install lanyon-plus theme
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shelley
parent
bf138a54e3
commit
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86 changed files with 3548 additions and 133 deletions
1
CNAME.sample
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1
CNAME.sample
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dyndna.github.io/lanyon-plus
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33
Gemfile
33
Gemfile
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@ -1,27 +1,14 @@
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source "https://rubygems.org"
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source 'https://rubygems.org'
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# Hello! This is where you manage which Jekyll version is used to run.
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# When you want to use a different version, change it below, save the
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# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
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#
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# bundle exec jekyll serve
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#
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# This will help ensure the proper Jekyll version is running.
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# Happy Jekylling!
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gem "jekyll", "3.5.1"
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# This is the default theme for new Jekyll sites. You may change this to anything you like.
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gem "minima", "~> 2.0"
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# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
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# uncomment the line below. To upgrade, run `bundle update github-pages`.
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# gem "github-pages", group: :jekyll_plugins
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# If you have any plugins, put them here!
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group :jekyll_plugins do
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group :jekyll_plugins do
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gem "jekyll-feed", "~> 0.6"
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gem 'jekyll'
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gem 'jekyll-sitemap'
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gem 'jemoji'
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gem 'jekyll-redirect-from'
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gem 'jekyll-paginate'
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gem 'jekyll-compose'
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end
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end
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# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
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gem 'font-awesome-sass'
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gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
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gem 'kramdown'
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gem 'rouge'
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101
Gemfile.lock
101
Gemfile.lock
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@ -1,58 +1,75 @@
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GEM
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GEM
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remote: https://rubygems.org/
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remote: https://rubygems.org/
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specs:
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specs:
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addressable (2.5.1)
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activesupport (4.2.5)
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public_suffix (~> 2.0, >= 2.0.2)
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i18n (~> 0.7)
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colorator (1.1.0)
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json (~> 1.7, >= 1.7.7)
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ffi (1.9.18)
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minitest (~> 5.1)
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forwardable-extended (2.6.0)
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thread_safe (~> 0.3, >= 0.3.4)
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jekyll (3.5.1)
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tzinfo (~> 1.1)
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addressable (~> 2.4)
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colorator (0.1)
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colorator (~> 1.0)
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ffi (1.9.10)
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font-awesome-sass (4.5.0)
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sass (>= 3.2)
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gemoji (2.1.0)
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html-pipeline (2.2.2)
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activesupport (>= 2, < 5)
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nokogiri (>= 1.4)
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i18n (0.7.0)
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jekyll (3.0.1)
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colorator (~> 0.1)
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jekyll-sass-converter (~> 1.0)
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jekyll-sass-converter (~> 1.0)
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jekyll-watch (~> 1.1)
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jekyll-watch (~> 1.1)
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kramdown (~> 1.3)
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kramdown (~> 1.3)
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liquid (~> 4.0)
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liquid (~> 3.0)
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mercenary (~> 0.3.3)
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mercenary (~> 0.3.3)
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pathutil (~> 0.9)
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rouge (~> 1.7)
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rouge (~> 1.7)
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safe_yaml (~> 1.0)
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safe_yaml (~> 1.0)
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jekyll-feed (0.9.2)
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jekyll-compose (0.4.1)
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jekyll (~> 3.3)
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jekyll (>= 2.5.0)
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jekyll-sass-converter (1.5.0)
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jekyll-paginate (1.1.0)
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jekyll-redirect-from (0.9.1)
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jekyll (>= 2.0)
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jekyll-sass-converter (1.4.0)
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sass (~> 3.4)
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sass (~> 3.4)
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jekyll-watch (1.5.0)
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jekyll-sitemap (0.9.0)
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listen (~> 3.0, < 3.1)
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jekyll-watch (1.3.0)
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kramdown (1.14.0)
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listen (~> 3.0)
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liquid (4.0.0)
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jemoji (0.5.1)
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listen (3.0.8)
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gemoji (~> 2.0)
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rb-fsevent (~> 0.9, >= 0.9.4)
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html-pipeline (~> 2.2)
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rb-inotify (~> 0.9, >= 0.9.7)
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jekyll (>= 2.0)
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mercenary (0.3.6)
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json (1.8.3)
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minima (2.1.1)
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kramdown (1.9.0)
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jekyll (~> 3.3)
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liquid (3.0.6)
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pathutil (0.14.0)
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listen (3.0.5)
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forwardable-extended (~> 2.6)
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rb-fsevent (>= 0.9.3)
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public_suffix (2.0.5)
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rb-inotify (>= 0.9)
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rb-fsevent (0.10.2)
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mercenary (0.3.5)
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rb-inotify (0.9.10)
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mini_portile2 (2.0.0)
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ffi (>= 0.5.0, < 2)
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minitest (5.8.3)
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rouge (1.11.1)
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nokogiri (1.6.7.1)
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mini_portile2 (~> 2.0.0.rc2)
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rb-fsevent (0.9.7)
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rb-inotify (0.9.5)
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ffi (>= 0.5.0)
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rouge (1.10.1)
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safe_yaml (1.0.4)
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safe_yaml (1.0.4)
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sass (3.5.1)
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sass (3.4.21)
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sass-listen (~> 4.0.0)
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thread_safe (0.3.5)
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sass-listen (4.0.0)
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tzinfo (1.2.2)
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rb-fsevent (~> 0.9, >= 0.9.4)
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thread_safe (~> 0.1)
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rb-inotify (~> 0.9, >= 0.9.7)
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PLATFORMS
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PLATFORMS
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ruby
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ruby
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DEPENDENCIES
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DEPENDENCIES
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jekyll (= 3.5.1)
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font-awesome-sass
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jekyll-feed (~> 0.6)
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jekyll
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minima (~> 2.0)
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jekyll-compose
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tzinfo-data
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jekyll-paginate
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jekyll-redirect-from
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BUNDLED WITH
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jekyll-sitemap
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1.15.3
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jemoji
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kramdown
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rouge
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9
LICENSE.md
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9
LICENSE.md
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# Released under MIT License
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Copyright (c) 2014 Mark Otto.
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Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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137
_config.yml
137
_config.yml
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# Welcome to Jekyll!
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# Permalinks
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#
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#
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# This config file is meant for settings that affect your whole blog, values
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# Use of `relative_permalinks` ensures post links from the index work properly.
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# which you are expected to set up once and rarely edit after that. If you find
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#permalink: pretty
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# yourself editing this file very often, consider using Jekyll's data files
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permalink: /blog/:year/:month/:day/:title/
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# feature for the data you need to update frequently.
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relative_permalinks: false
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#
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# For technical reasons, this file is *NOT* reloaded automatically when you use
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# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
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# Site settings
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# Setup
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# These are used to personalize your new site. If you look in the HTML files,
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title: foo
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# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
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#tagline: 'foo's website
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# You can create any custom variable you would like, and they will be accessible
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description: Foo's blog...
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# in the templates via {{ site.myvariable }}.
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url: https://dyndna.github.io/lanyon-plus
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title: Wild Toad
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baseurl: "/lanyon-plus"
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email: your-email@example.com
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urlimg: https://dyndna.github.io/lanyon-plus/images/
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description: > # this means to ignore newlines until "baseurl:"
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Write an awesome description for your new site here. You can edit this
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line in _config.yml. It will appear in your document head meta (for
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Google search results) and in your feed.xml site description.
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baseurl: "" # the subpath of your site, e.g. /blog
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url: "" # the base hostname & protocol for your site, e.g. http://example.com
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twitter_username: jekyllrb
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github_username: jekyll
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# Build settings
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markdown: kramdown
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markdown: kramdown
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theme: minima
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paginate: 5
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plugins:
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paginate_path: "/blog/page:num"
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- jekyll-feed
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excerpt_separator: <!--more-->
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default_bg: sitelogo.png
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safe: false
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#timezone: America/Chicago
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future: true
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# Exclude from processing.
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gems:
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# The following items will not be processed, by default. Create a custom list
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- jekyll-paginate
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# to override the default setting.
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- jemoji
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exclude:
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- font-awesome-sass
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- Gemfile
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- kramdown
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- Gemfile.lock
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- rouge
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- node_modules
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# - vendor/bundle/
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include: [".htaccess"]
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# - vendor/cache/
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exclude: ["lib", "config.rb", "Gemfile", "Capfile", "Gemfile.lock", "config", "log", "Rakefile", "Rakefile.rb", "rakefile", "README.md", "tmp", "less", "*.sublime-project", "*.sublime-workspace", "test", "spec", "Gruntfile.js", "package.json", "node_modules", "LICENSE", "vendor", "assets", "_plugins", "public/dormant"]
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# - vendor/gems/
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- vendor/ruby/
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# About/contact
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author:
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name: Foo Boo
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url: https://twitter.com/abcd
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avatar: foo.png
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#email:
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# Owner/author information
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owner:
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name: Foo Boo
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avatar: foo.png
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#email:
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# Use the coder's toolbox at http://coderstoolbox.net/string/#!encoding=xml&action=encode&charset=us_ascii to encode your description into XML string
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description:
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# Social networking links used in footer. Update and remove as you like.
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twitter: abcd
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facebook:
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github: xyz123abc
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stackexchange:
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linkedin: https://www.linkedin.com/in/foo
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instagram:
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flickr:
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tumblr:
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google_plus: https://plus.google.com/+foo
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# orcid and google scholar IDs are different than standard username.
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orcid: xyz123abc
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gscholar: xyz123abc
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## sidebar links:
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# For external links add external: true
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links:
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- title: <i class="iconside iconm-home"></i> Home
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url: /
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- title: <i class="iconside iconm-user"></i> About
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url: /about/
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- title: <i class="iconside iconm-quill"></i> Blog
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url: /blog/
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- title: <i class="fa fa-tags"></i> Tags
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url: /tags/
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- title: <i class="fa fa-archive"></i> Archive
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url: /archive/
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- title: <i class="iconside iconm-wordpress"></i> Old Blog
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url: https://foo.wordpress.com
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external: true
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- title: <i class="iconside iconm-envelop"></i> Contact
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url: /contact/
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- title: <i class="iconside iconm-twitter"></i> Twitter
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url: https://twitter.com/abcd
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external: true
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- title: <i class="iconside iconm-feed2"></i> Feed
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url: /feed.xml
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# Google Custom Search:
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#google_search: xyz123abc
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# Twitter stream widget:
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# Replace xyz123abc with your twitter widget id from https://twitter.com/settings/widgets
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#twitter_widget_id: xyz123abc
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# Add disqus username for Disqus comment board:
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disqus_shortname: foo
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# Analytics and webmaster tools stuff goes here
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#google_analytics: xyz123abc
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#### For dummy website only - remove if you wish ####
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github_repo: https://github.com/dyndna/lanyon-plus
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version: 1.1.0
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## END ##
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24
_data/socialmedia.yml
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24
_data/socialmedia.yml
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- name: Twitter
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url: https://twitter.com/abcd
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class: fa fa-twitter-square
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title: "Follow me @foo"
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- name: Google Plus
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url: https://plus.google.com/+foo
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class: fa fa-google-plus-square
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title: "Follow me +foo"
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- name: GitHub
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url: https://github.com/xyz123abc
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class: fa fa-github-square
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title: Code repository
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- name: Contact
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url: "/contact/"
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class: fa fa-envelope-square
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title: "Reach Us"
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- name: RSS
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url: "/feed.xml"
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class: fa fa-rss-square
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title: "Subscribe to RSS"
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102
_devconfig.yml
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102
_devconfig.yml
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# Permalinks
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|
#
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# Use of `relative_permalinks` ensures post links from the index work properly.
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||||||
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#permalink: pretty
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||||||
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permalink: /blog/:year/:month/:day/:title/
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relative_permalinks: false
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# Setup
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title: foo
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#tagline: 'foo's website
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description: Foo's blog...
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url: http://localhost:4000
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baseurl: ""
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urlimg: http://localhost:4000/images/
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markdown: kramdown
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paginate: 5
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paginate_path: "/blog/page:num"
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excerpt_separator: <!--more-->
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default_bg: sitelogo.png
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safe: false
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#timezone: America/Chicago
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||||||
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future: true
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||||||
|
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gems:
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- jekyll-paginate
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- jemoji
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||||||
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- font-awesome-sass
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||||||
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- kramdown
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||||||
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- rouge
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||||||
|
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include: [".htaccess"]
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exclude: ["lib", "config.rb", "Gemfile", "Capfile", "Gemfile.lock", "config", "log", "Rakefile", "Rakefile.rb", "rakefile", "README.md", "tmp", "less", "*.sublime-project", "*.sublime-workspace", "test", "spec", "Gruntfile.js", "package.json", "node_modules", "LICENSE", "vendor", "assets", "_plugins", "public/dormant"]
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# About/contact
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||||||
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author:
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||||||
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name: Foo Boo
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url: https://twitter.com/abcd
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||||||
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avatar: foo.png
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||||||
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#email:
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||||||
|
|
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|
# Owner/author information
|
||||||
|
owner:
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||||||
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name: Foo Boo
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||||||
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avatar: foo.png
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||||||
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#email:
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||||||
|
# Use the coder's toolbox at http://coderstoolbox.net/string/#!encoding=xml&action=encode&charset=us_ascii to encode your description into XML string
|
||||||
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description:
|
||||||
|
# Social networking links used in footer. Update and remove as you like.
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||||||
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twitter: abcd
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||||||
|
facebook:
|
||||||
|
github: xyz123abc
|
||||||
|
stackexchange:
|
||||||
|
linkedin: https://www.linkedin.com/in/foo
|
||||||
|
instagram:
|
||||||
|
flickr:
|
||||||
|
tumblr:
|
||||||
|
google_plus: https://plus.google.com/+foo
|
||||||
|
# orcid and google scholar IDs are different than standard username.
|
||||||
|
orcid: xyz123abc
|
||||||
|
gscholar: xyz123abc
|
||||||
|
|
||||||
|
## sidebar links:
|
||||||
|
# For external links add external: true
|
||||||
|
links:
|
||||||
|
- title: <i class="iconside iconm-home"></i> Home
|
||||||
|
url: /
|
||||||
|
- title: <i class="iconside iconm-user"></i> About
|
||||||
|
url: /about/
|
||||||
|
- title: <i class="iconside iconm-quill"></i> Blog
|
||||||
|
url: /blog/
|
||||||
|
- title: <i class="fa fa-tags"></i> Tags
|
||||||
|
url: /tags/
|
||||||
|
- title: <i class="fa fa-archive"></i> Archive
|
||||||
|
url: /archive/
|
||||||
|
- title: <i class="iconside iconm-wordpress"></i> Old Blog
|
||||||
|
url: https://foo.wordpress.com
|
||||||
|
external: true
|
||||||
|
- title: <i class="iconside iconm-envelop"></i> Contact
|
||||||
|
url: /contact/
|
||||||
|
- title: <i class="iconside iconm-twitter"></i> Twitter
|
||||||
|
url: https://twitter.com/abcd
|
||||||
|
external: true
|
||||||
|
- title: <i class="iconside iconm-feed2"></i> Feed
|
||||||
|
url: /feed.xml
|
||||||
|
|
||||||
|
# Google Custom Search:
|
||||||
|
#google_search: xyz123abc
|
||||||
|
|
||||||
|
# Twitter stream widget:
|
||||||
|
# Replace xyz123abc with your twitter widget id from https://twitter.com/settings/widgets
|
||||||
|
#twitter_widget_id: xyz123abc
|
||||||
|
|
||||||
|
# Add disqus username for Disqus comment board:
|
||||||
|
disqus_shortname: foo
|
||||||
|
|
||||||
|
# Analytics and webmaster tools stuff goes here
|
||||||
|
#google_analytics: xyz123abc
|
||||||
|
|
||||||
|
#### For dummy website only - remove if you wish ####
|
||||||
|
github_repo: https://github.com/dyndna/lanyon-plus
|
||||||
|
version: 1.1.0
|
||||||
|
## END ##
|
||||||
40
_drafts/2014-01-02-introducing-lanyon.md
Normal file
40
_drafts/2014-01-02-introducing-lanyon.md
Normal file
|
|
@ -0,0 +1,40 @@
|
||||||
|
---
|
||||||
|
layout: post
|
||||||
|
title: Introducing Lanyon
|
||||||
|
---
|
||||||
|
|
||||||
|
Lanyon is an unassuming [Jekyll](http://jekyllrb.com) theme that places content first by tucking away navigation in a hidden drawer. It's based on [Poole](http://getpoole.com), the Jekyll butler.
|
||||||
|
|
||||||
|
<!--more-->
|
||||||
|
|
||||||
|
### Built on Poole
|
||||||
|
|
||||||
|
Poole is the Jekyll Butler, serving as an upstanding and effective foundation for Jekyll themes by [@mdo](https://twitter.com/mdo). Poole, and every theme built on it (like Lanyon here) includes the following:
|
||||||
|
|
||||||
|
* Complete Jekyll setup included (layouts, config, [404](/404), [RSS feed](/atom.xml), posts, and [example page](/about))
|
||||||
|
* Mobile friendly design and development
|
||||||
|
* Easily scalable text and component sizing with `rem` units in the CSS
|
||||||
|
* Support for a wide gamut of HTML elements
|
||||||
|
* Related posts (time-based, because Jekyll) below each post
|
||||||
|
* Syntax highlighting, courtesy Pygments (the Python-based code snippet highlighter)
|
||||||
|
|
||||||
|
### Lanyon features
|
||||||
|
|
||||||
|
In addition to the features of Poole, Lanyon adds the following:
|
||||||
|
|
||||||
|
* Toggleable sliding sidebar (built with only CSS) via **☰** link in top corner
|
||||||
|
* Sidebar includes support for textual modules and a dynamically generated navigation with active link support
|
||||||
|
* Two orientations for content and sidebar, default (left sidebar) and [reverse](https://github.com/poole/lanyon#reverse-layout) (right sidebar), available via `<body>` classes
|
||||||
|
* [Eight optional color schemes](https://github.com/poole/lanyon#themes), available via `<body>` classes
|
||||||
|
|
||||||
|
[Head to the readme](https://github.com/poole/lanyon#readme) to learn more.
|
||||||
|
|
||||||
|
### Browser support
|
||||||
|
|
||||||
|
Lanyon is by preference a forward-thinking project. In addition to the latest versions of Chrome, Safari (mobile and desktop), and Firefox, it is only compatible with Internet Explorer 9 and above.
|
||||||
|
|
||||||
|
### Download
|
||||||
|
|
||||||
|
Lanyon is developed on and hosted with GitHub. Head to the <a href="https://github.com/poole/lanyon">GitHub repository</a> for downloads, bug reports, and features requests.
|
||||||
|
|
||||||
|
Thanks!
|
||||||
1
_includes/crosspost.html
Normal file
1
_includes/crosspost.html
Normal file
|
|
@ -0,0 +1 @@
|
||||||
|
<hr><a href="https://twitter.com/share?text={{ post.title }}&url={{ post.url | prepend: site.baseurl | prepend: site.url }}&via={{ site.owner.twitter }} @rbloggers" target="_blank" title="tweet author @{{ site.owner.twitter }}">tweet author</a> | <a href="https://plus.google.com/share?url={{ post.url | prepend: site.baseurl | prepend: site.url }}" target="_blank" title="Share on Google+">share on Google+</a>{% if page.comments %} | <a href="{{ post.url | prepend: site.baseurl | prepend: site.url }}#disqus_thread" title="Comment at author's website">Comments</a>{% endif %}
|
||||||
13
_includes/disqus_comments.html
Normal file
13
_includes/disqus_comments.html
Normal file
|
|
@ -0,0 +1,13 @@
|
||||||
|
<script type="text/javascript">
|
||||||
|
/* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
|
||||||
|
var disqus_shortname = '{{ site.disqus_shortname }}';
|
||||||
|
var disqus_identifier = '{{ site.url }}{{ page.url }}';
|
||||||
|
|
||||||
|
/* * * DON'T EDIT BELOW THIS LINE * * */
|
||||||
|
(function() {
|
||||||
|
var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
|
||||||
|
dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js';
|
||||||
|
(document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
|
||||||
|
})();
|
||||||
|
</script>
|
||||||
|
<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
|
||||||
1
_includes/feedfooter.html
Normal file
1
_includes/feedfooter.html
Normal file
|
|
@ -0,0 +1 @@
|
||||||
|
<hr><a href="https://twitter.com/share?text={{ post.title }}&url={{ post.url | prepend: site.baseurl | prepend: site.url }}&via={{ site.owner.twitter }}" target="_blank" title="tweet author @{{ site.owner.twitter }}">tweet author</a> | <a href="https://plus.google.com/share?url={{ post.url | prepend: site.baseurl | prepend: site.url }}" target="_blank" title="Share on Google+">share on Google+</a>{% if page.comments %} | <a href="{{ post.url | prepend: site.baseurl | prepend: site.url }}#disqus_thread" title="Comment at author's website">Comments</a>{% endif %}
|
||||||
15
_includes/footer.html
Normal file
15
_includes/footer.html
Normal file
|
|
@ -0,0 +1,15 @@
|
||||||
|
<div class="custom-footer" style="display: block;">
|
||||||
|
<div class="footer-social-icons">
|
||||||
|
<ul class="social-icons">
|
||||||
|
{% for social_item in site.data.socialmedia %}
|
||||||
|
{% if social_item.url contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.url %}
|
||||||
|
{% endif %}
|
||||||
|
<li><a href="{{ domain }}{{ social_item.url }}" rel="me" {% if social_item.url contains 'http' %} target="_blank" {% endif %} class="social-icons" title="{{ social_item.title }}"> <i class="{{ social_item.class }} fa-2x"></i></a></li>
|
||||||
|
{% endfor %}
|
||||||
|
</ul>
|
||||||
|
</div>
|
||||||
|
<h6 class="text-footer"><a rel="license" href="{{ site.url }}/disclosure/" title="CC BY-NC-SA 4.0 License, link to site disclosure" class="social-icon"><i class="fa fa-creative-commons"></i></a> <a rel="license" href="{{ site.url }}/disclosure/" title="CC BY-NC-SA 4.0 License, link to site disclosure">2015-{{ site.time | date: '%Y' }}</a>: <a href="{{ site.url }}" title="Home">example.com</a> | <a href="{{ site.url }}/about/" rel="me">About</a></h6>
|
||||||
|
</div>
|
||||||
3
_includes/gist_embed.html
Normal file
3
_includes/gist_embed.html
Normal file
|
|
@ -0,0 +1,3 @@
|
||||||
|
<!--Gist embed -->
|
||||||
|
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js"></script>
|
||||||
|
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/gist-embed/2.4/gist-embed.min.js"></script>
|
||||||
105
_includes/head.html
Normal file
105
_includes/head.html
Normal file
|
|
@ -0,0 +1,105 @@
|
||||||
|
<head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb#">
|
||||||
|
<!-- link href="http://gmpg.org/xfn/11" rel="profile" -->
|
||||||
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||||
|
<meta http-equiv="content-type" content="text/html; charset=utf-8">
|
||||||
|
|
||||||
|
<!-- Enable responsiveness on mobile devices-->
|
||||||
|
<meta name="HandheldFriendly" content="True">
|
||||||
|
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1">
|
||||||
|
|
||||||
|
<title>
|
||||||
|
{% if page.title == "Home" %}
|
||||||
|
{{ site.title }} · {{ site.tagline }}
|
||||||
|
{% else %}
|
||||||
|
{{ page.title }} · {{ site.title }}
|
||||||
|
{% endif %}
|
||||||
|
</title>
|
||||||
|
|
||||||
|
<!-- Search Engine Optimization -->
|
||||||
|
<meta name="description" content="{% if page.description %}{{ page.description }}{% elsif page.content %}{{ page.content | strip_html | truncatewords: 50 }}{% else %}{{ site.description }}{% endif %}">
|
||||||
|
{% if page.tags %}<meta name="keywords" content="{{ page.tags | join: ', ' }}">{% endif %}
|
||||||
|
{% if page.noindex == true %}<meta name="robots" content="noindex">{% endif %}
|
||||||
|
{% if page.nofollow == true %}<meta name="robots" content="nofollow">{% endif %}
|
||||||
|
{% if site.google_verify %}<meta name="google-site-verification" content="{{ site.google_verify }}">{% endif %}
|
||||||
|
|
||||||
|
{% if site.owner.twitter %}<!-- Twitter Cards -->
|
||||||
|
{% include twitter_card.html %}
|
||||||
|
{% endif %}
|
||||||
|
<meta name="twitter:title" content="{% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}">
|
||||||
|
<meta name="twitter:description" content="{% if page.description %}{{ page.description }}{% elsif page.content %}{{ page.content | strip_html | truncatewords: 50 }}{% else %}{{ site.description }}{% endif %}">
|
||||||
|
<meta name="twitter:creator" content="@{{ site.owner.twitter }}">
|
||||||
|
<!-- End Twitter Cards -->
|
||||||
|
|
||||||
|
<!-- Open Graph -->
|
||||||
|
<meta property="og:locale" content="en_US">
|
||||||
|
<meta property="og:type" content="article">
|
||||||
|
<meta property="og:title" content="{% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}">
|
||||||
|
<meta property="og:description" content="{% if page.description %}{{ page.description }}{% elsif page.content %}{{ page.content | strip_html | truncatewords: 50 }}{% else %}{{ site.description }}{% endif %}">
|
||||||
|
<meta property="og:url" content="{{ site.url }}{{ page.url }}">
|
||||||
|
<meta property="og:site_name" content="{{ site.title }}">
|
||||||
|
{% if page.imagefeature %}
|
||||||
|
{% if page.imagefeature contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.urlimg %}
|
||||||
|
{% endif %}
|
||||||
|
<meta property="og:image" content="{{ domain }}{{ page.imagefeature }}">{% else %}
|
||||||
|
<meta property="og:image" content="{% if page.imagesummary %}{{ site.urlimg }}{{ page.imagesummary }}{% else %}{{ site.urlimg }}{{ site.default_bg }}{% endif %}">{% endif %}
|
||||||
|
{% if page.videofeature %}<meta property="og:video" content="{{ page.videofeature }}">{% endif %}
|
||||||
|
<meta property="fb:app_id" content="1003108156422006">
|
||||||
|
<meta property="fb:admins" content="817465054">
|
||||||
|
|
||||||
|
<!-- Fonts -->
|
||||||
|
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=PT+Serif:400,400italic,700%7CPT+Sans:400|Tangerine|Inconsolata">
|
||||||
|
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/iconmoon.css">
|
||||||
|
|
||||||
|
<!-- CSS -->
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/style.min.css">
|
||||||
|
{% if page.category contains 'mypubs' or page.category contains 'myaoi' %}
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/publ.css">
|
||||||
|
<script src="{{ site.baseurl }}/public/js/jquery.min.js"></script>
|
||||||
|
{% endif %}
|
||||||
|
<!-- Add-on CSS to override system-wide defaults -->
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/addon.css">
|
||||||
|
|
||||||
|
<!-- CSS override per page -->
|
||||||
|
{% if page.style %}
|
||||||
|
<style type="text/css">
|
||||||
|
{{ page.style }}
|
||||||
|
</style>
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
<!-- Java scripts -->
|
||||||
|
<!-- <script src="{{ site.baseurl }}/public/js/jquery.min.js"></script> -->
|
||||||
|
|
||||||
|
<!-- Icons -->
|
||||||
|
<!-- 16x16 -->
|
||||||
|
<link rel="shortcut icon" href="{{ site.url }}/favicon.ico">
|
||||||
|
<!-- 32x32 -->
|
||||||
|
<link rel="shortcut icon" href="{{ site.url }}/favicon.png">
|
||||||
|
<!-- 57x57 (precomposed) for iPhone 3GS, pre-2011 iPod Touch and older Android devices -->
|
||||||
|
<link rel="apple-touch-icon-precomposed" href="{{ site.url }}/images/icons/apple-touch-icon-precomposed.png">
|
||||||
|
<!-- 72x72 (precomposed) for 1st generation iPad, iPad 2 and iPad mini -->
|
||||||
|
<link rel="apple-touch-icon-precomposed" sizes="72x72" href="{{ site.url }}/images/icons/apple-touch-icon-72x72-precomposed.png">
|
||||||
|
<!-- 114x114 (precomposed) for iPhone 4, 4S, 5 and post-2011 iPod Touch -->
|
||||||
|
<link rel="apple-touch-icon-precomposed" sizes="114x114" href="{{ site.url }}/images/icons/apple-touch-icon-114x114-precomposed.png">
|
||||||
|
<!-- 144x144 (precomposed) for iPad 3rd and 4th generation -->
|
||||||
|
<link rel="apple-touch-icon-precomposed" sizes="144x144" href="{{ site.url }}/images/icons/apple-touch-icon-144x144-precomposed.png">
|
||||||
|
<!-- 180x180 (precomposed) for iPhone 6 -->
|
||||||
|
<link rel="apple-touch-icon-precomposed" sizes="180x180" href="{{ site.url }}/images/icons/apple-touch-icon-180x180.png">
|
||||||
|
<!-- 192x192 (precomposed) for Android -->
|
||||||
|
<link rel="icon" type="image/png" sizes="192x192" href="{{ site.url }}/images/icons/android-icon-192x192.png">
|
||||||
|
|
||||||
|
{% capture canonical %}{{ site.url }}{% if site.permalink contains '.html' %}{{ page.url }}{% else %}{{ page.url | remove:'index.html' | strip_slash }}{% endif %}{% endcapture %}
|
||||||
|
<link rel="canonical" href="{{ canonical }}">
|
||||||
|
{% if site.owner.google_plus %}<link rel="author" href="{{ site.owner.google_plus }}?rel=author">{% endif %}
|
||||||
|
|
||||||
|
<!-- RSS -->
|
||||||
|
<link rel="alternate" type="application/rss+xml" title="RSS" href="{{ site.url }}/feed.xml">
|
||||||
|
|
||||||
|
{% if page.mathjax %}
|
||||||
|
{% include mathjax_support.html %}
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
</head>
|
||||||
73
_includes/head_minimal.html
Normal file
73
_includes/head_minimal.html
Normal file
|
|
@ -0,0 +1,73 @@
|
||||||
|
<head>
|
||||||
|
<!-- link href="http://gmpg.org/xfn/11" rel="profile" -->
|
||||||
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||||
|
<meta http-equiv="content-type" content="text/html; charset=utf-8">
|
||||||
|
|
||||||
|
<!-- Enable responsiveness on mobile devices-->
|
||||||
|
<meta name="HandheldFriendly" content="True">
|
||||||
|
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1">
|
||||||
|
|
||||||
|
<title>
|
||||||
|
{% if page.title == "Home" %}
|
||||||
|
{{ site.title }} · {{ site.tagline }}
|
||||||
|
{% else %}
|
||||||
|
{{ page.title }} · {{ site.title }}
|
||||||
|
{% endif %}
|
||||||
|
</title>
|
||||||
|
|
||||||
|
<!-- Search Engine Optimization -->
|
||||||
|
<meta name="description" content="{% if page.description %}{{ page.description }}{% else %}{{ site.description }}{% endif %}">
|
||||||
|
|
||||||
|
{% if page.noindex == true %}<meta name="robots" content="noindex">{% endif %}
|
||||||
|
{% if page.nofollow == true %}<meta name="robots" content="nofollow">{% endif %}
|
||||||
|
|
||||||
|
<meta name="twitter:creator" content="@{{ site.owner.twitter }}">
|
||||||
|
|
||||||
|
<!-- Fonts -->
|
||||||
|
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=PT+Serif:400,400italic,700%7CPT+Sans:400|Tangerine|Inconsolata">
|
||||||
|
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/iconmoon.css">
|
||||||
|
|
||||||
|
<!-- CSS -->
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/style.min.css">
|
||||||
|
{% if page.category contains 'mypubs' or page.category contains 'myaoi' %}
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/publ.css">
|
||||||
|
<script src="{{ site.baseurl }}/public/js/jquery.min.js"></script>
|
||||||
|
{% endif %}
|
||||||
|
<!-- Add-on CSS to override system-wide defaults -->
|
||||||
|
<link rel="stylesheet" href="{{ site.baseurl }}/public/css/addon.css">
|
||||||
|
|
||||||
|
<!-- CSS override per page -->
|
||||||
|
{% if page.style %}
|
||||||
|
<style type="text/css">
|
||||||
|
{{ page.style }}
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<div class="full-bib-section"><div class="bib-item"><div class="csl-entry">Beerenwinkel, N., Greenman, C. D., & Lagergren, J. (2016). <a class="doctitle" href="http://dx.doi.org/10.1371/journal.pcbi.1004717">Computational Cancer Biology: An Evolutionary Perspective.</a> <i>PLoS Comput Biol</i>, <i>12</i>(2), e1004717. http://doi.org/10.1371/journal.pcbi.1004717</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{beerenwinkel_computational_2016,
|
||||||
|
title = {Computational {Cancer} {Biology}: {An} {Evolutionary} {Perspective}},
|
||||||
|
volume = {12},
|
||||||
|
shorttitle = {Computational {Cancer} {Biology}},
|
||||||
|
url = {http://dx.doi.org/10.1371/journal.pcbi.1004717},
|
||||||
|
doi = {10.1371/journal.pcbi.1004717},
|
||||||
|
number = {2},
|
||||||
|
urldate = {2016-02-05TZ},
|
||||||
|
journal = {PLoS Comput Biol},
|
||||||
|
author = {Beerenwinkel, Niko and Greenman, Chris D. and Lagergren, Jens},
|
||||||
|
month = feb,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {cancer, concepts, darwinian, epigenetics, evolution, mathematical modeling, review, statistics, variant},
|
||||||
|
pages = {e1004717}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - Computational Cancer Biology: An Evolutionary Perspective
|
||||||
|
AU - Beerenwinkel, Niko
|
||||||
|
AU - Greenman, Chris D.
|
||||||
|
AU - Lagergren, Jens
|
||||||
|
T2 - PLoS Comput Biol
|
||||||
|
DA - 2016/02/04/
|
||||||
|
PY - 2016
|
||||||
|
DO - 10.1371/journal.pcbi.1004717
|
||||||
|
DP - PLoS Journals
|
||||||
|
VL - 12
|
||||||
|
IS - 2
|
||||||
|
SP - e1004717
|
||||||
|
J2 - PLoS Comput Biol
|
||||||
|
ST - Computational Cancer Biology
|
||||||
|
UR - http://dx.doi.org/10.1371/journal.pcbi.1004717
|
||||||
|
Y2 - 2016/02/05/T20:21:50Z
|
||||||
|
KW - cancer
|
||||||
|
KW - concepts
|
||||||
|
KW - darwinian
|
||||||
|
KW - epigenetics
|
||||||
|
KW - evolution
|
||||||
|
KW - mathematical modeling
|
||||||
|
KW - review
|
||||||
|
KW - statistics
|
||||||
|
KW - variant
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Kaufman, C. K., Mosimann, C., Fan, Z. P., Yang, S., Thomas, A. J., Ablain, J., … Zon, L. I. (2016). <a class="doctitle" href="http://science.sciencemag.org/content/351/6272/aad2197">A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation.</a> <i>Science</i>, <i>351</i>(6272), aad2197. http://doi.org/10.1126/science.aad2197</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">Visualizing the beginnings of melanoma
|
||||||
|
In cancer biology‚ a tumor begins from a single cell within a group of precancerous cells that share genetic mutations. Kaufman et al. used a zebrafish melanoma model to visualize cancer initiation (see the Perspective by Boumahdi and Blanpain). They used a fluorescent reporter that specifically lit up neural crest progenitors that are only present during embryogenesis or during adult melanoma tumor formation. The appearance of this tumor correlated with a set of gene regulatory elements‚ called super-enhancers‚ whose identification and manipulation may prove beneficial in detecting and preventing melanoma initiation.
|
||||||
|
Science‚ this issue p. 10.1126/science.aad3867; see also p. 453
|
||||||
|
Structured Abstract
|
||||||
|
INTRODUCTIONThe “cancerized field” concept posits that cells in a given tissue sharing an oncogenic mutation are cancer-prone‚ yet only discreet clones within the field initiate tumors. Studying the process of cancer initiation has remained challenging because of (i) the rarity of these events‚ (ii) the difficulty of visiualizing initiating clones in living organisms‚ and (iii) the transient nature of a newly transformed clone emerging before it expands to form an early tumor. A more complete understanding of the molecular processes that regulate cancer initiation could provide important prognostic information about which precancerous lesions are most prone to becoming cancer and also implicate druggable molecular pathways that‚ when inhibited‚ may prevent the cancer from ever starting.
|
||||||
|
RATIONALEThe majority of benign nevi carry oncogenic BRAFV600E mutations and can be considered a cancerized field of melanocytes‚ but they only rarely convert to melanoma. In an effort to define events that initiate cancer‚ we used a melanoma model in the zebrafish in which the human BRAFV600E oncogene is driven by the melanocyte-specific mitfa promoter. When bred into a p53 mutant background‚ these fish develop melanoma tumors over the course of many months. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and is specifically reexpressed only in melanoma tumors‚ making it an ideal candidate for tracking melanoma from initiation onward.
|
||||||
|
RESULTSWe developed a crestin:EGFP reporter that recapitulates the embryonic neural crest expression pattern of crestin and its expression in melanoma tumors. We show through live imaging of transgenic zebrafish crestin reporters that within a cancerized field (BRAFV600E-mutant; p53-deficient)‚ a single melanocyte reactivates the NCP state‚ and this establishes that a fate change occurs at melanoma initiation in this model. Early crestin+ patches of cells expand and are transplantable in a manner consistent with their possessing tumorigenic activity‚ and they exhibit a gene expression pattern consistent with the NCP identity readout by the crestin reporter. The crestin element is regulated by NCP transcription factors‚ including sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation‚ whereas CRISPR/Cas9 targeting of sox10 delayed melanoma onset. We show activation of super-enhancers at NCP genes in both zebrafish and human melanomas‚ identifying an epigenetic mechanism for control of this NCP signature leading to melanoma.
|
||||||
|
CONCLUSIONThis work using our zebrafish melanoma model and in vivo reporter of NCP identity allows us to see cancer from its birth as a single cell and shows the importance of NCP-state reemergence as a key event in melanoma initiation from a field of cancer-prone melanocytes. Thus‚ in addition to the typical fixed genetic alterations in oncogenes and tumor supressors that are required for cancer development‚ the reemergence of progenitor identity may be an additional rate-limiting step in the formation of melanoma. Preventing NCP reemergence in a field of cancer-prone melanocytes may thus prove therapeutically useful‚ and the association of NCP genes with super-enhancer regulatory elements implicates the associated druggable epigenetic machinery in this process. Download high-res image Open in new tab Download Powerpoint Neural crest reporter expression in melanoma.The crestin:EGFP transgene is specifically expressed in melanoma in BRAFV600E/p53 mutant melanoma-prone zebrafish. (Top) A single cell expressing crestin:EGFP expands into a small patch of cells over the course of 2 weeks‚ capturing the initiation of melanoma formation (bracket). (Bottom) A fully formed melanoma specifically expresses crestin:EGFP‚ whereas the rest of the fish remains EGFP-negative.
|
||||||
|
The “cancerized field” concept posits that cancer-prone cells in a given tissue share an oncogenic mutation‚ but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAFV600E mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAFV600E-mutant; p53-deficient)‚ a single melanocyte reactivates the NCP state‚ revealing a fate change at melanoma initiation in this model. NCP transcription factors‚ including sox10‚ regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation‚ which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{kaufman_zebrafish_2016,
|
||||||
|
title = {A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation},
|
||||||
|
volume = {351},
|
||||||
|
copyright = {Copyright © 2016, American Association for the Advancement of Science},
|
||||||
|
issn = {0036-8075, 1095-9203},
|
||||||
|
url = {http://science.sciencemag.org/content/351/6272/aad2197},
|
||||||
|
doi = {10.1126/science.aad2197},
|
||||||
|
language = {en},
|
||||||
|
number = {6272},
|
||||||
|
urldate = {2016-01-29TZ},
|
||||||
|
journal = {Science},
|
||||||
|
author = {Kaufman, Charles K. and Mosimann, Christian and Fan, Zi Peng and Yang, Song and Thomas, Andrew J. and Ablain, Julien and Tan, Justin L. and Fogley, Rachel D. and Rooijen, Ellen van and Hagedorn, Elliott J. and Ciarlo, Christie and White, Richard M. and Matos, Dominick A. and Puller, Ann-Christin and Santoriello, Cristina and Liao, Eric C. and Young, Richard A. and Zon, Leonard I.},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {Development, SKCM, classics, epigenetics, evolution, melanoma, super\_enhancer, zebrafish},
|
||||||
|
pages = {aad2197}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation
|
||||||
|
AU - Kaufman, Charles K.
|
||||||
|
AU - Mosimann, Christian
|
||||||
|
AU - Fan, Zi Peng
|
||||||
|
AU - Yang, Song
|
||||||
|
AU - Thomas, Andrew J.
|
||||||
|
AU - Ablain, Julien
|
||||||
|
AU - Tan, Justin L.
|
||||||
|
AU - Fogley, Rachel D.
|
||||||
|
AU - Rooijen, Ellen van
|
||||||
|
AU - Hagedorn, Elliott J.
|
||||||
|
AU - Ciarlo, Christie
|
||||||
|
AU - White, Richard M.
|
||||||
|
AU - Matos, Dominick A.
|
||||||
|
AU - Puller, Ann-Christin
|
||||||
|
AU - Santoriello, Cristina
|
||||||
|
AU - Liao, Eric C.
|
||||||
|
AU - Young, Richard A.
|
||||||
|
AU - Zon, Leonard I.
|
||||||
|
T2 - Science
|
||||||
|
AB - Visualizing the beginnings of melanoma
|
||||||
|
In cancer biology, a tumor begins from a single cell within a group of precancerous cells that share genetic mutations. Kaufman et al. used a zebrafish melanoma model to visualize cancer initiation (see the Perspective by Boumahdi and Blanpain). They used a fluorescent reporter that specifically lit up neural crest progenitors that are only present during embryogenesis or during adult melanoma tumor formation. The appearance of this tumor correlated with a set of gene regulatory elements, called super-enhancers, whose identification and manipulation may prove beneficial in detecting and preventing melanoma initiation.
|
||||||
|
Science, this issue p. 10.1126/science.aad3867; see also p. 453
|
||||||
|
Structured Abstract
|
||||||
|
INTRODUCTIONThe “cancerized field” concept posits that cells in a given tissue sharing an oncogenic mutation are cancer-prone, yet only discreet clones within the field initiate tumors. Studying the process of cancer initiation has remained challenging because of (i) the rarity of these events, (ii) the difficulty of visiualizing initiating clones in living organisms, and (iii) the transient nature of a newly transformed clone emerging before it expands to form an early tumor. A more complete understanding of the molecular processes that regulate cancer initiation could provide important prognostic information about which precancerous lesions are most prone to becoming cancer and also implicate druggable molecular pathways that, when inhibited, may prevent the cancer from ever starting.
|
||||||
|
RATIONALEThe majority of benign nevi carry oncogenic BRAFV600E mutations and can be considered a cancerized field of melanocytes, but they only rarely convert to melanoma. In an effort to define events that initiate cancer, we used a melanoma model in the zebrafish in which the human BRAFV600E oncogene is driven by the melanocyte-specific mitfa promoter. When bred into a p53 mutant background, these fish develop melanoma tumors over the course of many months. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and is specifically reexpressed only in melanoma tumors, making it an ideal candidate for tracking melanoma from initiation onward.
|
||||||
|
RESULTSWe developed a crestin:EGFP reporter that recapitulates the embryonic neural crest expression pattern of crestin and its expression in melanoma tumors. We show through live imaging of transgenic zebrafish crestin reporters that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, and this establishes that a fate change occurs at melanoma initiation in this model. Early crestin+ patches of cells expand and are transplantable in a manner consistent with their possessing tumorigenic activity, and they exhibit a gene expression pattern consistent with the NCP identity readout by the crestin reporter. The crestin element is regulated by NCP transcription factors, including sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation, whereas CRISPR/Cas9 targeting of sox10 delayed melanoma onset. We show activation of super-enhancers at NCP genes in both zebrafish and human melanomas, identifying an epigenetic mechanism for control of this NCP signature leading to melanoma.
|
||||||
|
CONCLUSIONThis work using our zebrafish melanoma model and in vivo reporter of NCP identity allows us to see cancer from its birth as a single cell and shows the importance of NCP-state reemergence as a key event in melanoma initiation from a field of cancer-prone melanocytes. Thus, in addition to the typical fixed genetic alterations in oncogenes and tumor supressors that are required for cancer development, the reemergence of progenitor identity may be an additional rate-limiting step in the formation of melanoma. Preventing NCP reemergence in a field of cancer-prone melanocytes may thus prove therapeutically useful, and the association of NCP genes with super-enhancer regulatory elements implicates the associated druggable epigenetic machinery in this process. Download high-res image Open in new tab Download Powerpoint Neural crest reporter expression in melanoma.The crestin:EGFP transgene is specifically expressed in melanoma in BRAFV600E/p53 mutant melanoma-prone zebrafish. (Top) A single cell expressing crestin:EGFP expands into a small patch of cells over the course of 2 weeks, capturing the initiation of melanoma formation (bracket). (Bottom) A fully formed melanoma specifically expresses crestin:EGFP, whereas the rest of the fish remains EGFP-negative.
|
||||||
|
The “cancerized field” concept posits that cancer-prone cells in a given tissue share an oncogenic mutation, but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAFV600E mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, revealing a fate change at melanoma initiation in this model. NCP transcription factors, including sox10, regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation, which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
DA - 2016/01/29/
|
||||||
|
PY - 2016
|
||||||
|
DO - 10.1126/science.aad2197
|
||||||
|
DP - science.sciencemag.org
|
||||||
|
VL - 351
|
||||||
|
IS - 6272
|
||||||
|
SP - aad2197
|
||||||
|
LA - en
|
||||||
|
SN - 0036-8075, 1095-9203
|
||||||
|
UR - http://science.sciencemag.org/content/351/6272/aad2197
|
||||||
|
Y2 - 2016/01/29/T14:40:26Z
|
||||||
|
KW - Development
|
||||||
|
KW - SKCM
|
||||||
|
KW - classics
|
||||||
|
KW - epigenetics
|
||||||
|
KW - evolution
|
||||||
|
KW - melanoma
|
||||||
|
KW - super_enhancer
|
||||||
|
KW - zebrafish
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Lipinski, K. A., Barber, L. J., Davies, M. N., Ashenden, M., Sottoriva, A., & Gerlinger, M. (2016). <a class="doctitle" href="http://www.sciencedirect.com/science/article/pii/S2405803315000692">Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine.</a> <i>Trends in Cancer</i>, <i>2</i>(1), 49–63. http://doi.org/10.1016/j.trecan.2015.11.003</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection‚ which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes‚ which have been extensively studied in evolutionary biology‚ limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{lipinski_cancer_2016,
|
||||||
|
title = {Cancer {Evolution} and the {Limits} of {Predictability} in {Precision} {Cancer} {Medicine}},
|
||||||
|
volume = {2},
|
||||||
|
issn = {2405-8033},
|
||||||
|
url = {http://www.sciencedirect.com/science/article/pii/S2405803315000692},
|
||||||
|
doi = {10.1016/j.trecan.2015.11.003},
|
||||||
|
number = {1},
|
||||||
|
urldate = {2016-01-30TZ},
|
||||||
|
journal = {Trends in Cancer},
|
||||||
|
author = {Lipinski, Kamil A. and Barber, Louise J. and Davies, Matthew N. and Ashenden, Matthew and Sottoriva, Andrea and Gerlinger, Marco},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {classics, evolution, heterogeneity, resistance, review},
|
||||||
|
pages = {49--63}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine
|
||||||
|
AU - Lipinski, Kamil A.
|
||||||
|
AU - Barber, Louise J.
|
||||||
|
AU - Davies, Matthew N.
|
||||||
|
AU - Ashenden, Matthew
|
||||||
|
AU - Sottoriva, Andrea
|
||||||
|
AU - Gerlinger, Marco
|
||||||
|
T2 - Trends in Cancer
|
||||||
|
AB - The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.
|
||||||
|
DA - 2016/01//
|
||||||
|
PY - 2016
|
||||||
|
DO - 10.1016/j.trecan.2015.11.003
|
||||||
|
DP - ScienceDirect
|
||||||
|
VL - 2
|
||||||
|
IS - 1
|
||||||
|
SP - 49
|
||||||
|
EP - 63
|
||||||
|
J2 - Trends in Cancer
|
||||||
|
SN - 2405-8033
|
||||||
|
UR - http://www.sciencedirect.com/science/article/pii/S2405803315000692
|
||||||
|
Y2 - 2016/01/30/T22:58:32Z
|
||||||
|
KW - classics
|
||||||
|
KW - evolution
|
||||||
|
KW - heterogeneity
|
||||||
|
KW - resistance
|
||||||
|
KW - review
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Trapnell, C. (2015). <a class="doctitle" href="http://genome.cshlp.org/content/25/10/1491">Defining cell types and states with single-cell genomics.</a> <i>Genome Research</i>, <i>25</i>(10), 1491–1498. http://doi.org/10.1101/gr.190595.115</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">A revolution in cellular measurement technology is under way: For the first time‚ we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state‚ but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states‚ over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape‚ but illuminates the molecular mechanisms that shape the landscape itself. However‚ single-cell genomics is a field in its infancy‚ with many experimental and computational advances needed to fully realize its full potential.</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{trapnell_defining_2015,
|
||||||
|
title = {Defining cell types and states with single-cell genomics},
|
||||||
|
volume = {25},
|
||||||
|
issn = {1088-9051, 1549-5469},
|
||||||
|
url = {http://genome.cshlp.org/content/25/10/1491},
|
||||||
|
doi = {10.1101/gr.190595.115},
|
||||||
|
language = {en},
|
||||||
|
number = {10},
|
||||||
|
urldate = {2015-10-14TZ},
|
||||||
|
journal = {Genome Research},
|
||||||
|
author = {Trapnell, Cole},
|
||||||
|
month = oct,
|
||||||
|
year = {2015},
|
||||||
|
pmid = {26430159},
|
||||||
|
keywords = {Waddington, capacitance, chromatin, classics, epigenetics, evolution, genomics, ideas, oped, review, single-cell},
|
||||||
|
pages = {1491--1498}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - Defining cell types and states with single-cell genomics
|
||||||
|
AU - Trapnell, Cole
|
||||||
|
T2 - Genome Research
|
||||||
|
AB - A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.
|
||||||
|
DA - 2015/10/01/
|
||||||
|
PY - 2015
|
||||||
|
DO - 10.1101/gr.190595.115
|
||||||
|
DP - genome.cshlp.org
|
||||||
|
VL - 25
|
||||||
|
IS - 10
|
||||||
|
SP - 1491
|
||||||
|
EP - 1498
|
||||||
|
J2 - Genome Res.
|
||||||
|
LA - en
|
||||||
|
SN - 1088-9051, 1549-5469
|
||||||
|
UR - http://genome.cshlp.org/content/25/10/1491
|
||||||
|
Y2 - 2015/10/14/T06:07:23Z
|
||||||
|
KW - Waddington
|
||||||
|
KW - capacitance
|
||||||
|
KW - chromatin
|
||||||
|
KW - classics
|
||||||
|
KW - epigenetics
|
||||||
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|
||||||
|
KW - genomics
|
||||||
|
KW - ideas
|
||||||
|
KW - oped
|
||||||
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KW - review
|
||||||
|
KW - single-cell
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Jacobs, F. M. J., Greenberg, D., Nguyen, N., Haeussler, M., Ewing, A. D., Katzman, S., … Haussler, D. (2014). <a class="doctitle" href="http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html">An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.</a> <i>Nature</i>, <i>516</i>(7530), 242–245. http://doi.org/10.1038/nature13760</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave‚ the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells‚ transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex‚ which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However‚ the identity of KZNF genes battling retrotransposons currently active in the human genome‚ such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1)‚ is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until [sim]12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93/’s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes‚ and this is followed by mutations in these retrotransposons to evade repression‚ a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{jacobs_evolutionary_2014,
|
||||||
|
title = {An evolutionary arms race between {KRAB} zinc-finger genes {ZNF}91/93 and {SVA}/{L}1 retrotransposons},
|
||||||
|
volume = {516},
|
||||||
|
copyright = {© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
|
||||||
|
issn = {0028-0836},
|
||||||
|
url = {http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html},
|
||||||
|
doi = {10.1038/nature13760},
|
||||||
|
language = {en},
|
||||||
|
number = {7530},
|
||||||
|
urldate = {2015-10-12TZ},
|
||||||
|
journal = {Nature},
|
||||||
|
author = {Jacobs, Frank M. J. and Greenberg, David and Nguyen, Ngan and Haeussler, Maximilian and Ewing, Adam D. and Katzman, Sol and Paten, Benedict and Salama, Sofie R. and Haussler, David},
|
||||||
|
month = dec,
|
||||||
|
year = {2014},
|
||||||
|
keywords = {classics, genereg, ideas, interactions, lncrna, network, transposon},
|
||||||
|
pages = {242--245}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
|
||||||
|
AU - Jacobs, Frank M. J.
|
||||||
|
AU - Greenberg, David
|
||||||
|
AU - Nguyen, Ngan
|
||||||
|
AU - Haeussler, Maximilian
|
||||||
|
AU - Ewing, Adam D.
|
||||||
|
AU - Katzman, Sol
|
||||||
|
AU - Paten, Benedict
|
||||||
|
AU - Salama, Sofie R.
|
||||||
|
AU - Haussler, David
|
||||||
|
T2 - Nature
|
||||||
|
AB - Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex, which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1), is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until [sim]12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93/'s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.
|
||||||
|
DA - 2014/12/11/
|
||||||
|
PY - 2014
|
||||||
|
DO - 10.1038/nature13760
|
||||||
|
DP - www.nature.com
|
||||||
|
VL - 516
|
||||||
|
IS - 7530
|
||||||
|
SP - 242
|
||||||
|
EP - 245
|
||||||
|
J2 - Nature
|
||||||
|
LA - en
|
||||||
|
SN - 0028-0836
|
||||||
|
UR - http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html
|
||||||
|
Y2 - 2015/10/12/T21:07:51Z
|
||||||
|
KW - classics
|
||||||
|
KW - genereg
|
||||||
|
KW - ideas
|
||||||
|
KW - interactions
|
||||||
|
KW - lncrna
|
||||||
|
KW - network
|
||||||
|
KW - transposon
|
||||||
|
ER -</div></div></div></div></div></div>
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<div class="full-bib-section"><div class="bib-item"><div class="csl-entry">Beerenwinkel, N., Greenman, C. D., & Lagergren, J. (2016). <a class="doctitle" href="http://dx.doi.org/10.1371/journal.pcbi.1004717">Computational Cancer Biology: An Evolutionary Perspective.</a> <i>PLoS Comput Biol</i>, <i>12</i>(2), e1004717. http://doi.org/10.1371/journal.pcbi.1004717</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{beerenwinkel_computational_2016,
|
||||||
|
title = {Computational {Cancer} {Biology}: {An} {Evolutionary} {Perspective}},
|
||||||
|
volume = {12},
|
||||||
|
shorttitle = {Computational {Cancer} {Biology}},
|
||||||
|
url = {http://dx.doi.org/10.1371/journal.pcbi.1004717},
|
||||||
|
doi = {10.1371/journal.pcbi.1004717},
|
||||||
|
number = {2},
|
||||||
|
urldate = {2016-02-05TZ},
|
||||||
|
journal = {PLoS Comput Biol},
|
||||||
|
author = {Beerenwinkel, Niko and Greenman, Chris D. and Lagergren, Jens},
|
||||||
|
month = feb,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {cancer, concepts, darwinian, epigenetics, evolution, mathematical modeling, review, statistics, variant},
|
||||||
|
pages = {e1004717}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - Computational Cancer Biology: An Evolutionary Perspective
|
||||||
|
AU - Beerenwinkel, Niko
|
||||||
|
AU - Greenman, Chris D.
|
||||||
|
AU - Lagergren, Jens
|
||||||
|
T2 - PLoS Comput Biol
|
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DA - 2016/02/04/
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PY - 2016
|
||||||
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DO - 10.1371/journal.pcbi.1004717
|
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DP - PLoS Journals
|
||||||
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VL - 12
|
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IS - 2
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SP - e1004717
|
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J2 - PLoS Comput Biol
|
||||||
|
ST - Computational Cancer Biology
|
||||||
|
UR - http://dx.doi.org/10.1371/journal.pcbi.1004717
|
||||||
|
Y2 - 2016/02/05/T20:21:50Z
|
||||||
|
KW - cancer
|
||||||
|
KW - concepts
|
||||||
|
KW - darwinian
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|
KW - epigenetics
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|
KW - evolution
|
||||||
|
KW - mathematical modeling
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KW - review
|
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KW - statistics
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KW - variant
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|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Kaufman, C. K., Mosimann, C., Fan, Z. P., Yang, S., Thomas, A. J., Ablain, J., … Zon, L. I. (2016). <a class="doctitle" href="http://science.sciencemag.org/content/351/6272/aad2197">A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation.</a> <i>Science</i>, <i>351</i>(6272), aad2197. http://doi.org/10.1126/science.aad2197</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">Visualizing the beginnings of melanoma
|
||||||
|
In cancer biology‚ a tumor begins from a single cell within a group of precancerous cells that share genetic mutations. Kaufman et al. used a zebrafish melanoma model to visualize cancer initiation (see the Perspective by Boumahdi and Blanpain). They used a fluorescent reporter that specifically lit up neural crest progenitors that are only present during embryogenesis or during adult melanoma tumor formation. The appearance of this tumor correlated with a set of gene regulatory elements‚ called super-enhancers‚ whose identification and manipulation may prove beneficial in detecting and preventing melanoma initiation.
|
||||||
|
Science‚ this issue p. 10.1126/science.aad3867; see also p. 453
|
||||||
|
Structured Abstract
|
||||||
|
INTRODUCTIONThe “cancerized field” concept posits that cells in a given tissue sharing an oncogenic mutation are cancer-prone‚ yet only discreet clones within the field initiate tumors. Studying the process of cancer initiation has remained challenging because of (i) the rarity of these events‚ (ii) the difficulty of visiualizing initiating clones in living organisms‚ and (iii) the transient nature of a newly transformed clone emerging before it expands to form an early tumor. A more complete understanding of the molecular processes that regulate cancer initiation could provide important prognostic information about which precancerous lesions are most prone to becoming cancer and also implicate druggable molecular pathways that‚ when inhibited‚ may prevent the cancer from ever starting.
|
||||||
|
RATIONALEThe majority of benign nevi carry oncogenic BRAFV600E mutations and can be considered a cancerized field of melanocytes‚ but they only rarely convert to melanoma. In an effort to define events that initiate cancer‚ we used a melanoma model in the zebrafish in which the human BRAFV600E oncogene is driven by the melanocyte-specific mitfa promoter. When bred into a p53 mutant background‚ these fish develop melanoma tumors over the course of many months. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and is specifically reexpressed only in melanoma tumors‚ making it an ideal candidate for tracking melanoma from initiation onward.
|
||||||
|
RESULTSWe developed a crestin:EGFP reporter that recapitulates the embryonic neural crest expression pattern of crestin and its expression in melanoma tumors. We show through live imaging of transgenic zebrafish crestin reporters that within a cancerized field (BRAFV600E-mutant; p53-deficient)‚ a single melanocyte reactivates the NCP state‚ and this establishes that a fate change occurs at melanoma initiation in this model. Early crestin+ patches of cells expand and are transplantable in a manner consistent with their possessing tumorigenic activity‚ and they exhibit a gene expression pattern consistent with the NCP identity readout by the crestin reporter. The crestin element is regulated by NCP transcription factors‚ including sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation‚ whereas CRISPR/Cas9 targeting of sox10 delayed melanoma onset. We show activation of super-enhancers at NCP genes in both zebrafish and human melanomas‚ identifying an epigenetic mechanism for control of this NCP signature leading to melanoma.
|
||||||
|
CONCLUSIONThis work using our zebrafish melanoma model and in vivo reporter of NCP identity allows us to see cancer from its birth as a single cell and shows the importance of NCP-state reemergence as a key event in melanoma initiation from a field of cancer-prone melanocytes. Thus‚ in addition to the typical fixed genetic alterations in oncogenes and tumor supressors that are required for cancer development‚ the reemergence of progenitor identity may be an additional rate-limiting step in the formation of melanoma. Preventing NCP reemergence in a field of cancer-prone melanocytes may thus prove therapeutically useful‚ and the association of NCP genes with super-enhancer regulatory elements implicates the associated druggable epigenetic machinery in this process. Download high-res image Open in new tab Download Powerpoint Neural crest reporter expression in melanoma.The crestin:EGFP transgene is specifically expressed in melanoma in BRAFV600E/p53 mutant melanoma-prone zebrafish. (Top) A single cell expressing crestin:EGFP expands into a small patch of cells over the course of 2 weeks‚ capturing the initiation of melanoma formation (bracket). (Bottom) A fully formed melanoma specifically expresses crestin:EGFP‚ whereas the rest of the fish remains EGFP-negative.
|
||||||
|
The “cancerized field” concept posits that cancer-prone cells in a given tissue share an oncogenic mutation‚ but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAFV600E mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAFV600E-mutant; p53-deficient)‚ a single melanocyte reactivates the NCP state‚ revealing a fate change at melanoma initiation in this model. NCP transcription factors‚ including sox10‚ regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation‚ which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{kaufman_zebrafish_2016,
|
||||||
|
title = {A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation},
|
||||||
|
volume = {351},
|
||||||
|
copyright = {Copyright © 2016, American Association for the Advancement of Science},
|
||||||
|
issn = {0036-8075, 1095-9203},
|
||||||
|
url = {http://science.sciencemag.org/content/351/6272/aad2197},
|
||||||
|
doi = {10.1126/science.aad2197},
|
||||||
|
language = {en},
|
||||||
|
number = {6272},
|
||||||
|
urldate = {2016-01-29TZ},
|
||||||
|
journal = {Science},
|
||||||
|
author = {Kaufman, Charles K. and Mosimann, Christian and Fan, Zi Peng and Yang, Song and Thomas, Andrew J. and Ablain, Julien and Tan, Justin L. and Fogley, Rachel D. and Rooijen, Ellen van and Hagedorn, Elliott J. and Ciarlo, Christie and White, Richard M. and Matos, Dominick A. and Puller, Ann-Christin and Santoriello, Cristina and Liao, Eric C. and Young, Richard A. and Zon, Leonard I.},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {Development, SKCM, classics, epigenetics, evolution, melanoma, super\_enhancer, zebrafish},
|
||||||
|
pages = {aad2197}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation
|
||||||
|
AU - Kaufman, Charles K.
|
||||||
|
AU - Mosimann, Christian
|
||||||
|
AU - Fan, Zi Peng
|
||||||
|
AU - Yang, Song
|
||||||
|
AU - Thomas, Andrew J.
|
||||||
|
AU - Ablain, Julien
|
||||||
|
AU - Tan, Justin L.
|
||||||
|
AU - Fogley, Rachel D.
|
||||||
|
AU - Rooijen, Ellen van
|
||||||
|
AU - Hagedorn, Elliott J.
|
||||||
|
AU - Ciarlo, Christie
|
||||||
|
AU - White, Richard M.
|
||||||
|
AU - Matos, Dominick A.
|
||||||
|
AU - Puller, Ann-Christin
|
||||||
|
AU - Santoriello, Cristina
|
||||||
|
AU - Liao, Eric C.
|
||||||
|
AU - Young, Richard A.
|
||||||
|
AU - Zon, Leonard I.
|
||||||
|
T2 - Science
|
||||||
|
AB - Visualizing the beginnings of melanoma
|
||||||
|
In cancer biology, a tumor begins from a single cell within a group of precancerous cells that share genetic mutations. Kaufman et al. used a zebrafish melanoma model to visualize cancer initiation (see the Perspective by Boumahdi and Blanpain). They used a fluorescent reporter that specifically lit up neural crest progenitors that are only present during embryogenesis or during adult melanoma tumor formation. The appearance of this tumor correlated with a set of gene regulatory elements, called super-enhancers, whose identification and manipulation may prove beneficial in detecting and preventing melanoma initiation.
|
||||||
|
Science, this issue p. 10.1126/science.aad3867; see also p. 453
|
||||||
|
Structured Abstract
|
||||||
|
INTRODUCTIONThe “cancerized field” concept posits that cells in a given tissue sharing an oncogenic mutation are cancer-prone, yet only discreet clones within the field initiate tumors. Studying the process of cancer initiation has remained challenging because of (i) the rarity of these events, (ii) the difficulty of visiualizing initiating clones in living organisms, and (iii) the transient nature of a newly transformed clone emerging before it expands to form an early tumor. A more complete understanding of the molecular processes that regulate cancer initiation could provide important prognostic information about which precancerous lesions are most prone to becoming cancer and also implicate druggable molecular pathways that, when inhibited, may prevent the cancer from ever starting.
|
||||||
|
RATIONALEThe majority of benign nevi carry oncogenic BRAFV600E mutations and can be considered a cancerized field of melanocytes, but they only rarely convert to melanoma. In an effort to define events that initiate cancer, we used a melanoma model in the zebrafish in which the human BRAFV600E oncogene is driven by the melanocyte-specific mitfa promoter. When bred into a p53 mutant background, these fish develop melanoma tumors over the course of many months. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and is specifically reexpressed only in melanoma tumors, making it an ideal candidate for tracking melanoma from initiation onward.
|
||||||
|
RESULTSWe developed a crestin:EGFP reporter that recapitulates the embryonic neural crest expression pattern of crestin and its expression in melanoma tumors. We show through live imaging of transgenic zebrafish crestin reporters that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, and this establishes that a fate change occurs at melanoma initiation in this model. Early crestin+ patches of cells expand and are transplantable in a manner consistent with their possessing tumorigenic activity, and they exhibit a gene expression pattern consistent with the NCP identity readout by the crestin reporter. The crestin element is regulated by NCP transcription factors, including sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation, whereas CRISPR/Cas9 targeting of sox10 delayed melanoma onset. We show activation of super-enhancers at NCP genes in both zebrafish and human melanomas, identifying an epigenetic mechanism for control of this NCP signature leading to melanoma.
|
||||||
|
CONCLUSIONThis work using our zebrafish melanoma model and in vivo reporter of NCP identity allows us to see cancer from its birth as a single cell and shows the importance of NCP-state reemergence as a key event in melanoma initiation from a field of cancer-prone melanocytes. Thus, in addition to the typical fixed genetic alterations in oncogenes and tumor supressors that are required for cancer development, the reemergence of progenitor identity may be an additional rate-limiting step in the formation of melanoma. Preventing NCP reemergence in a field of cancer-prone melanocytes may thus prove therapeutically useful, and the association of NCP genes with super-enhancer regulatory elements implicates the associated druggable epigenetic machinery in this process. Download high-res image Open in new tab Download Powerpoint Neural crest reporter expression in melanoma.The crestin:EGFP transgene is specifically expressed in melanoma in BRAFV600E/p53 mutant melanoma-prone zebrafish. (Top) A single cell expressing crestin:EGFP expands into a small patch of cells over the course of 2 weeks, capturing the initiation of melanoma formation (bracket). (Bottom) A fully formed melanoma specifically expresses crestin:EGFP, whereas the rest of the fish remains EGFP-negative.
|
||||||
|
The “cancerized field” concept posits that cancer-prone cells in a given tissue share an oncogenic mutation, but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAFV600E mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, revealing a fate change at melanoma initiation in this model. NCP transcription factors, including sox10, regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation, which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
DA - 2016/01/29/
|
||||||
|
PY - 2016
|
||||||
|
DO - 10.1126/science.aad2197
|
||||||
|
DP - science.sciencemag.org
|
||||||
|
VL - 351
|
||||||
|
IS - 6272
|
||||||
|
SP - aad2197
|
||||||
|
LA - en
|
||||||
|
SN - 0036-8075, 1095-9203
|
||||||
|
UR - http://science.sciencemag.org/content/351/6272/aad2197
|
||||||
|
Y2 - 2016/01/29/T14:40:26Z
|
||||||
|
KW - Development
|
||||||
|
KW - SKCM
|
||||||
|
KW - classics
|
||||||
|
KW - epigenetics
|
||||||
|
KW - evolution
|
||||||
|
KW - melanoma
|
||||||
|
KW - super_enhancer
|
||||||
|
KW - zebrafish
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Lipinski, K. A., Barber, L. J., Davies, M. N., Ashenden, M., Sottoriva, A., & Gerlinger, M. (2016). <a class="doctitle" href="http://www.sciencedirect.com/science/article/pii/S2405803315000692">Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine.</a> <i>Trends in Cancer</i>, <i>2</i>(1), 49–63. http://doi.org/10.1016/j.trecan.2015.11.003</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection‚ which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes‚ which have been extensively studied in evolutionary biology‚ limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{lipinski_cancer_2016,
|
||||||
|
title = {Cancer {Evolution} and the {Limits} of {Predictability} in {Precision} {Cancer} {Medicine}},
|
||||||
|
volume = {2},
|
||||||
|
issn = {2405-8033},
|
||||||
|
url = {http://www.sciencedirect.com/science/article/pii/S2405803315000692},
|
||||||
|
doi = {10.1016/j.trecan.2015.11.003},
|
||||||
|
number = {1},
|
||||||
|
urldate = {2016-01-30TZ},
|
||||||
|
journal = {Trends in Cancer},
|
||||||
|
author = {Lipinski, Kamil A. and Barber, Louise J. and Davies, Matthew N. and Ashenden, Matthew and Sottoriva, Andrea and Gerlinger, Marco},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {classics, evolution, heterogeneity, resistance, review},
|
||||||
|
pages = {49--63}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine
|
||||||
|
AU - Lipinski, Kamil A.
|
||||||
|
AU - Barber, Louise J.
|
||||||
|
AU - Davies, Matthew N.
|
||||||
|
AU - Ashenden, Matthew
|
||||||
|
AU - Sottoriva, Andrea
|
||||||
|
AU - Gerlinger, Marco
|
||||||
|
T2 - Trends in Cancer
|
||||||
|
AB - The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.
|
||||||
|
DA - 2016/01//
|
||||||
|
PY - 2016
|
||||||
|
DO - 10.1016/j.trecan.2015.11.003
|
||||||
|
DP - ScienceDirect
|
||||||
|
VL - 2
|
||||||
|
IS - 1
|
||||||
|
SP - 49
|
||||||
|
EP - 63
|
||||||
|
J2 - Trends in Cancer
|
||||||
|
SN - 2405-8033
|
||||||
|
UR - http://www.sciencedirect.com/science/article/pii/S2405803315000692
|
||||||
|
Y2 - 2016/01/30/T22:58:32Z
|
||||||
|
KW - classics
|
||||||
|
KW - evolution
|
||||||
|
KW - heterogeneity
|
||||||
|
KW - resistance
|
||||||
|
KW - review
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Trapnell, C. (2015). <a class="doctitle" href="http://genome.cshlp.org/content/25/10/1491">Defining cell types and states with single-cell genomics.</a> <i>Genome Research</i>, <i>25</i>(10), 1491–1498. http://doi.org/10.1101/gr.190595.115</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">A revolution in cellular measurement technology is under way: For the first time‚ we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state‚ but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states‚ over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape‚ but illuminates the molecular mechanisms that shape the landscape itself. However‚ single-cell genomics is a field in its infancy‚ with many experimental and computational advances needed to fully realize its full potential.</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{trapnell_defining_2015,
|
||||||
|
title = {Defining cell types and states with single-cell genomics},
|
||||||
|
volume = {25},
|
||||||
|
issn = {1088-9051, 1549-5469},
|
||||||
|
url = {http://genome.cshlp.org/content/25/10/1491},
|
||||||
|
doi = {10.1101/gr.190595.115},
|
||||||
|
language = {en},
|
||||||
|
number = {10},
|
||||||
|
urldate = {2015-10-14TZ},
|
||||||
|
journal = {Genome Research},
|
||||||
|
author = {Trapnell, Cole},
|
||||||
|
month = oct,
|
||||||
|
year = {2015},
|
||||||
|
pmid = {26430159},
|
||||||
|
keywords = {Waddington, capacitance, chromatin, classics, epigenetics, evolution, genomics, ideas, oped, review, single-cell},
|
||||||
|
pages = {1491--1498}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - Defining cell types and states with single-cell genomics
|
||||||
|
AU - Trapnell, Cole
|
||||||
|
T2 - Genome Research
|
||||||
|
AB - A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.
|
||||||
|
DA - 2015/10/01/
|
||||||
|
PY - 2015
|
||||||
|
DO - 10.1101/gr.190595.115
|
||||||
|
DP - genome.cshlp.org
|
||||||
|
VL - 25
|
||||||
|
IS - 10
|
||||||
|
SP - 1491
|
||||||
|
EP - 1498
|
||||||
|
J2 - Genome Res.
|
||||||
|
LA - en
|
||||||
|
SN - 1088-9051, 1549-5469
|
||||||
|
UR - http://genome.cshlp.org/content/25/10/1491
|
||||||
|
Y2 - 2015/10/14/T06:07:23Z
|
||||||
|
KW - Waddington
|
||||||
|
KW - capacitance
|
||||||
|
KW - chromatin
|
||||||
|
KW - classics
|
||||||
|
KW - epigenetics
|
||||||
|
KW - evolution
|
||||||
|
KW - genomics
|
||||||
|
KW - ideas
|
||||||
|
KW - oped
|
||||||
|
KW - review
|
||||||
|
KW - single-cell
|
||||||
|
ER -</div></div></div></div><div class="bib-item"><div class="csl-entry">Jacobs, F. M. J., Greenberg, D., Nguyen, N., Haeussler, M., Ewing, A. D., Katzman, S., … Haussler, D. (2014). <a class="doctitle" href="http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html">An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.</a> <i>Nature</i>, <i>516</i>(7530), 242–245. http://doi.org/10.1038/nature13760</div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">abstract</a><div class="bibshowhide"><div class="abstract">Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave‚ the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells‚ transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex‚ which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However‚ the identity of KZNF genes battling retrotransposons currently active in the human genome‚ such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1)‚ is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until [sim]12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93/’s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes‚ and this is followed by mutations in these retrotransposons to evade repression‚ a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.</div></div></div><div class="blink"><a href="javascript:show(this);" onclick="show(this);">bib</a><div class="bibshowhide"><div class="bib">@article{jacobs_evolutionary_2014,
|
||||||
|
title = {An evolutionary arms race between {KRAB} zinc-finger genes {ZNF}91/93 and {SVA}/{L}1 retrotransposons},
|
||||||
|
volume = {516},
|
||||||
|
copyright = {© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
|
||||||
|
issn = {0028-0836},
|
||||||
|
url = {http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html},
|
||||||
|
doi = {10.1038/nature13760},
|
||||||
|
language = {en},
|
||||||
|
number = {7530},
|
||||||
|
urldate = {2015-10-12TZ},
|
||||||
|
journal = {Nature},
|
||||||
|
author = {Jacobs, Frank M. J. and Greenberg, David and Nguyen, Ngan and Haeussler, Maximilian and Ewing, Adam D. and Katzman, Sol and Paten, Benedict and Salama, Sofie R. and Haussler, David},
|
||||||
|
month = dec,
|
||||||
|
year = {2014},
|
||||||
|
keywords = {classics, genereg, ideas, interactions, lncrna, network, transposon},
|
||||||
|
pages = {242--245}
|
||||||
|
}</div></div></div><div class="blink"><a title="Download EndNote record" href="javascript:downloadFile(this);" onclick="downloadFile(this);">ris</a><div class="bibshowhide"><div class="ris">TY - JOUR
|
||||||
|
TI - An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
|
||||||
|
AU - Jacobs, Frank M. J.
|
||||||
|
AU - Greenberg, David
|
||||||
|
AU - Nguyen, Ngan
|
||||||
|
AU - Haeussler, Maximilian
|
||||||
|
AU - Ewing, Adam D.
|
||||||
|
AU - Katzman, Sol
|
||||||
|
AU - Paten, Benedict
|
||||||
|
AU - Salama, Sofie R.
|
||||||
|
AU - Haussler, David
|
||||||
|
T2 - Nature
|
||||||
|
AB - Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex, which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1), is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until [sim]12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93/'s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.
|
||||||
|
DA - 2014/12/11/
|
||||||
|
PY - 2014
|
||||||
|
DO - 10.1038/nature13760
|
||||||
|
DP - www.nature.com
|
||||||
|
VL - 516
|
||||||
|
IS - 7530
|
||||||
|
SP - 242
|
||||||
|
EP - 245
|
||||||
|
J2 - Nature
|
||||||
|
LA - en
|
||||||
|
SN - 0028-0836
|
||||||
|
UR - http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html
|
||||||
|
Y2 - 2015/10/12/T21:07:51Z
|
||||||
|
KW - classics
|
||||||
|
KW - genereg
|
||||||
|
KW - ideas
|
||||||
|
KW - interactions
|
||||||
|
KW - lncrna
|
||||||
|
KW - network
|
||||||
|
KW - transposon
|
||||||
|
ER -</div></div></div></div></div></div>
|
||||||
16
_includes/printmsgpages.html
Normal file
16
_includes/printmsgpages.html
Normal file
|
|
@ -0,0 +1,16 @@
|
||||||
|
<div class="printMsg">
|
||||||
|
<table>
|
||||||
|
<thead>
|
||||||
|
<tr>
|
||||||
|
<th><i class="fa fa-twitter">@{{ site.owner.twitter }}</i></th>
|
||||||
|
<th>QR code</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td><i class="fa fa-anchor"> {{ site.url }}{{ page.url }}</i><br /><i class="fa fa-calendar"> {% if page.modified.size > 2 %}{{ page.modified }}{% else %}{{ site.time | date: "%d-%b-%y" }}{% endif %}</i><br /><i class="fa fa-creative-commons"> BY-NC-SA 4.0 {{ site.url }}/disclosure</i></td>
|
||||||
|
<td><img src="https://chart.googleapis.com/chart?chs=150x150&cht=qr&chl={{ site.url }}{{ page.url }}&choe=UTF-8" alt="{{ site.url }}{{ page.url }}" /></td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</div>
|
||||||
16
_includes/printmsgposts.html
Normal file
16
_includes/printmsgposts.html
Normal file
|
|
@ -0,0 +1,16 @@
|
||||||
|
<div class="printMsg">
|
||||||
|
<table>
|
||||||
|
<thead>
|
||||||
|
<tr>
|
||||||
|
<th><i class="fa fa-twitter">@{{ site.owner.twitter }}</i></th>
|
||||||
|
<th>QR code</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td><i class="fa fa-anchor"> {{ site.url }}{{ page.url }}</i><br /><i class="fa fa-calendar"> {% if page.modified.size > 2 %}{{ page.modified }}{% else %}{{ page.date | date: "%d-%b-%y" }}{% endif %}</i><br /><i class="fa fa-creative-commons"> BY-NC-SA 4.0 {{ site.url }}/disclosure</i></td>
|
||||||
|
<td><img src="https://chart.googleapis.com/chart?chs=150x150&cht=qr&chl={{ site.url }}{{ page.url }}&choe=UTF-8" alt="{{ site.url }}{{ page.url }}" /></td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
</div>
|
||||||
1
_includes/rblogger.html
Normal file
1
_includes/rblogger.html
Normal file
|
|
@ -0,0 +1 @@
|
||||||
|
<p>This post may be cross-posted at <a href="http://www.r-bloggers.com" rel="external">R-bloggers.com</a> - blog on <code class="highlighter-rouge">R</code> news and tutorials contributed by more than 500 <code class="highlighter-rouge">R</code> bloggers. <a href="https://feeds.feedburner.com/RBloggers" title="RSS feed of latest posts from R-blogger" rel="external"> <i class="fa fa-rss"></i></a></p>
|
||||||
25
_includes/scripts.html
Normal file
25
_includes/scripts.html
Normal file
|
|
@ -0,0 +1,25 @@
|
||||||
|
{% if site.google_analytics %}
|
||||||
|
<!-- Asynchronous Google Analytics snippet -->
|
||||||
|
<script>
|
||||||
|
var _gaq = _gaq || [];
|
||||||
|
var pluginUrl =
|
||||||
|
'//www.google-analytics.com/plugins/ga/inpage_linkid.js';
|
||||||
|
_gaq.push(['_require', 'inpage_linkid', pluginUrl]);
|
||||||
|
_gaq.push(['_setAccount', '{{ site.google_analytics }}']);
|
||||||
|
_gaq.push(['_trackPageview']);
|
||||||
|
|
||||||
|
(function() {
|
||||||
|
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
|
||||||
|
ga.src = ('https:' == document.location.protocol ? 'https://' : 'http://') + 'stats.g.doubleclick.net/dc.js';
|
||||||
|
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
|
||||||
|
})();
|
||||||
|
</script>
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
<!-- gist embed -->
|
||||||
|
{% if page.gistembed %}
|
||||||
|
{% include gist_embed.html %}
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
<!-- disqus comments -->
|
||||||
|
{% if page.comments %}{% include disqus_comments.html %}{% endif %}
|
||||||
61
_includes/sidebar.html
Normal file
61
_includes/sidebar.html
Normal file
|
|
@ -0,0 +1,61 @@
|
||||||
|
<!-- Target for toggling the sidebar `.sidebar-checkbox` is for regular
|
||||||
|
styles, `#sidebar-checkbox` for behavior. -->
|
||||||
|
<input type="checkbox" class="sidebar-checkbox" id="sidebar-checkbox">
|
||||||
|
|
||||||
|
<!-- Toggleable sidebar -->
|
||||||
|
<div class="sidebar" id="sidebar">
|
||||||
|
<!-- <div class="sidebar-item">
|
||||||
|
<p>{{ site.description }}</p>
|
||||||
|
</div> -->
|
||||||
|
|
||||||
|
<nav class="sidebar-nav">
|
||||||
|
<!-- a class="sidebar-nav-item{% if page.url == site.baseurl %} active{% endif %}" href="{{ site.baseurl }}/">Home</a-->
|
||||||
|
|
||||||
|
{% comment %}
|
||||||
|
The code below dynamically generates a sidebar nav of pages with
|
||||||
|
`layout: page` in the front-matter. See readme for usage.
|
||||||
|
{% endcomment %}
|
||||||
|
|
||||||
|
{% comment %}
|
||||||
|
<!-- DISABLE AUTO LINKS -->
|
||||||
|
{% assign pages_list = site.pages | sort:"url" %}
|
||||||
|
{% for node in pages_list %}
|
||||||
|
{% if node.title != null %}
|
||||||
|
{% if node.layout == "page" %}
|
||||||
|
<a class="sidebar-nav-item{% if page.url == node.url %} active{% endif %}" href="{{ node.url }}">{{ node.title }}</a>
|
||||||
|
{% endif %}
|
||||||
|
{% endif %}
|
||||||
|
{% endfor %}
|
||||||
|
{% endcomment %}
|
||||||
|
|
||||||
|
{% for link in site.links %}
|
||||||
|
{% if link.external %}
|
||||||
|
<a class="sidebar-nav-item{% if page.url == link.url %} active{% endif %}" href="{{ link.url }}" target="_blank">{{ link.title }}</a>
|
||||||
|
{% else %}
|
||||||
|
<a class="sidebar-nav-item{% if page.url == link.url %} active{% endif %}" href="{{ site.url }}{{ link.url }}">{{ link.title }}</a>
|
||||||
|
{% endif %}
|
||||||
|
{% endfor %}
|
||||||
|
|
||||||
|
{% if site.version %}
|
||||||
|
<a class="sidebar-nav-item" href="{{ site.github_repo }}"><em>lanyon-plus project</em></a>
|
||||||
|
<a class="sidebar-nav-item" href="{{ site.github_repo }}/releases/tag/v{{ site.version }}">Download v{{ site.version }}</a>
|
||||||
|
{% endif %}
|
||||||
|
</nav>
|
||||||
|
|
||||||
|
<hr class="gh">
|
||||||
|
|
||||||
|
{% if site.google_search %}
|
||||||
|
<div id="searchbox2" style="margin:0 auto; display: table;">
|
||||||
|
<div class="searchcont2">
|
||||||
|
<!-- span class="searchicon2"><i class="fa fa-search fa-2x"></i></span -->
|
||||||
|
<form role="search" method="get" action="{{ site.url }}/cse/">
|
||||||
|
<input id="searchString2" name="searchString2"
|
||||||
|
placeholder=" Search" type="text">
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
{% else %}
|
||||||
|
Search box will show up here if Google Custom Search key is set in <code>_config.yml</code>
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
</div>
|
||||||
28
_includes/twitter_card.html
Normal file
28
_includes/twitter_card.html
Normal file
|
|
@ -0,0 +1,28 @@
|
||||||
|
{% if page.videofeature %}
|
||||||
|
<meta name="twitter:card" content="player">
|
||||||
|
{% if page.videocredit %}<meta name="twitter:site" content="@{{ page.videocredit }}">{% else %}
|
||||||
|
<meta name="twitter:site" content="@youtube">{% endif %}
|
||||||
|
{% if page.videoimage %}<meta name="twitter:image" content="{{ page.videoimage }}">{% elsif page.imagefeature %}
|
||||||
|
{% if page.imagefeature contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.urlimg %}
|
||||||
|
{% endif %}
|
||||||
|
<meta name="twitter:image" content="{{ domain }}{{ page.imagefeature }}">{% else %}
|
||||||
|
<meta name="twitter:image" content="{{ site.urlimg }}{{ site.default_bg }}">{% endif %}
|
||||||
|
<meta name="twitter:player" content="{{ page.videofeature }}">
|
||||||
|
<meta name="twitter:player:width" content="1920">
|
||||||
|
<meta name="twitter:player:height" content="1080">
|
||||||
|
{% elsif page.imagefeature %}
|
||||||
|
{% if page.imagefeature contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.urlimg %}
|
||||||
|
{% endif %}
|
||||||
|
<meta name="twitter:card" content="summary_large_image">
|
||||||
|
<meta name="twitter:site" content="@{{ site.owner.twitter }}">
|
||||||
|
<meta name="twitter:image" content="{{ domain }}{{ page.imagefeature }}">
|
||||||
|
{% else %}
|
||||||
|
<meta name="twitter:card" content="summary">
|
||||||
|
<meta name="twitter:site" content="@{{ site.owner.twitter }}">
|
||||||
|
<meta name="twitter:image" content="{% if page.imagesummary %}{{ site.urlimg }}{{ page.imagesummary }}{% else %}{{ site.urlimg }}{{ site.default_bg }}{% endif %}">{% endif %}
|
||||||
5
_includes/youtube.html
Normal file
5
_includes/youtube.html
Normal file
|
|
@ -0,0 +1,5 @@
|
||||||
|
<hr class="transp">
|
||||||
|
<div class="ytube-video-container">
|
||||||
|
<iframe width="560" height="315" src="{{ page.videofeature }}" frameborder="0" allowfullscreen></iframe>
|
||||||
|
</div>
|
||||||
|
<hr class="transp">
|
||||||
59
_layouts/default.html
Normal file
59
_layouts/default.html
Normal file
|
|
@ -0,0 +1,59 @@
|
||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="en-us">
|
||||||
|
<!--
|
||||||
|
====================================================
|
||||||
|
Homepage: {{ site.url }}
|
||||||
|
Credits: {{ site.url }}/disclosure
|
||||||
|
====================================================
|
||||||
|
-->
|
||||||
|
{% include head.html %}
|
||||||
|
|
||||||
|
<body>
|
||||||
|
|
||||||
|
{% include sidebar.html %}
|
||||||
|
|
||||||
|
<!-- Wrap is the content to shift when toggling the sidebar. We wrap the
|
||||||
|
content to avoid any CSS collisions with our real content. -->
|
||||||
|
<div class="wrap">
|
||||||
|
<div class="masthead">
|
||||||
|
<div class="container">
|
||||||
|
<h3 class="masthead-title">
|
||||||
|
<a href="{{ site.baseurl }}/" title="Home">{{ site.title }}</a>
|
||||||
|
<!-- <small>{{ site.tagline }}</small> -->
|
||||||
|
<div class="headicons">
|
||||||
|
<small><a href="{{ site.url }}/about" rel="me" title="About"><i class="iconm iconm-user"></i></a></small>
|
||||||
|
<small><a href="{{ site.url }}/blog" rel="me" title="Blog"><i class="iconm iconm-quill"></i></a></small>
|
||||||
|
<small><a href="{{ site.url }}/contact" rel="me" title="Contact"><i class="iconm iconm-envelop"></i></a></small>
|
||||||
|
</div>
|
||||||
|
</h3>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="container content">
|
||||||
|
{{ content }}
|
||||||
|
{% include footer.html %}
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<label for="sidebar-checkbox" class="sidebar-toggle"></label>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
(function(document) {
|
||||||
|
var toggle = document.querySelector('.sidebar-toggle');
|
||||||
|
var sidebar = document.querySelector('#sidebar');
|
||||||
|
var checkbox = document.querySelector('#sidebar-checkbox');
|
||||||
|
|
||||||
|
document.addEventListener('click', function(e) {
|
||||||
|
var target = e.target;
|
||||||
|
|
||||||
|
if(!checkbox.checked ||
|
||||||
|
sidebar.contains(target) ||
|
||||||
|
(target === checkbox || target === toggle)) return;
|
||||||
|
|
||||||
|
checkbox.checked = false;
|
||||||
|
}, false);
|
||||||
|
})(document);
|
||||||
|
</script>
|
||||||
|
{% include scripts.html %}
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
59
_layouts/default_minimal.html
Normal file
59
_layouts/default_minimal.html
Normal file
|
|
@ -0,0 +1,59 @@
|
||||||
|
<!DOCTYPE html>
|
||||||
|
<html lang="en-us">
|
||||||
|
<!--
|
||||||
|
====================================================
|
||||||
|
Homepage: {{ site.url }}
|
||||||
|
Credits: {{ site.url }}/disclosure
|
||||||
|
====================================================
|
||||||
|
-->
|
||||||
|
{% include head_minimal.html %}
|
||||||
|
|
||||||
|
<body>
|
||||||
|
|
||||||
|
{% include sidebar.html %}
|
||||||
|
|
||||||
|
<!-- Wrap is the content to shift when toggling the sidebar. We wrap the
|
||||||
|
content to avoid any CSS collisions with our real content. -->
|
||||||
|
<div class="wrap">
|
||||||
|
<div class="masthead">
|
||||||
|
<div class="container">
|
||||||
|
<h3 class="masthead-title">
|
||||||
|
<a href="{{ site.baseurl }}/" title="Home">{{ site.title }}</a>
|
||||||
|
<!-- <small>{{ site.tagline }}</small> -->
|
||||||
|
<div class="headicons">
|
||||||
|
<small><a href="{{ site.url }}/about" rel="me" title="About"><i class="iconm iconm-user"></i></a></small>
|
||||||
|
<small><a href="{{ site.url }}/blog" rel="me" title="Blog"><i class="iconm iconm-quill"></i></a></small>
|
||||||
|
<small><a href="{{ site.url }}/contact" rel="me" title="Contact"><i class="iconm iconm-envelop"></i></a></small>
|
||||||
|
</div>
|
||||||
|
</h3>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="container content">
|
||||||
|
{{ content }}
|
||||||
|
{% include footer.html %}
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<label for="sidebar-checkbox" class="sidebar-toggle"></label>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
(function(document) {
|
||||||
|
var toggle = document.querySelector('.sidebar-toggle');
|
||||||
|
var sidebar = document.querySelector('#sidebar');
|
||||||
|
var checkbox = document.querySelector('#sidebar-checkbox');
|
||||||
|
|
||||||
|
document.addEventListener('click', function(e) {
|
||||||
|
var target = e.target;
|
||||||
|
|
||||||
|
if(!checkbox.checked ||
|
||||||
|
sidebar.contains(target) ||
|
||||||
|
(target === checkbox || target === toggle)) return;
|
||||||
|
|
||||||
|
checkbox.checked = false;
|
||||||
|
}, false);
|
||||||
|
})(document);
|
||||||
|
</script>
|
||||||
|
{% include scripts.html %}
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
21
_layouts/page.html
Normal file
21
_layouts/page.html
Normal file
|
|
@ -0,0 +1,21 @@
|
||||||
|
---
|
||||||
|
layout: default
|
||||||
|
---
|
||||||
|
|
||||||
|
<div class="page">
|
||||||
|
<h1 class="page-title">{{ page.title }}</h1>
|
||||||
|
{% if page.show_meta == true %}
|
||||||
|
{% include meta_info.html %}
|
||||||
|
{% endif %}
|
||||||
|
{{ content }}
|
||||||
|
{% if page.show_meta == true %}
|
||||||
|
{% include meta_info.html %}
|
||||||
|
{% endif %}
|
||||||
|
</div>
|
||||||
|
|
||||||
|
{% unless page.hide_printmsg == true %}
|
||||||
|
{% include printmsgpages.html %}
|
||||||
|
{% endunless %}
|
||||||
|
|
||||||
|
<div class="page-break"></div>
|
||||||
|
{% if site.disqus_shortname and page.comments == true %}<div id="disqus_thread"></div><!-- /#disqus_thread -->{% endif %}
|
||||||
62
_layouts/post.html
Normal file
62
_layouts/post.html
Normal file
|
|
@ -0,0 +1,62 @@
|
||||||
|
---
|
||||||
|
layout: default
|
||||||
|
---
|
||||||
|
|
||||||
|
<div class="post">
|
||||||
|
<h1 itemprop="name" class="post-title">{{ page.title }}</h1>
|
||||||
|
<span class="post-date" itemprop="datePublished" content="{{ page.date | date: "%Y-%m-%d" }}"><i class="fa fa-calendar" title="Date published"> <a class="permalink" href="{{ site.url }}{{ page.url }}" itemprop="url" title="Permanent link to this post">{{ page.date | date_to_string }}</a> </i></span>
|
||||||
|
{% if page.modified.size > 2 %}{% assign moddate = page.modified | date_to_string %}{% assign pgdate = page.date | date_to_string %}{% unless moddate == pgdate | date_to_string %}<span class="post-date" itemprop="dateModified" content="{{ page.modified | date: "%Y-%m-%d" }}"><i class="fa fa-edit" title="Last updated"> {{ page.modified | date_to_string }}</i></span>{% endunless %}{% endif %}
|
||||||
|
<span class="post-tags" itemprop="keywords" content="{{ page.tags | array_to_sentence_string }}">{% for tag in page.tags %}{% if forloop.first %}<i class="fa fa-tags" title="page tags"></i>{% endif %} <a href="{{ site.url }}/tags/#{{ tag | cgi_escape }}" title="Pages tagged {{ tag }}" rel="tag">{{ tag }}</a>{% unless forloop.last %} • {% endunless %}{% endfor %}</span>
|
||||||
|
{% unless page.show_meta == false %}
|
||||||
|
{% include meta_info.html %}
|
||||||
|
{% endunless %}
|
||||||
|
{{ content }}
|
||||||
|
<hr>
|
||||||
|
{% if page.tags contains 'R' %}
|
||||||
|
{% include rblogger.html %}
|
||||||
|
{% endif %}
|
||||||
|
<span class="post-date metafoot" itemprop="datePublished" content="{{ page.date | date: "%Y-%m-%d" }}"><i class="fa fa-calendar" title="Date published"> <a class="permalink" href="{{ site.url }}{{ page.url }}" itemprop="url" title="Permanent link to this post">{{ page.date | date_to_string }}</a> </i></span>
|
||||||
|
{% if page.modified.size > 2 %}{% assign moddate = page.modified | date_to_string %}{% assign pgdate = page.date | date_to_string %}{% unless moddate == pgdate | date_to_string %}<span class="post-date metafoot" itemprop="dateModified" content="{{ page.modified | date: "%Y-%m-%d" }}"><i class="fa fa-edit" title="Last updated"> {{ page.modified | date_to_string }}</i></span>{% endunless %}{% endif %}
|
||||||
|
<span class="post-tags" itemprop="keywords" content="{{ page.tags | array_to_sentence_string }}">{% for tag in page.tags %}{% if forloop.first %}<i class="fa fa-tags" title="page tags"></i>{% endif %} <a href="{{ site.url }}/tags/#{{ tag | cgi_escape }}" title="Pages tagged {{ tag }}" rel="tag">{{ tag }}</a>{% unless forloop.last %} • {% endunless %}{% endfor %}</span>
|
||||||
|
{% unless page.show_meta == false %}
|
||||||
|
{% include meta_info.html %}
|
||||||
|
{% endunless %}
|
||||||
|
</div>
|
||||||
|
|
||||||
|
{% unless page.hide_printmsg == true %}
|
||||||
|
{% include printmsgposts.html %}
|
||||||
|
{% endunless %}
|
||||||
|
|
||||||
|
<div class="page-break"></div>
|
||||||
|
<div class="related">
|
||||||
|
<h2>Related Posts</h2>
|
||||||
|
<ul>
|
||||||
|
{% for post in site.posts %}
|
||||||
|
{% if post.url != page.url %}
|
||||||
|
{% for tag in page.tags %}
|
||||||
|
{% if post.tags contains tag %}
|
||||||
|
<li><a href="{{ site.url }}{{ post.url }}">{{ post.title }}</a><br /></li>
|
||||||
|
{% break %}
|
||||||
|
{% endif %}
|
||||||
|
{% endfor %}
|
||||||
|
{% endif %}
|
||||||
|
{% endfor %}
|
||||||
|
</ul>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="prevnext">
|
||||||
|
{% if page.previous.url %}
|
||||||
|
<a class="prevnext-item older" href="{{ site.url }}{{page.previous.url}}" title="{{ page.previous.title }}">Older</a>
|
||||||
|
{% else %}
|
||||||
|
<span class="prevnext-item older">Older</span>
|
||||||
|
{% endif %}
|
||||||
|
{% if page.next.url %}
|
||||||
|
<a class="prevnext-item older" href="{{ site.url }}{{page.next.url}}" title="{{ page.next.title }}">Newer</a>
|
||||||
|
{% else %}
|
||||||
|
<span class="prevnext-item older">Newer</span>
|
||||||
|
{% endif %}
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="page-break"></div>
|
||||||
|
|
||||||
|
{% if site.disqus_shortname and page.comments == true %}<div id="disqus_thread"></div><!-- /#disqus_thread -->{% endif %}
|
||||||
27
_layouts/publ.html
Normal file
27
_layouts/publ.html
Normal file
|
|
@ -0,0 +1,27 @@
|
||||||
|
---
|
||||||
|
layout: default
|
||||||
|
---
|
||||||
|
|
||||||
|
<div class="page">
|
||||||
|
<h1 class="page-title">{{ page.title }}</h1>
|
||||||
|
{% if page.show_meta == true %}
|
||||||
|
{% include meta_info.html %}
|
||||||
|
{% endif %}
|
||||||
|
{{ content }}
|
||||||
|
{% if page.category contains "mypubs" %}
|
||||||
|
{% include mypubs.html %}
|
||||||
|
{% elsif page.category contains "myaoi" %}
|
||||||
|
{% include myaoi.html %}
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
{% if page.show_meta == true %}
|
||||||
|
{% include meta_info.html %}
|
||||||
|
{% endif %}
|
||||||
|
</div>
|
||||||
|
|
||||||
|
{% unless page.hide_printmsg == true %}
|
||||||
|
{% include printmsgpages.html %}
|
||||||
|
{% endunless %}
|
||||||
|
|
||||||
|
<div class="page-break"></div>
|
||||||
|
{% if site.disqus_shortname and page.comments == true %}<div id="disqus_thread"></div><!-- /#disqus_thread -->{% endif %}
|
||||||
34
_layouts/redirect.html
Normal file
34
_layouts/redirect.html
Normal file
|
|
@ -0,0 +1,34 @@
|
||||||
|
---
|
||||||
|
# This layout is used to redirect pages, if you moved them.
|
||||||
|
# Use the following settings in front matter:
|
||||||
|
#
|
||||||
|
# layout: redirect
|
||||||
|
# sitemap: false
|
||||||
|
# permalink: /old-location/
|
||||||
|
# redirect_to: /new-location/
|
||||||
|
#
|
||||||
|
# Idea and Code by: http://codingtips.kanishkkunal.in/about/
|
||||||
|
---
|
||||||
|
<!DOCTYPE html>
|
||||||
|
<html>
|
||||||
|
<head>
|
||||||
|
{% if page.redirect_to contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.url %}
|
||||||
|
{% endif %}
|
||||||
|
<link rel="canonical" href="{{ domain }}{{ page.redirect_to }}"/>
|
||||||
|
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
|
||||||
|
<meta http-equiv="refresh" content="1;url={{ domain }}{{ page.redirect_to }}" />
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<h1>Redirecting...</h1>
|
||||||
|
{% if page.redirect_to contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.url %}
|
||||||
|
{% endif %}
|
||||||
|
If you are not redirected automatically, visit <a href="{{ domain }}{{ page.redirect_to }}">{{ domain }}{{ page.redirect_to }}<a>.
|
||||||
|
<script>location='{{ domain }}{{ page.redirect_to }}'</script>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
288
_posts/2013-01-01-example-content.md
Normal file
288
_posts/2013-01-01-example-content.md
Normal file
|
|
@ -0,0 +1,288 @@
|
||||||
|
---
|
||||||
|
layout: post
|
||||||
|
title: "Example content"
|
||||||
|
date: "2013-01-01"
|
||||||
|
slug: "example_content"
|
||||||
|
description: "Example content from lanyon. If page description is more than 140 words, it will be shown as post summary on home page and blog index else post excerpt will be shown. Same rule is for html meta description: >140 words in description or first 50 words of posts will be shown as summary. Page excerpt supports markdown formatted summary."
|
||||||
|
category:
|
||||||
|
- views
|
||||||
|
- featured
|
||||||
|
# tags will also be used as html meta keywords.
|
||||||
|
tags:
|
||||||
|
- examples
|
||||||
|
- common_tag
|
||||||
|
show_meta: true
|
||||||
|
comments: true
|
||||||
|
mathjax: true
|
||||||
|
gistembed: true
|
||||||
|
published: true
|
||||||
|
noindex: false
|
||||||
|
nofollow: false
|
||||||
|
# hide QR code, permalink block while printing.
|
||||||
|
hide_printmsg: false
|
||||||
|
# show post summary or full post in RSS feed.
|
||||||
|
summaryfeed: false
|
||||||
|
## for twitter summary card with squared image and page description or page excerpt:
|
||||||
|
# imagesummary: foo.png
|
||||||
|
## for twitter card with large image:
|
||||||
|
# imagefeature: "http://img.youtube.com/vi/VEIrQUXm_hY/0.jpg"
|
||||||
|
## for twitter video card: (active for this page)
|
||||||
|
videofeature: "https://www.youtube.com/embed/iG9CE55wbtY"
|
||||||
|
imagefeature: "http://img.youtube.com/vi/iG9CE55wbtY/0.jpg"
|
||||||
|
videocredit: tedtalks
|
||||||
|
---
|
||||||
|
|
||||||
|
Howdy! This is an example blog post that shows features supported in **lanyon-plus** theme. See [raw post](https://raw.githubusercontent.com/dyndna/lanyon-plus/master/_posts/2013-01-01-example-content.md) for required YAML header and liquid tag specifications.
|
||||||
|
|
||||||
|
<!--more-->
|
||||||
|
|
||||||
|
* TOC
|
||||||
|
{:toc}
|
||||||
|
|
||||||
|
### Heading
|
||||||
|
|
||||||
|
# H1
|
||||||
|
{:.no_toc}
|
||||||
|
|
||||||
|
## H2
|
||||||
|
{:.no_toc}
|
||||||
|
|
||||||
|
### H3
|
||||||
|
{:.no_toc}
|
||||||
|
|
||||||
|
#### H4
|
||||||
|
{:.no_toc}
|
||||||
|
|
||||||
|
##### H5
|
||||||
|
{:.no_toc}
|
||||||
|
|
||||||
|
###### H6
|
||||||
|
{:.no_toc}
|
||||||
|
|
||||||
|
Vivamus sagittis lacus vel augue rutrum faucibus dolor auctor. Duis mollis, est non commodo luctus, nisi erat porttitor ligula, eget lacinia odio sem nec elit. Morbi leo risus, porta ac consectetur ac, vestibulum at eros.
|
||||||
|
|
||||||
|
### Inline HTML elements
|
||||||
|
|
||||||
|
HTML defines a long list of available inline tags, a complete list of which can be found on the [Mozilla Developer Network](https://developer.mozilla.org/en-US/docs/Web/HTML/Element).
|
||||||
|
|
||||||
|
- **To bold text**, use `<strong>`.
|
||||||
|
- *To italicize text*, use `<em>`.
|
||||||
|
- Abbreviations, like <abbr title="HyperText Markup Langage">HTML</abbr> should use `<abbr>`, with an optional `title` attribute for the full phrase.
|
||||||
|
- Citations, like <cite>— Mark otto</cite>, should use `<cite>`.
|
||||||
|
- <del>Deleted</del> text should use `<del>` and <ins>inserted</ins> text should use `<ins>`.
|
||||||
|
- Superscript <sup>text</sup> uses `<sup>` and subscript <sub>text</sub> uses `<sub>`.
|
||||||
|
|
||||||
|
Most of these elements are styled by browsers with few modifications on our part.
|
||||||
|
|
||||||
|
### Code
|
||||||
|
|
||||||
|
Cum sociis natoque penatibus et magnis dis `code element` montes, nascetur ridiculus mus.
|
||||||
|
|
||||||
|
{% highlight js %}
|
||||||
|
// Example can be run directly in your JavaScript console
|
||||||
|
|
||||||
|
// Create a function that takes two arguments and returns the sum of those arguments
|
||||||
|
var adder = new Function("a", "b", "return a + b");
|
||||||
|
|
||||||
|
// Call the function
|
||||||
|
adder(2, 6);
|
||||||
|
// > 8
|
||||||
|
{% endhighlight %}
|
||||||
|
|
||||||
|
Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa.
|
||||||
|
|
||||||
|
#### Alternate code block:
|
||||||
|
|
||||||
|
~~~r
|
||||||
|
library(uuid)
|
||||||
|
library(stringr)
|
||||||
|
library(parallel)
|
||||||
|
library(data.table)
|
||||||
|
~~~
|
||||||
|
|
||||||
|
#### `pygments` based highlighting (deprecated)
|
||||||
|
|
||||||
|
{% highlight bash %}
|
||||||
|
library(uuid)
|
||||||
|
library(stringr)
|
||||||
|
library(parallel)
|
||||||
|
library(data.table)
|
||||||
|
{% endhighlight %}
|
||||||
|
|
||||||
|
### Lists
|
||||||
|
|
||||||
|
Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus.
|
||||||
|
|
||||||
|
* Praesent commodo cursus magna, vel scelerisque nisl consectetur et.
|
||||||
|
* Donec id elit non mi porta gravida at eget metus.
|
||||||
|
* Nulla vitae elit libero, a pharetra augue.
|
||||||
|
|
||||||
|
Donec ullamcorper nulla non metus auctor fringilla. Nulla vitae elit libero, a pharetra augue.
|
||||||
|
|
||||||
|
1. Vestibulum id ligula porta felis euismod semper.
|
||||||
|
2. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.
|
||||||
|
3. Maecenas sed diam eget risus varius blandit sit amet non magna.
|
||||||
|
|
||||||
|
Cras mattis consectetur purus sit amet fermentum. Sed posuere consectetur est at lobortis.
|
||||||
|
|
||||||
|
<dl>
|
||||||
|
<dt>HyperText Markup Language (HTML)</dt>
|
||||||
|
<dd>The language used to describe and define the content of a Web page</dd>
|
||||||
|
|
||||||
|
<dt>Cascading Style Sheets (CSS)</dt>
|
||||||
|
<dd>Used to describe the appearance of Web content</dd>
|
||||||
|
|
||||||
|
<dt>JavaScript (JS)</dt>
|
||||||
|
<dd>The programming language used to build advanced Web sites and applications</dd>
|
||||||
|
</dl>
|
||||||
|
|
||||||
|
Integer posuere erat a ante venenatis dapibus posuere velit aliquet. Morbi leo risus, porta ac consectetur ac, vestibulum at eros. Nullam quis risus eget urna mollis ornare vel eu leo.
|
||||||
|
|
||||||
|
### Tables
|
||||||
|
|
||||||
|
#### markdown formatted:
|
||||||
|
|
||||||
|
| Heading 1 | Heading 2 | Heading 3 |
|
||||||
|
| :--- | --- | ---: |
|
||||||
|
| Hello | World | <i class="fa fa-twitter"> @foo</i> |
|
||||||
|
|
||||||
|
Aenean lacinia bibendum nulla sed consectetur. Lorem ipsum dolor sit amet, consectetur adipiscing elit.
|
||||||
|
|
||||||
|
#### html table:
|
||||||
|
|
||||||
|
<table>
|
||||||
|
<thead>
|
||||||
|
<tr>
|
||||||
|
<th>Name</th>
|
||||||
|
<th>Upvotes</th>
|
||||||
|
<th>Downvotes</th>
|
||||||
|
</tr>
|
||||||
|
</thead>
|
||||||
|
<tfoot>
|
||||||
|
<tr>
|
||||||
|
<td>Totals</td>
|
||||||
|
<td>21</td>
|
||||||
|
<td>23</td>
|
||||||
|
</tr>
|
||||||
|
</tfoot>
|
||||||
|
<tbody>
|
||||||
|
<tr>
|
||||||
|
<td>Alice</td>
|
||||||
|
<td>10</td>
|
||||||
|
<td>11</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>Bob</td>
|
||||||
|
<td>4</td>
|
||||||
|
<td>3</td>
|
||||||
|
</tr>
|
||||||
|
<tr>
|
||||||
|
<td>Charlie</td>
|
||||||
|
<td>7</td>
|
||||||
|
<td>9</td>
|
||||||
|
</tr>
|
||||||
|
</tbody>
|
||||||
|
</table>
|
||||||
|
|
||||||
|
### Text highlight:
|
||||||
|
|
||||||
|
Nullam id dolor id nibh ultricies vehicula ut id elit. Sed posuere consectetur est at lobortis. Nullam quis risus eget urna mollis ornare vel eu leo. `Nullam id dolor id nibh ultricies vehicula ut id elit. Highlighted color will be removed during prinintg and replaced with underline.`{:.yelhglt}
|
||||||
|
|
||||||
|
### Blockquotes
|
||||||
|
|
||||||
|
#### stylized
|
||||||
|
|
||||||
|
<blockquote class="style1">
|
||||||
|
Aenean lacinia bibendum nulla sed consectetur. Etiam porta sem malesuada magna mollis euismod.
|
||||||
|
</blockquote>
|
||||||
|
|
||||||
|
#### regular
|
||||||
|
|
||||||
|
>When you bring new things into a society, you can either, it's like the balance of the force. You can either use it for good or you can use it for evil. And what happens when something new: People have a tendency to overdo it; they abuse it.
|
||||||
|
|
||||||
|
### Embed video
|
||||||
|
|
||||||
|
{% include youtube.html %}
|
||||||
|
|
||||||
|
### Embed picture
|
||||||
|
|
||||||
|
{:.text-center img}
|
||||||
|
|
||||||
|
|
||||||
|
### Inline css attributes
|
||||||
|
|
||||||
|
[MahJax source - link open in new window](http://haixing-hu.github.io/programming/2013/09/20/how-to-use-mathjax-in-jekyll-generated-github-pages/){:target="_blank"}
|
||||||
|
|
||||||
|
### MathJax
|
||||||
|
|
||||||
|
Let's test some inline math $x$, $y$, $x_1$, $y_1$.
|
||||||
|
|
||||||
|
Now a inline math with special character: $\|\psi\rangle$, $x'$, $x^\*$ and $\|\psi_1\rangle = a\|0\rangle + b\|1\rangle$
|
||||||
|
|
||||||
|
Test a display math:
|
||||||
|
$$
|
||||||
|
|\psi_1\rangle = a|0\rangle + b|1\rangle
|
||||||
|
$$
|
||||||
|
Is it O.K.?
|
||||||
|
|
||||||
|
Test a display math with equation number:
|
||||||
|
\begin{equation}
|
||||||
|
|\psi_1\rangle = a|0\rangle + b|1\rangle
|
||||||
|
\end{equation}
|
||||||
|
Is it O.K.?
|
||||||
|
|
||||||
|
Test a display math with equation number:
|
||||||
|
|
||||||
|
$$
|
||||||
|
\begin{align}
|
||||||
|
|\psi_1\rangle &= a|0\rangle + b|1\rangle \\
|
||||||
|
|\psi_2\rangle &= c|0\rangle + d|1\rangle
|
||||||
|
\end{align}
|
||||||
|
$$
|
||||||
|
Is it O.K.?
|
||||||
|
|
||||||
|
And test a display math without equaltion number:
|
||||||
|
$$
|
||||||
|
\begin{align*}
|
||||||
|
|\psi_1\rangle &= a|0\rangle + b|1\rangle \\
|
||||||
|
|\psi_2\rangle &= c|0\rangle + d|1\rangle
|
||||||
|
\end{align*}
|
||||||
|
$$
|
||||||
|
Is it O.K.?
|
||||||
|
|
||||||
|
Test a display math with equation number:
|
||||||
|
$$
|
||||||
|
\begin{align}
|
||||||
|
|\psi_1\rangle &= a|0\rangle + b|1\rangle \\
|
||||||
|
|\psi_2\rangle &= c|0\rangle + d|1\rangle
|
||||||
|
\end{align}
|
||||||
|
$$
|
||||||
|
Is it O.K.?
|
||||||
|
|
||||||
|
And test a display math without equaltion number:
|
||||||
|
$$
|
||||||
|
\begin{align*}
|
||||||
|
|\psi_1\rangle &= a|0\rangle + b|1\rangle \\
|
||||||
|
|\psi_2\rangle &= c|0\rangle + d|1\rangle
|
||||||
|
\end{align*}
|
||||||
|
$$
|
||||||
|
|
||||||
|
### gist embed
|
||||||
|
|
||||||
|
Below is a partial code showing main steps of merge function.
|
||||||
|
|
||||||
|
<code data-gist-id="0fe211678316cc53370c" data-gist-file="merge_tables_datatable.R" data-gist-line="50-52,57,65-69,80,88-90,100-106"></code>
|
||||||
|
|
||||||
|
### References
|
||||||
|
|
||||||
|
Multiple[^1]<sup>,</sup>[^3] and with comments[^2]
|
||||||
|
|
||||||
|
Want to see something else added? <a href="https://github.com/dyndna/lanyon-plus/issues/new">Open an issue.</a>
|
||||||
|
|
||||||
|
[^1]: [lanyon theme](http://lanyon.getpoole.com)
|
||||||
|
[^2]:
|
||||||
|
[lanyon-plus theme](https://github.com/dyndna/lanyon-plus "accessed on {{ page.date | date: '%B %d, %Y' }}")
|
||||||
|
|
||||||
|
>Excerpt: Sample post showing enabled features for post: `inline code`, `text highlight`{:.yelhglt}, code block with syntax highlights, embed gist, stylized blockquotes, video and image cards for twitter, markdown tables, inline and code bocks having mathjax support, references, print format, disqus comments, related posts, tags.
|
||||||
|
|
||||||
|
[^3]: [About]({{ site.url }}/about)
|
||||||
19
_posts/2013-12-31-whats-jekyll.md
Normal file
19
_posts/2013-12-31-whats-jekyll.md
Normal file
|
|
@ -0,0 +1,19 @@
|
||||||
|
---
|
||||||
|
layout: post
|
||||||
|
title: What's Jekyll?
|
||||||
|
# date element overrides date in title format.
|
||||||
|
date: 2015-1-31
|
||||||
|
tag:
|
||||||
|
- common_tag
|
||||||
|
- other_tag
|
||||||
|
---
|
||||||
|
|
||||||
|
[Jekyll](http://jekyllrb.com) is a static site generator, an open-source tool for creating simple yet powerful websites of all shapes and sizes. From [the project's readme](https://github.com/mojombo/jekyll/blob/master/README.markdown):
|
||||||
|
|
||||||
|
<!--more-->
|
||||||
|
|
||||||
|
> Jekyll is a simple, blog aware, static site generator. It takes a template directory [...] and spits out a complete, static website suitable for serving with Apache or your favorite web server. This is also the engine behind GitHub Pages, which you can use to host your project’s page or blog right here from GitHub.
|
||||||
|
|
||||||
|
It's an immensely useful tool and one we encourage you to use here with Lanyon.
|
||||||
|
|
||||||
|
Find out more by [visiting the project on GitHub](https://github.com/mojombo/jekyll).
|
||||||
|
|
@ -1,25 +0,0 @@
|
||||||
---
|
|
||||||
layout: post
|
|
||||||
title: "Welcome to Jekyll!"
|
|
||||||
date: 2017-08-03 16:54:51 +0200
|
|
||||||
categories: jekyll update
|
|
||||||
---
|
|
||||||
You’ll find this post in your `_posts` directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run `jekyll serve`, which launches a web server and auto-regenerates your site when a file is updated.
|
|
||||||
|
|
||||||
To add new posts, simply add a file in the `_posts` directory that follows the convention `YYYY-MM-DD-name-of-post.ext` and includes the necessary front matter. Take a look at the source for this post to get an idea about how it works.
|
|
||||||
|
|
||||||
Jekyll also offers powerful support for code snippets:
|
|
||||||
|
|
||||||
{% highlight ruby %}
|
|
||||||
def print_hi(name)
|
|
||||||
puts "Hi, #{name}"
|
|
||||||
end
|
|
||||||
print_hi('Tom')
|
|
||||||
#=> prints 'Hi, Tom' to STDOUT.
|
|
||||||
{% endhighlight %}
|
|
||||||
|
|
||||||
Check out the [Jekyll docs][jekyll-docs] for more info on how to get the most out of Jekyll. File all bugs/feature requests at [Jekyll’s GitHub repo][jekyll-gh]. If you have questions, you can ask them on [Jekyll Talk][jekyll-talk].
|
|
||||||
|
|
||||||
[jekyll-docs]: https://jekyllrb.com/docs/home
|
|
||||||
[jekyll-gh]: https://github.com/jekyll/jekyll
|
|
||||||
[jekyll-talk]: https://talk.jekyllrb.com/
|
|
||||||
213
_prose.yml
Normal file
213
_prose.yml
Normal file
|
|
@ -0,0 +1,213 @@
|
||||||
|
prose:
|
||||||
|
rooturl: ''
|
||||||
|
siteurl: 'http://example.com/'
|
||||||
|
relativeLinks: 'http://example.com/links.jsonp'
|
||||||
|
media: 'images/media'
|
||||||
|
ignore:
|
||||||
|
- /_data
|
||||||
|
- /_includes
|
||||||
|
- /_layouts
|
||||||
|
- /blog
|
||||||
|
- .htaccess
|
||||||
|
- _config.yml
|
||||||
|
- Gemfile
|
||||||
|
- Gemfile.lock
|
||||||
|
- .gitignore
|
||||||
|
- .editorconfig
|
||||||
|
- .gitattributes
|
||||||
|
- favicon.ico
|
||||||
|
- favicon.png
|
||||||
|
metadata:
|
||||||
|
_posts:
|
||||||
|
- name: "published"
|
||||||
|
field:
|
||||||
|
label: "Published"
|
||||||
|
element: "checkbox"
|
||||||
|
value: "true"
|
||||||
|
- name: "layout"
|
||||||
|
field:
|
||||||
|
element: "hidden"
|
||||||
|
label: "Layout"
|
||||||
|
value: "post"
|
||||||
|
- name: "title"
|
||||||
|
field:
|
||||||
|
label: "Title"
|
||||||
|
element: "text"
|
||||||
|
value: "An Awesome Headline!"
|
||||||
|
- name: "description"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Description"
|
||||||
|
placeholder: "Enter Post Description"
|
||||||
|
- name: "date"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Post date - this will override date given in file name and permalink will change accordingly"
|
||||||
|
placeholder: "YYYY-MM-DD"
|
||||||
|
value: CURRENT_DATETIME
|
||||||
|
- name: "modified"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Last modified in quotes"
|
||||||
|
placeholder: "YYYY-MM-DD"
|
||||||
|
value: CURRENT_DATETIME
|
||||||
|
- name: "category"
|
||||||
|
field:
|
||||||
|
element: "select"
|
||||||
|
label: "Add categories"
|
||||||
|
placeholder: "Choose category"
|
||||||
|
value: base
|
||||||
|
options:
|
||||||
|
- name: "info"
|
||||||
|
value: info
|
||||||
|
- name: "news"
|
||||||
|
value: news
|
||||||
|
- name: "base"
|
||||||
|
value: base
|
||||||
|
alterable: true
|
||||||
|
- name: "tags"
|
||||||
|
field:
|
||||||
|
element: "multiselect"
|
||||||
|
label: "Add tags"
|
||||||
|
placeholder: "Choose tags"
|
||||||
|
value: default
|
||||||
|
options:
|
||||||
|
- name: "default"
|
||||||
|
value: default
|
||||||
|
alterable: true
|
||||||
|
- name: "imagefeature"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Featured Image or Video frame jpg for twitter card"
|
||||||
|
placeholder: "http url or path relative to images dir"
|
||||||
|
value: "sitelogo.png"
|
||||||
|
- name: "show_meta"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Show tags and share buttons"
|
||||||
|
value: true
|
||||||
|
- name: "comments"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Comments"
|
||||||
|
value: true
|
||||||
|
- name: "mathjax"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "MathJax"
|
||||||
|
value: false
|
||||||
|
- name: "gistembed"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "embed gist?"
|
||||||
|
value: false
|
||||||
|
- name: "noindex"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "noindex in robots.txt?"
|
||||||
|
value: false
|
||||||
|
- name: "hide_printmsg"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "hide info box while printing?"
|
||||||
|
value: false
|
||||||
|
- name: "sitemap"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Keep in sitemap?"
|
||||||
|
value: true
|
||||||
|
- name: "summaryfeed"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Show summary and not full post in rss feed?"
|
||||||
|
value: false
|
||||||
|
pages:
|
||||||
|
- name: "published"
|
||||||
|
field:
|
||||||
|
label: "Published"
|
||||||
|
element: "checkbox"
|
||||||
|
value: true
|
||||||
|
- name: "layout"
|
||||||
|
field:
|
||||||
|
element: "hidden"
|
||||||
|
label: "Layout"
|
||||||
|
value: "page"
|
||||||
|
- name: "title"
|
||||||
|
field:
|
||||||
|
label: "Title"
|
||||||
|
element: "text"
|
||||||
|
value: "An Awesome Headline!"
|
||||||
|
- name: "description"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Description"
|
||||||
|
placeholder: "Enter Page Description"
|
||||||
|
- name: "permalink"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Permalink - relative to root directory"
|
||||||
|
- name: "modified"
|
||||||
|
field:
|
||||||
|
element: "text"
|
||||||
|
label: "Last modified in quotes"
|
||||||
|
placeholder: "YYYY-MM-DD"
|
||||||
|
value: CURRENT_DATETIME
|
||||||
|
- name: "category"
|
||||||
|
field:
|
||||||
|
element: "select"
|
||||||
|
label: "Add categories"
|
||||||
|
placeholder: "Choose category"
|
||||||
|
value: info
|
||||||
|
options:
|
||||||
|
- name: "info"
|
||||||
|
value: info
|
||||||
|
- name: "news"
|
||||||
|
value: news
|
||||||
|
alterable: true
|
||||||
|
- name: "author"
|
||||||
|
field:
|
||||||
|
element: "select"
|
||||||
|
label: "Add author"
|
||||||
|
placeholder: "Choose author"
|
||||||
|
value: author1
|
||||||
|
options:
|
||||||
|
- name: "author1"
|
||||||
|
value: author1
|
||||||
|
- name: "author2"
|
||||||
|
value: author2
|
||||||
|
alterable: true
|
||||||
|
- name: "show_meta"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Show tags and share buttons"
|
||||||
|
value: false
|
||||||
|
- name: "comments"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Comments"
|
||||||
|
value: false
|
||||||
|
- name: "mathjax"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "MathJax"
|
||||||
|
value: false
|
||||||
|
- name: "gistembed"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "embed gist?"
|
||||||
|
value: false
|
||||||
|
- name: "noindex"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "noindex in robots.txt?"
|
||||||
|
value: false
|
||||||
|
- name: "hide_printmsg"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "hide info box while printing?"
|
||||||
|
value: false
|
||||||
|
- name: "sitemap"
|
||||||
|
field:
|
||||||
|
element: "checkbox"
|
||||||
|
label: "Keep in sitemap?"
|
||||||
|
value: true
|
||||||
39
blog/index.html
Normal file
39
blog/index.html
Normal file
|
|
@ -0,0 +1,39 @@
|
||||||
|
---
|
||||||
|
layout: default
|
||||||
|
title: Blog @ example.com
|
||||||
|
description: "Blogging on ...."
|
||||||
|
---
|
||||||
|
|
||||||
|
<div class="posts">
|
||||||
|
{% for post in paginator.posts %}
|
||||||
|
<div class="post">
|
||||||
|
<h1 class="post-title">
|
||||||
|
<a href="{{ site.url }}{{ post.url }}">
|
||||||
|
{{ post.title }}
|
||||||
|
</a>
|
||||||
|
</h1>
|
||||||
|
|
||||||
|
{% if post.modified.size > 2 %}<span class="post-date indexpg" itemprop="dateModified" content="{{ post.modified | date: "%Y-%m-%d" }}"><i class="fa fa-edit" title="Last updated"> {{ post.modified | date_to_string }}</i> {% if post.category contains "featured" %}<a href="{{ site.url }}/featured" title="Featured posts"><i class="fa fa-paperclip" title="Featured" class="social-icons"></i></a>{% endif %}</span>{% else %}<span class="post-date indexpg" itemprop="datePublished" content="{{ post.date | date: "%Y-%m-%d" }}"><i class="fa fa-calendar" title="Date published"> {{ post.date | date_to_string }}</i> {% if post.category contains "featured" %}<a href="{{ site.url }}/featured" title="Featured posts"><i class="fa fa-paperclip" title="Featured" class="social-icons"></i></a>{% endif %}</span>{% endif %}
|
||||||
|
|
||||||
|
{% if post.description.size > 140 %}{{ post.description | markdownify | remove: '<p>' | remove: '</p>' }}{% else %}{{ post.excerpt | markdownify | remove: '<p>' | remove: '</p>' }}{% endif %} <a href="{{ site.url }}{{ post.url }}" title="Read more"><strong>Read more...</strong></a>
|
||||||
|
</div>
|
||||||
|
{% unless forloop.last %}<hr class="transp">{% endunless %}
|
||||||
|
{% endfor %}
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="pagination">
|
||||||
|
{% if paginator.next_page %}
|
||||||
|
<a class="pagination-item older" href="{{ site.url }}/blog/page{{paginator.next_page}}">Older</a>
|
||||||
|
{% else %}
|
||||||
|
<span class="pagination-item older">Older</span>
|
||||||
|
{% endif %}
|
||||||
|
{% if paginator.previous_page %}
|
||||||
|
{% if paginator.page == 2 %}
|
||||||
|
<a class="pagination-item newer" href="{{ site.url }}/blog/">Newer</a>
|
||||||
|
{% else %}
|
||||||
|
<a class="pagination-item newer" href="{{ site.url }}/blog/page{{paginator.previous_page}}">Newer</a>
|
||||||
|
{% endif %}
|
||||||
|
{% else %}
|
||||||
|
<span class="pagination-item newer">Newer</span>
|
||||||
|
{% endif %}
|
||||||
|
</div>
|
||||||
BIN
favicon.ico
Normal file
BIN
favicon.ico
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 1.1 KiB |
BIN
favicon.png
Normal file
BIN
favicon.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 5.7 KiB |
31
feed.xml
Normal file
31
feed.xml
Normal file
|
|
@ -0,0 +1,31 @@
|
||||||
|
---
|
||||||
|
layout: null
|
||||||
|
---
|
||||||
|
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>{{ site.title | xml_escape }}</title>
|
||||||
|
<description>{{ site.description | xml_escape }}</description>
|
||||||
|
<link>{{ site.url }}{{ site.baseurl }}/</link>
|
||||||
|
<atom:link href="{{ "/feed.xml" | prepend: site.baseurl | prepend: site.url }}" rel="self" type="application/rss+xml" />
|
||||||
|
<updated>{{ site.time | date_to_xmlschema }}</updated>
|
||||||
|
<id>{{ site.url }}</id>
|
||||||
|
<author>
|
||||||
|
<name>{{ site.owner.name }}</name>
|
||||||
|
</author>
|
||||||
|
{% for post in site.posts limit:10 %}
|
||||||
|
<item>
|
||||||
|
<title>{{ post.title | xml_escape }}</title>
|
||||||
|
{% if post.summaryfeed and post.excerpt %}
|
||||||
|
<description>{{ post.excerpt | xml_escape }}</description>
|
||||||
|
{% else %}
|
||||||
|
<description>{{ post.content | xml_escape }}</description>
|
||||||
|
{% endif %}
|
||||||
|
<pubDate>{{ post.date | date: "%a, %d %b %Y %H:%M:%S %z" }}</pubDate>
|
||||||
|
<link>{{ post.url | prepend: site.baseurl | prepend: site.url }}</link>
|
||||||
|
<guid isPermaLink="true">{{ post.url | prepend: site.baseurl | prepend: site.url }}</guid>
|
||||||
|
</item>
|
||||||
|
{% endfor %}
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
BIN
files/cv.pdf
Normal file
BIN
files/cv.pdf
Normal file
Binary file not shown.
103
files/myaoi.bib
Normal file
103
files/myaoi.bib
Normal file
|
|
@ -0,0 +1,103 @@
|
||||||
|
|
||||||
|
@article{jacobs_evolutionary_2014,
|
||||||
|
title = {An evolutionary arms race between {KRAB} zinc-finger genes {ZNF}91/93 and {SVA}/{L}1 retrotransposons},
|
||||||
|
volume = {516},
|
||||||
|
copyright = {© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
|
||||||
|
issn = {0028-0836},
|
||||||
|
url = {http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html},
|
||||||
|
doi = {10.1038/nature13760},
|
||||||
|
abstract = {Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex, which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1), is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until [sim]12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93/'s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.},
|
||||||
|
language = {en},
|
||||||
|
number = {7530},
|
||||||
|
urldate = {2015-10-12},
|
||||||
|
journal = {Nature},
|
||||||
|
author = {Jacobs, Frank M. J. and Greenberg, David and Nguyen, Ngan and Haeussler, Maximilian and Ewing, Adam D. and Katzman, Sol and Paten, Benedict and Salama, Sofie R. and Haussler, David},
|
||||||
|
month = dec,
|
||||||
|
year = {2014},
|
||||||
|
pmid = {25274305},
|
||||||
|
keywords = {evolution, interactions, transposon},
|
||||||
|
pages = {242--245}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{trapnell_defining_2015,
|
||||||
|
title = {Defining cell types and states with single-cell genomics},
|
||||||
|
volume = {25},
|
||||||
|
issn = {1088-9051, 1549-5469},
|
||||||
|
url = {http://genome.cshlp.org/content/25/10/1491},
|
||||||
|
doi = {10.1101/gr.190595.115},
|
||||||
|
abstract = {A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.},
|
||||||
|
language = {en},
|
||||||
|
number = {10},
|
||||||
|
urldate = {2015-10-14},
|
||||||
|
journal = {Genome Research},
|
||||||
|
author = {Trapnell, Cole},
|
||||||
|
month = oct,
|
||||||
|
year = {2015},
|
||||||
|
pmid = {26430159},
|
||||||
|
keywords = {chromatin, evolution, review, single-cell, Waddington},
|
||||||
|
pages = {1491--1498}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{kaufman_zebrafish_2016,
|
||||||
|
title = {A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation},
|
||||||
|
volume = {351},
|
||||||
|
copyright = {Copyright © 2016, American Association for the Advancement of Science},
|
||||||
|
issn = {0036-8075, 1095-9203},
|
||||||
|
url = {http://science.sciencemag.org/content/351/6272/aad2197},
|
||||||
|
doi = {10.1126/science.aad2197},
|
||||||
|
abstract = {Visualizing the beginnings of melanoma
|
||||||
|
In cancer biology, a tumor begins from a single cell within a group of precancerous cells that share genetic mutations. Kaufman et al. used a zebrafish melanoma model to visualize cancer initiation (see the Perspective by Boumahdi and Blanpain). They used a fluorescent reporter that specifically lit up neural crest progenitors that are only present during embryogenesis or during adult melanoma tumor formation. The appearance of this tumor correlated with a set of gene regulatory elements, called super-enhancers, whose identification and manipulation may prove beneficial in detecting and preventing melanoma initiation.
|
||||||
|
Science, this issue p. 10.1126/science.aad3867; see also p. 453
|
||||||
|
Structured Abstract
|
||||||
|
INTRODUCTIONThe “cancerized field” concept posits that cells in a given tissue sharing an oncogenic mutation are cancer-prone, yet only discreet clones within the field initiate tumors. Studying the process of cancer initiation has remained challenging because of (i) the rarity of these events, (ii) the difficulty of visiualizing initiating clones in living organisms, and (iii) the transient nature of a newly transformed clone emerging before it expands to form an early tumor. A more complete understanding of the molecular processes that regulate cancer initiation could provide important prognostic information about which precancerous lesions are most prone to becoming cancer and also implicate druggable molecular pathways that, when inhibited, may prevent the cancer from ever starting.
|
||||||
|
RATIONALEThe majority of benign nevi carry oncogenic BRAFV600E mutations and can be considered a cancerized field of melanocytes, but they only rarely convert to melanoma. In an effort to define events that initiate cancer, we used a melanoma model in the zebrafish in which the human BRAFV600E oncogene is driven by the melanocyte-specific mitfa promoter. When bred into a p53 mutant background, these fish develop melanoma tumors over the course of many months. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and is specifically reexpressed only in melanoma tumors, making it an ideal candidate for tracking melanoma from initiation onward.
|
||||||
|
RESULTSWe developed a crestin:EGFP reporter that recapitulates the embryonic neural crest expression pattern of crestin and its expression in melanoma tumors. We show through live imaging of transgenic zebrafish crestin reporters that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, and this establishes that a fate change occurs at melanoma initiation in this model. Early crestin+ patches of cells expand and are transplantable in a manner consistent with their possessing tumorigenic activity, and they exhibit a gene expression pattern consistent with the NCP identity readout by the crestin reporter. The crestin element is regulated by NCP transcription factors, including sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation, whereas CRISPR/Cas9 targeting of sox10 delayed melanoma onset. We show activation of super-enhancers at NCP genes in both zebrafish and human melanomas, identifying an epigenetic mechanism for control of this NCP signature leading to melanoma.
|
||||||
|
CONCLUSIONThis work using our zebrafish melanoma model and in vivo reporter of NCP identity allows us to see cancer from its birth as a single cell and shows the importance of NCP-state reemergence as a key event in melanoma initiation from a field of cancer-prone melanocytes. Thus, in addition to the typical fixed genetic alterations in oncogenes and tumor supressors that are required for cancer development, the reemergence of progenitor identity may be an additional rate-limiting step in the formation of melanoma. Preventing NCP reemergence in a field of cancer-prone melanocytes may thus prove therapeutically useful, and the association of NCP genes with super-enhancer regulatory elements implicates the associated druggable epigenetic machinery in this process. Download high-res image Open in new tab Download Powerpoint Neural crest reporter expression in melanoma.The crestin:EGFP transgene is specifically expressed in melanoma in BRAFV600E/p53 mutant melanoma-prone zebrafish. (Top) A single cell expressing crestin:EGFP expands into a small patch of cells over the course of 2 weeks, capturing the initiation of melanoma formation (bracket). (Bottom) A fully formed melanoma specifically expresses crestin:EGFP, whereas the rest of the fish remains EGFP-negative.
|
||||||
|
The “cancerized field” concept posits that cancer-prone cells in a given tissue share an oncogenic mutation, but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAFV600E mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, revealing a fate change at melanoma initiation in this model. NCP transcription factors, including sox10, regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation, which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]},
|
||||||
|
language = {en},
|
||||||
|
number = {6272},
|
||||||
|
urldate = {2016-01-29},
|
||||||
|
journal = {Science},
|
||||||
|
author = {Kaufman, Charles K. and Mosimann, Christian and Fan, Zi Peng and Yang, Song and Thomas, Andrew J. and Ablain, Julien and Tan, Justin L. and Fogley, Rachel D. and Rooijen, Ellen van and Hagedorn, Elliott J. and Ciarlo, Christie and White, Richard M. and Matos, Dominick A. and Puller, Ann-Christin and Santoriello, Cristina and Liao, Eric C. and Young, Richard A. and Zon, Leonard I.},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
pmid = {26823433},
|
||||||
|
keywords = {Development, epigenetics, evolution, melanoma, super\_enhancer, zebrafish},
|
||||||
|
pages = {aad2197}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{lipinski_cancer_2016,
|
||||||
|
title = {Cancer {Evolution} and the {Limits} of {Predictability} in {Precision} {Cancer} {Medicine}},
|
||||||
|
volume = {2},
|
||||||
|
issn = {2405-8033},
|
||||||
|
url = {http://www.sciencedirect.com/science/article/pii/S2405803315000692},
|
||||||
|
doi = {10.1016/j.trecan.2015.11.003},
|
||||||
|
abstract = {The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.},
|
||||||
|
number = {1},
|
||||||
|
urldate = {2016-01-30},
|
||||||
|
journal = {Trends in Cancer},
|
||||||
|
author = {Lipinski, Kamil A. and Barber, Louise J. and Davies, Matthew N. and Ashenden, Matthew and Sottoriva, Andrea and Gerlinger, Marco},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {evolution, heterogeneity, resistance, review},
|
||||||
|
pages = {49--63}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{beerenwinkel_computational_2016,
|
||||||
|
title = {Computational {Cancer} {Biology}: {An} {Evolutionary} {Perspective}},
|
||||||
|
volume = {12},
|
||||||
|
shorttitle = {Computational {Cancer} {Biology}},
|
||||||
|
url = {http://dx.doi.org/10.1371/journal.pcbi.1004717},
|
||||||
|
doi = {10.1371/journal.pcbi.1004717},
|
||||||
|
number = {2},
|
||||||
|
urldate = {2016-02-05},
|
||||||
|
journal = {PLoS Comput Biol},
|
||||||
|
author = {Beerenwinkel, Niko and Greenman, Chris D. and Lagergren, Jens},
|
||||||
|
month = feb,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {cancer, concepts, darwinian, epigenetics, evolution, mathematical modeling, review, statistics, variant},
|
||||||
|
pages = {e1004717},
|
||||||
|
pmid = {26845763}
|
||||||
|
}
|
||||||
103
files/mypubs.bib
Normal file
103
files/mypubs.bib
Normal file
|
|
@ -0,0 +1,103 @@
|
||||||
|
|
||||||
|
@article{jacobs_evolutionary_2014,
|
||||||
|
title = {An evolutionary arms race between {KRAB} zinc-finger genes {ZNF}91/93 and {SVA}/{L}1 retrotransposons},
|
||||||
|
volume = {516},
|
||||||
|
copyright = {© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
|
||||||
|
issn = {0028-0836},
|
||||||
|
url = {http://www.nature.com/nature/journal/v516/n7530/full/nature13760.html},
|
||||||
|
doi = {10.1038/nature13760},
|
||||||
|
abstract = {Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex, which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1), is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until [sim]12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93/'s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.},
|
||||||
|
language = {en},
|
||||||
|
number = {7530},
|
||||||
|
urldate = {2015-10-12},
|
||||||
|
journal = {Nature},
|
||||||
|
author = {Jacobs, Frank M. J. and Greenberg, David and Nguyen, Ngan and Haeussler, Maximilian and Ewing, Adam D. and Katzman, Sol and Paten, Benedict and Salama, Sofie R. and Haussler, David},
|
||||||
|
month = dec,
|
||||||
|
year = {2014},
|
||||||
|
pmid = {25274305},
|
||||||
|
keywords = {evolution, interactions, transposon},
|
||||||
|
pages = {242--245}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{trapnell_defining_2015,
|
||||||
|
title = {Defining cell types and states with single-cell genomics},
|
||||||
|
volume = {25},
|
||||||
|
issn = {1088-9051, 1549-5469},
|
||||||
|
url = {http://genome.cshlp.org/content/25/10/1491},
|
||||||
|
doi = {10.1101/gr.190595.115},
|
||||||
|
abstract = {A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.},
|
||||||
|
language = {en},
|
||||||
|
number = {10},
|
||||||
|
urldate = {2015-10-14},
|
||||||
|
journal = {Genome Research},
|
||||||
|
author = {Trapnell, Cole},
|
||||||
|
month = oct,
|
||||||
|
year = {2015},
|
||||||
|
pmid = {26430159},
|
||||||
|
keywords = {chromatin, evolution, review, single-cell, Waddington},
|
||||||
|
pages = {1491--1498}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{kaufman_zebrafish_2016,
|
||||||
|
title = {A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation},
|
||||||
|
volume = {351},
|
||||||
|
copyright = {Copyright © 2016, American Association for the Advancement of Science},
|
||||||
|
issn = {0036-8075, 1095-9203},
|
||||||
|
url = {http://science.sciencemag.org/content/351/6272/aad2197},
|
||||||
|
doi = {10.1126/science.aad2197},
|
||||||
|
abstract = {Visualizing the beginnings of melanoma
|
||||||
|
In cancer biology, a tumor begins from a single cell within a group of precancerous cells that share genetic mutations. Kaufman et al. used a zebrafish melanoma model to visualize cancer initiation (see the Perspective by Boumahdi and Blanpain). They used a fluorescent reporter that specifically lit up neural crest progenitors that are only present during embryogenesis or during adult melanoma tumor formation. The appearance of this tumor correlated with a set of gene regulatory elements, called super-enhancers, whose identification and manipulation may prove beneficial in detecting and preventing melanoma initiation.
|
||||||
|
Science, this issue p. 10.1126/science.aad3867; see also p. 453
|
||||||
|
Structured Abstract
|
||||||
|
INTRODUCTIONThe “cancerized field” concept posits that cells in a given tissue sharing an oncogenic mutation are cancer-prone, yet only discreet clones within the field initiate tumors. Studying the process of cancer initiation has remained challenging because of (i) the rarity of these events, (ii) the difficulty of visiualizing initiating clones in living organisms, and (iii) the transient nature of a newly transformed clone emerging before it expands to form an early tumor. A more complete understanding of the molecular processes that regulate cancer initiation could provide important prognostic information about which precancerous lesions are most prone to becoming cancer and also implicate druggable molecular pathways that, when inhibited, may prevent the cancer from ever starting.
|
||||||
|
RATIONALEThe majority of benign nevi carry oncogenic BRAFV600E mutations and can be considered a cancerized field of melanocytes, but they only rarely convert to melanoma. In an effort to define events that initiate cancer, we used a melanoma model in the zebrafish in which the human BRAFV600E oncogene is driven by the melanocyte-specific mitfa promoter. When bred into a p53 mutant background, these fish develop melanoma tumors over the course of many months. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and is specifically reexpressed only in melanoma tumors, making it an ideal candidate for tracking melanoma from initiation onward.
|
||||||
|
RESULTSWe developed a crestin:EGFP reporter that recapitulates the embryonic neural crest expression pattern of crestin and its expression in melanoma tumors. We show through live imaging of transgenic zebrafish crestin reporters that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, and this establishes that a fate change occurs at melanoma initiation in this model. Early crestin+ patches of cells expand and are transplantable in a manner consistent with their possessing tumorigenic activity, and they exhibit a gene expression pattern consistent with the NCP identity readout by the crestin reporter. The crestin element is regulated by NCP transcription factors, including sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation, whereas CRISPR/Cas9 targeting of sox10 delayed melanoma onset. We show activation of super-enhancers at NCP genes in both zebrafish and human melanomas, identifying an epigenetic mechanism for control of this NCP signature leading to melanoma.
|
||||||
|
CONCLUSIONThis work using our zebrafish melanoma model and in vivo reporter of NCP identity allows us to see cancer from its birth as a single cell and shows the importance of NCP-state reemergence as a key event in melanoma initiation from a field of cancer-prone melanocytes. Thus, in addition to the typical fixed genetic alterations in oncogenes and tumor supressors that are required for cancer development, the reemergence of progenitor identity may be an additional rate-limiting step in the formation of melanoma. Preventing NCP reemergence in a field of cancer-prone melanocytes may thus prove therapeutically useful, and the association of NCP genes with super-enhancer regulatory elements implicates the associated druggable epigenetic machinery in this process. Download high-res image Open in new tab Download Powerpoint Neural crest reporter expression in melanoma.The crestin:EGFP transgene is specifically expressed in melanoma in BRAFV600E/p53 mutant melanoma-prone zebrafish. (Top) A single cell expressing crestin:EGFP expands into a small patch of cells over the course of 2 weeks, capturing the initiation of melanoma formation (bracket). (Bottom) A fully formed melanoma specifically expresses crestin:EGFP, whereas the rest of the fish remains EGFP-negative.
|
||||||
|
The “cancerized field” concept posits that cancer-prone cells in a given tissue share an oncogenic mutation, but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAFV600E mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAFV600E-mutant; p53-deficient), a single melanocyte reactivates the NCP state, revealing a fate change at melanoma initiation in this model. NCP transcription factors, including sox10, regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation, which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]
|
||||||
|
Melanocytes with oncogenic or tumor suppressor mutations revert to expressing the crestin gene early in melanoma formation. [Also see Perspective by Boumahdi and Blanpain]},
|
||||||
|
language = {en},
|
||||||
|
number = {6272},
|
||||||
|
urldate = {2016-01-29},
|
||||||
|
journal = {Science},
|
||||||
|
author = {Kaufman, Charles K. and Mosimann, Christian and Fan, Zi Peng and Yang, Song and Thomas, Andrew J. and Ablain, Julien and Tan, Justin L. and Fogley, Rachel D. and Rooijen, Ellen van and Hagedorn, Elliott J. and Ciarlo, Christie and White, Richard M. and Matos, Dominick A. and Puller, Ann-Christin and Santoriello, Cristina and Liao, Eric C. and Young, Richard A. and Zon, Leonard I.},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
pmid = {26823433},
|
||||||
|
keywords = {Development, epigenetics, evolution, melanoma, super\_enhancer, zebrafish},
|
||||||
|
pages = {aad2197}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{lipinski_cancer_2016,
|
||||||
|
title = {Cancer {Evolution} and the {Limits} of {Predictability} in {Precision} {Cancer} {Medicine}},
|
||||||
|
volume = {2},
|
||||||
|
issn = {2405-8033},
|
||||||
|
url = {http://www.sciencedirect.com/science/article/pii/S2405803315000692},
|
||||||
|
doi = {10.1016/j.trecan.2015.11.003},
|
||||||
|
abstract = {The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.},
|
||||||
|
number = {1},
|
||||||
|
urldate = {2016-01-30},
|
||||||
|
journal = {Trends in Cancer},
|
||||||
|
author = {Lipinski, Kamil A. and Barber, Louise J. and Davies, Matthew N. and Ashenden, Matthew and Sottoriva, Andrea and Gerlinger, Marco},
|
||||||
|
month = jan,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {evolution, heterogeneity, resistance, review},
|
||||||
|
pages = {49--63}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{beerenwinkel_computational_2016,
|
||||||
|
title = {Computational {Cancer} {Biology}: {An} {Evolutionary} {Perspective}},
|
||||||
|
volume = {12},
|
||||||
|
shorttitle = {Computational {Cancer} {Biology}},
|
||||||
|
url = {http://dx.doi.org/10.1371/journal.pcbi.1004717},
|
||||||
|
doi = {10.1371/journal.pcbi.1004717},
|
||||||
|
number = {2},
|
||||||
|
urldate = {2016-02-05},
|
||||||
|
journal = {PLoS Comput Biol},
|
||||||
|
author = {Beerenwinkel, Niko and Greenman, Chris D. and Lagergren, Jens},
|
||||||
|
month = feb,
|
||||||
|
year = {2016},
|
||||||
|
keywords = {cancer, concepts, darwinian, epigenetics, evolution, mathematical modeling, review, statistics, variant},
|
||||||
|
pages = {e1004717},
|
||||||
|
pmid = {26845763}
|
||||||
|
}
|
||||||
15
humans.txt
Normal file
15
humans.txt
Normal file
|
|
@ -0,0 +1,15 @@
|
||||||
|
---
|
||||||
|
---
|
||||||
|
|
||||||
|
/* TEAM */
|
||||||
|
Primary Contact: foo
|
||||||
|
Site: {{ site.url }}/about/
|
||||||
|
Twitter: https://twitter.com/{{ site.owner.twitter }}
|
||||||
|
|
||||||
|
/* THANKS */
|
||||||
|
Design Contributors: {{ site.url }}/disclosure/
|
||||||
|
|
||||||
|
/* SITE */
|
||||||
|
Last Updated: {{ site.time | date:"%Y/%m/%d" }}
|
||||||
|
Standards: HTML5, CSS3
|
||||||
|
Software: Sublime Text, Chrome, Jekyll, Git, Sass
|
||||||
BIN
images/foo.png
Normal file
BIN
images/foo.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 19 KiB |
BIN
images/icons/android-icon-192x192.png
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BIN
images/icons/android-icon-192x192.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 18 KiB |
BIN
images/icons/apple-icon-precomposed.png
Normal file
BIN
images/icons/apple-icon-precomposed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 18 KiB |
BIN
images/icons/apple-icon.png
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BIN
images/icons/apple-icon.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 18 KiB |
BIN
images/icons/apple-touch-icon-114x114-precomposed.png
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BIN
images/icons/apple-touch-icon-114x114-precomposed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 10 KiB |
BIN
images/icons/apple-touch-icon-144x144-precomposed.png
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BIN
images/icons/apple-touch-icon-144x144-precomposed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 13 KiB |
BIN
images/icons/apple-touch-icon-180x180.png
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BIN
images/icons/apple-touch-icon-180x180.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 18 KiB |
BIN
images/icons/apple-touch-icon-72x72-precomposed.png
Normal file
BIN
images/icons/apple-touch-icon-72x72-precomposed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 5.7 KiB |
BIN
images/icons/apple-touch-icon-precomposed.png
Normal file
BIN
images/icons/apple-touch-icon-precomposed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 13 KiB |
BIN
images/media/apple-icon.png
Normal file
BIN
images/media/apple-icon.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 19 KiB |
BIN
images/sitebg.jpg
Normal file
BIN
images/sitebg.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 8.9 KiB |
BIN
images/sitelogo.png
Normal file
BIN
images/sitelogo.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 19 KiB |
81
index.md
81
index.md
|
|
@ -1,6 +1,79 @@
|
||||||
---
|
---
|
||||||
# You don't need to edit this file, it's empty on purpose.
|
layout: default
|
||||||
# Edit theme's home layout instead if you wanna make some changes
|
permalink: index.html
|
||||||
# See: https://jekyllrb.com/docs/themes/#overriding-theme-defaults
|
title: Personal Homepage of foo boo
|
||||||
layout: home
|
description: "Blogging on ...."
|
||||||
---
|
---
|
||||||
|
|
||||||
|
## [lanyon-plus](https://github.com/dyndna/lanyon-plus)
|
||||||
|
|
||||||
|
Based on Jekyll theme: [Lanyon](http://lanyon.getpoole.com) by [**Mark Otto**](https://github.com/mdo)
|
||||||
|
|
||||||
|
* add-ons by [Samir Amin](http://sbamin.com)
|
||||||
|
* [Site features]({{ site.url}}/disclosure#i-classfa-fa-thumbs-o-up-credits-for-site-featuresi)
|
||||||
|
* License: Open sourced under the [MIT license](http://sbamin.com/disclosure/#theme-major-credit--license).
|
||||||
|
|
||||||
|
Maximum four posts on front page where first two posts are featured, and remaining are date sorted.
|
||||||
|
|
||||||
|
{% if site.twitter_widget_id %}
|
||||||
|
<div class="text-tweets">
|
||||||
|
<div class="tweets">
|
||||||
|
<a class="twitter-timeline"
|
||||||
|
data-dnt="true"
|
||||||
|
width="600"
|
||||||
|
height="250"
|
||||||
|
href="https://twitter.com/{{ site.owner.twitter }}"
|
||||||
|
data-widget-id="{{ site.twitter_widget_id }}"
|
||||||
|
data-tweet-limit="2"
|
||||||
|
data-chrome="noheader nofooter noborders noscrollbar transparent">
|
||||||
|
Recent Tweets</a>
|
||||||
|
</div>
|
||||||
|
<script>
|
||||||
|
!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");
|
||||||
|
</script>
|
||||||
|
</div>
|
||||||
|
{% else %}
|
||||||
|
Twitter stream will show up here if `twitter_widget_id` is present is `_config.yml`. [Demo](http://sbamin.com)
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
<div class="posts">
|
||||||
|
{% for post in site.categories.featured limit:2 %}
|
||||||
|
<div class="post">
|
||||||
|
<h1 class="post-title">
|
||||||
|
<a href="{{ site.url }}{{ post.url }}">
|
||||||
|
{{ post.title }}
|
||||||
|
</a>
|
||||||
|
</h1>
|
||||||
|
|
||||||
|
{% if post.modified.size > 2 %}<span class="post-date indexpg" itemprop="dateModified" content="{{ post.modified | date: "%Y-%m-%d" }}"><i class="fa fa-edit" title="Last updated"> {{ post.modified | date_to_string }}</i> <a href="{{ site.url }}/featured" title="Featured posts"><i class="fa fa-paperclip" title="Featured" class="social-icons"></i></a></span>{% else %}<span class="post-date indexpg" itemprop="datePublished" content="{{ post.date | date: "%Y-%m-%d" }}"><i class="fa fa-calendar" title="Date published"> {{ post.date | date_to_string }}</i> <a href="{{ site.url }}/featured" title="Featured posts"><i class="fa fa-paperclip" title="Featured" class="social-icons"></i></a></span>{% endif %}
|
||||||
|
|
||||||
|
{% if post.description.size > 140 %}{{ post.description | markdownify | remove: '<p>' | remove: '</p>' }}{% else %}{{ post.excerpt | markdownify | remove: '<p>' | remove: '</p>' }}{% endif %} <a href="{{ site.url }}{{ post.url }}" title="Read more"><strong>Read more...</strong></a>
|
||||||
|
</div>
|
||||||
|
<hr class="transp">
|
||||||
|
{% endfor %}
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<div class="posts">
|
||||||
|
{% for post in site.posts limit:2 %}
|
||||||
|
{% unless post.category contains "featured" %}
|
||||||
|
<div class="post">
|
||||||
|
<h1 class="post-title">
|
||||||
|
<a href="{{ site.url }}{{ post.url }}">
|
||||||
|
{{ post.title }}
|
||||||
|
</a>
|
||||||
|
</h1>
|
||||||
|
|
||||||
|
{% if post.modified.size > 2 %}<span class="post-date indexpg" itemprop="dateModified" content="{{ post.modified | date: "%Y-%m-%d" }}"><i class="fa fa-edit" title="Last updated"> {{ post.modified | date_to_string }}</i></span>{% else %}<span class="post-date indexpg" itemprop="datePublished" content="{{ post.date | date: "%Y-%m-%d" }}"><i class="fa fa-calendar" title="Date published"> {{ post.date | date_to_string }}</i></span>{% endif %}
|
||||||
|
|
||||||
|
{% if post.description.size > 140 %}{{ post.description | markdownify | remove: '<p>' | remove: '</p>' }}{% else %}{{ post.excerpt | markdownify | remove: '<p>' | remove: '</p>' }}{% endif %} <a href="{{ site.url }}{{ post.url }}" title="Read more"><strong>Read more...</strong></a>
|
||||||
|
</div>
|
||||||
|
{% unless forloop.last %}<hr class="transp">{% endunless %}
|
||||||
|
{% endunless %}
|
||||||
|
{% endfor %}
|
||||||
|
</div>
|
||||||
|
<h3 class="post-title">
|
||||||
|
<div class="pagination" style="margin: 0.5rem;">
|
||||||
|
<a class="pagination-item older" href="{{ site.url }}/blog"><i class="fa fa-edit"> Blog</i></a>
|
||||||
|
<a class="pagination-item newer" href="{{ site.url }}/tags"><i class="fa fa-tags"> Tags</i></a>
|
||||||
|
</div>
|
||||||
|
</h3>
|
||||||
|
|
|
||||||
10
links.jsonp
Normal file
10
links.jsonp
Normal file
|
|
@ -0,0 +1,10 @@
|
||||||
|
---
|
||||||
|
---
|
||||||
|
callback([
|
||||||
|
{% for post in site.posts reversed | sort: title %}
|
||||||
|
{
|
||||||
|
"text": "{{post.title | replace:'"','\"'}}",
|
||||||
|
"href": "{{site.url}}{{post.url}}"
|
||||||
|
} {% unless forloop.last %},{% endunless%}
|
||||||
|
{% endfor %}
|
||||||
|
])
|
||||||
41
pages/about.md
Normal file
41
pages/about.md
Normal file
|
|
@ -0,0 +1,41 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
title: About
|
||||||
|
permalink: /about/
|
||||||
|
show_meta: true
|
||||||
|
# imagefeature path is relative to images/ directory.
|
||||||
|
imagefeature: foo.png
|
||||||
|
published: true
|
||||||
|
description: "About example.com...."
|
||||||
|
category: views
|
||||||
|
comments: false
|
||||||
|
mathjax: false
|
||||||
|
noindex: false
|
||||||
|
sitemap:
|
||||||
|
priority: 0.7
|
||||||
|
changefreq: 'monthly'
|
||||||
|
lastmod: 2016-02-13
|
||||||
|
# tags will be used as html meta keywords.
|
||||||
|
tags:
|
||||||
|
- "foo boo"
|
||||||
|
- "city tx"
|
||||||
|
---
|
||||||
|
|
||||||
|
<div class="post-author text-center">
|
||||||
|
<img src="{{ site.urlimg }}{{ site.owner.avatar }}" alt="{{ site.owner.name }}'s photo" itemprop="image" class="post-avatar img-circle img-responsive"/>
|
||||||
|
<span class="social-icons" style="padding-top: 10px; padding-bottom: 1px;">
|
||||||
|
<a href="{{ site.url }}/cv" title="Curriculum Vitae" class="social-icons"><i class="iconm iconm-profile" style="vertical-align: top;"></i></a>
|
||||||
|
<a href="{{ site.url }}/about/publications/" class="social-icons" title="Publications"><i class="iconm iconm-file-pdf"></i></a>
|
||||||
|
<a href="{{ site.owner.linkedin }}" class="social-icons" title="LinkedIn profile"><i class="iconm iconm-linkedin2"></i></a>
|
||||||
|
</span>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
Lorem ipsum dolor sit amet, consectetur adipiscing elit. In ornare lectus a purus rutrum, a hendrerit quam condimentum. Donec vel ante maximus, vulputate libero ac, rhoncus justo. Phasellus purus nisl, auctor id tristique eu, maximus quis leo. Mauris ultricies ante quis vehicula accumsan. Nulla facilisi. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Ut mi elit, feugiat non scelerisque eget, ultrices nec est. Morbi a est iaculis, commodo quam congue, posuere quam. Phasellus venenatis finibus eros, vitae malesuada nisl gravida vitae.
|
||||||
|
|
||||||
|
Praesent ac sem quis diam fermentum fermentum. Nullam turpis metus, elementum sit amet venenatis sed, placerat eget erat. Ut convallis ipsum vitae volutpat tristique. Cras a tempor lorem, quis aliquet dui. Nunc vel leo erat. Donec posuere massa sed justo luctus, accumsan porttitor ligula laoreet. Suspendisse sit amet nisi ultrices, venenatis lorem vel, posuere turpis. Fusce eget dictum nisi. Proin eu diam nisi. Quisque ut quam quis sem tincidunt efficitur vitae nec ex. Pellentesque ut dolor eros. Ut faucibus semper ultricies. Vestibulum nec nisl in magna porttitor dictum.
|
||||||
|
|
||||||
|
Donec egestas eros arcu, id fermentum orci faucibus ac. Pellentesque facilisis elit eu tellus ultrices pulvinar. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. In ut eros et mi dapibus condimentum. Sed ante metus, porttitor ut aliquet vitae, ullamcorper quis ex. Donec ac efficitur arcu, a malesuada dolor. Nulla magna arcu, semper quis augue sed, rhoncus porta urna. Duis dictum dapibus diam, ac sodales ipsum lobortis vel. Nulla ac dictum metus. Morbi sollicitudin tortor eu diam tristique, ut tincidunt tortor euismod. Integer non tincidunt metus. In tempus sem dapibus, venenatis mi placerat, condimentum orci. Nunc et tellus diam.
|
||||||
|
|
||||||
|
Nam imperdiet consequat lorem. Donec sagittis tortor eu dolor efficitur ullamcorper. Pellentesque dolor arcu, vestibulum quis laoreet at, tincidunt nec mauris. Praesent id laoreet arcu. Quisque blandit nunc at elit auctor, eget tempor nunc sodales. Cras venenatis lacinia tempus. Proin erat nisl, pharetra a massa volutpat, rhoncus pellentesque nisi. Mauris in elit dictum, egestas tellus et, laoreet velit. Nam auctor tempus augue sit amet fermentum. Nulla accumsan arcu quis efficitur aliquam. Nulla dapibus in neque eget facilisis. Nullam nisi augue, maximus at lectus sit amet, ornare malesuada ante. Morbi volutpat justo a urna pharetra elementum. Proin tempor ac felis ac consequat. Proin feugiat, nulla ac sagittis consequat, ante diam auctor tortor, in suscipit leo ante id dolor. Vivamus posuere pellentesque magna, sagittis blandit neque convallis sed.
|
||||||
|
|
||||||
|
*[volutpat]: Tooltip for abbreviation.
|
||||||
46
pages/aoi.md
Normal file
46
pages/aoi.md
Normal file
|
|
@ -0,0 +1,46 @@
|
||||||
|
---
|
||||||
|
layout: publ
|
||||||
|
category: myaoi
|
||||||
|
permalink: /about/aoi/
|
||||||
|
title: "Articles of interest"
|
||||||
|
published: true
|
||||||
|
description: "Sample page showing bookmarked papers"
|
||||||
|
tags:
|
||||||
|
- papers
|
||||||
|
- articles
|
||||||
|
- research
|
||||||
|
- starred
|
||||||
|
comments: true
|
||||||
|
modified: "2016-02-13"
|
||||||
|
bibtex: "/files/myaoi.bib"
|
||||||
|
#bibtex: "http://foo-alternate.com/files/myaoi.bib"
|
||||||
|
show_meta: true
|
||||||
|
noindex: false
|
||||||
|
nofollow: true
|
||||||
|
sitemap:
|
||||||
|
priority: 0.5
|
||||||
|
changefreq: 'monthly'
|
||||||
|
lastmod: 2016-02-13
|
||||||
|
style: |
|
||||||
|
.container {
|
||||||
|
max-width: 48rem;
|
||||||
|
}
|
||||||
|
---
|
||||||
|
|
||||||
|
{% comment %}
|
||||||
|
<!-- bibbase.org should work with following code unless you are hosting domain over https. -->
|
||||||
|
|
||||||
|
{% if page.bibtex %}
|
||||||
|
{% if page.bibtex contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.url %}
|
||||||
|
{% endif %}
|
||||||
|
{% capture biburl %}{{ domain }}{{ page.bibtex }}{% endcapture %}
|
||||||
|
<script src="http://bibbase.org/show?bib={{ biburl | cgi_escape }}&jsonp=1&authorFirst=1"></script>
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
{% endcomment %}
|
||||||
|
|
||||||
|
If category is *myaoi*, then html content from bibtex file at `_includes/myaoi.html` will be shown below.
|
||||||
|
|
||||||
53
pages/contact.md
Normal file
53
pages/contact.md
Normal file
|
|
@ -0,0 +1,53 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
permalink: /contact/
|
||||||
|
title: Contact
|
||||||
|
show_meta: false
|
||||||
|
published: true
|
||||||
|
description: "Contact example.com"
|
||||||
|
comments: false
|
||||||
|
mathjax: false
|
||||||
|
noindex: false
|
||||||
|
sitemap:
|
||||||
|
priority: 0.5
|
||||||
|
changefreq: 'monthly'
|
||||||
|
lastmod: 2016-02-13
|
||||||
|
tags:
|
||||||
|
- "foo boo"
|
||||||
|
- "driving directions"
|
||||||
|
- address
|
||||||
|
---
|
||||||
|
|
||||||
|
| <i class="fa fa-twitter"></i> | [@{{ site.owner.twitter }}](https://twitter.com/{{ site.owner.twitter }}) |
|
||||||
|
| - | :- |
|
||||||
|
| <i class="fa fa-envelope"></i> | foo<br>XYZ<br>1234 ABC ST<br>Washington, DC 11111 |
|
||||||
|
| - | :- |
|
||||||
|
| <i class="fa fa-car"></i> | [Driving directions]({{ site.url }}/directions) |
|
||||||
|
| - | :- |
|
||||||
|
| <i class="fa fa-paper-plane"> | foo@xyz |
|
||||||
|
| - | :- |
|
||||||
|
|
||||||
|
<a href="https://twitter.com/share" class="twitter-share-button" data-via="{{ site.owner.twitter }}" data-size="small" data-dnt="true">Tweet</a> <a href="javascript:window.print()" class="social-icons" title="Printer friendly format"><i class="fa fa-print"></i></a>
|
||||||
|
|
||||||
|
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs');</script>
|
||||||
|
|
||||||
|
{% if site.twitter_widget_id %}
|
||||||
|
<div class="text-tweets">
|
||||||
|
<div class="tweets">
|
||||||
|
<a class="twitter-timeline"
|
||||||
|
data-dnt="true"
|
||||||
|
width="600"
|
||||||
|
height="250"
|
||||||
|
href="https://twitter.com/{{ site.owner.twitter }}"
|
||||||
|
data-widget-id="{{ site.twitter_widget_id }}"
|
||||||
|
data-tweet-limit="2"
|
||||||
|
data-chrome="noheader nofooter noborders noscrollbar transparent">
|
||||||
|
Recent Tweets</a>
|
||||||
|
</div>
|
||||||
|
<script>
|
||||||
|
!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");
|
||||||
|
</script>
|
||||||
|
</div>
|
||||||
|
{% else %}
|
||||||
|
Twitter stream will show up here if `twitter_widget_id` is present is `_config.yml`
|
||||||
|
{% endif %}
|
||||||
36
pages/cv.md
Normal file
36
pages/cv.md
Normal file
|
|
@ -0,0 +1,36 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
permalink: /cv/
|
||||||
|
title: Curriculum Vitae
|
||||||
|
category: base
|
||||||
|
published: true
|
||||||
|
description: "Curriculum Vitae / Resume"
|
||||||
|
tags:
|
||||||
|
- cv
|
||||||
|
- resume
|
||||||
|
- "foo boo"
|
||||||
|
comments: false
|
||||||
|
imagesummary: foo.png
|
||||||
|
modified: "2016-02-13"
|
||||||
|
sitemap:
|
||||||
|
priority: 0.7
|
||||||
|
changefreq: 'monthly'
|
||||||
|
lastmod: 2016-02-13
|
||||||
|
style: |
|
||||||
|
.container {
|
||||||
|
max-width: 48rem;
|
||||||
|
}
|
||||||
|
---
|
||||||
|
|
||||||
|
<span class="social-icons">
|
||||||
|
<a href="https://twitter.com/share?text=Curriculum Vitae - {{ site.owner.name }}&url={{ site.url }}/cv&via={{ site.owner.twitter }}" class="social-icons" target="_blank" title="Share on twitter"> <i class="fa fa-twitter meta"></i></a>
|
||||||
|
<a href="https://plus.google.com/share?url={{ site.url }}/cv" class="social-icons" target="_blank" title="Share on Google+"> <i class="fa fa-google-plus"></i></a>
|
||||||
|
<a href="{{ site.owner.linkedin }}" class="social-icons" title="LinkedIn profile"><i class="fa fa-linkedin"></i></a>
|
||||||
|
<a href="{{ site.url }}/files/cv.pdf" class="social-icons" title="Printer friendly format"><i class="fa fa-print"></i></a>
|
||||||
|
</span>
|
||||||
|
|
||||||
|
{:.text-center}
|
||||||
|
[Publications]({{ site.url }}/about/publications/) \| [ORCID profile](https://orcid.org/{{ site.owner.orcid }}) \| [Google Scholar profile](https://scholar.google.com/citations?user={{ site.owner.gscholar }}&hl=en)
|
||||||
|
|
||||||
|
<!-- Alternaetly, user html5 embed tag -->
|
||||||
|
<iframe src="{{ site.url }}/files/cv.pdf" width="100%" style="height: 100vh;"></iframe>
|
||||||
56
pages/disclosure.md
Normal file
56
pages/disclosure.md
Normal file
|
|
@ -0,0 +1,56 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
permalink: /disclosure/
|
||||||
|
title: "Disclosure"
|
||||||
|
description: "This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License"
|
||||||
|
nofollow: false
|
||||||
|
published: true
|
||||||
|
modified: "2016-01-13"
|
||||||
|
---
|
||||||
|
|
||||||
|
This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.
|
||||||
|
|
||||||
|
### Theme Credit:
|
||||||
|
|
||||||
|
* Base: [*lanyon*](https://github.com/poole/lanyon) by [Mark Otto](https://github.com/mdo)
|
||||||
|
* Add-ons: [Samir B. Amin](https://twitter.com/sbamin) at [SBAmin.com](http://www.sbamin.com)
|
||||||
|
|
||||||
|
{% highlight c %}
|
||||||
|
Released under MIT License
|
||||||
|
|
||||||
|
Copyright (c) 2014 Mark Otto.
|
||||||
|
|
||||||
|
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
|
||||||
|
|
||||||
|
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
|
||||||
|
|
||||||
|
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
{% endhighlight %}
|
||||||
|
|
||||||
|
***
|
||||||
|
|
||||||
|
### <i class="fa fa-thumbs-o-up"> Credits for site features</i>:
|
||||||
|
|
||||||
|
* [Jekyll](https://jekyllrb.com){:target="_blank"}
|
||||||
|
* [Footer social icons by Lauren Clark](http://codepen.io/Deadlymuffin/pen/hGiqo/){:target="_blank"}
|
||||||
|
* [CSS and jekyll tips from HMFAYSAL OMEGA by HMFAYSAL](https://github.com/hmfaysal/hmfaysal-omega-theme){:target="_blank"}
|
||||||
|
* Icons by [Font Awesome Icons](http://fortawesome.github.io/Font-Awesome/icons/){:target="_blank"} and [IcoMoon](https://icomoon.io){:target="_blank"}
|
||||||
|
* [Responsive YouTube Playlist Embedding by John](http://avexdesigns.com/responsive-youtube-embed/){:target="_blank"}
|
||||||
|
* [Related posts without plugin by Ross Gardler](http://rgardler.github.io/2015/07/28/adding-related-posts-to-jekyll-blog/){:target="_blank"}
|
||||||
|
* [Archive page by Reyhan Dhuny and Michael Rowe](http://reyhan.org/2013/03/jekyll-archive-without-plugins.html){:target="_blank"}
|
||||||
|
* [Print css by Pieter Beulque and David Walsh](http://www.webdesignerdepot.com/2010/01/10-tips-for-better-print-style-sheets/){:target="_blank"}
|
||||||
|
* [Embed gists by Blair Vanderhoof](https://github.com/blairvanderhoof/gist-embed){:target="_blank"}
|
||||||
|
* [code highlighting css from *jekyll-now* by Barry Clark](https://github.com/barryclark/jekyll-now){:target="_blank"}
|
||||||
|
* CSS minify via [refresh-sf](http://refresh-sf.com){:target="_blank"}
|
||||||
|
* Search box:
|
||||||
|
* By [Justin James](https://github.com/digitaldrummerj){:target="_blank"}
|
||||||
|
* By [Paula Borowska](https://twitter.com/paulaborowska){:target="_blank"} at [envato tuts+](http://webdesign.tutsplus.com/tutorials/css-experiments-with-a-search-form-input-and-button--cms-22069){:target="_blank"}
|
||||||
|
* By [Amit Agrawal](http://www.labnol.org/about/){:target="_blank"} at [Digital Inspiration](http://www.labnol.org/internet/google-custom-search-css/28360/){:target="_blank"}
|
||||||
|
* Tag cloud:
|
||||||
|
* By [Tobias Sjosten](https://github.com/tobiassjosten/tobiassjosten.github.io){:target="_blank"}
|
||||||
|
* By [Thibaut Courouble](https://github.com/Thibaut){:target="_blank"} at [cssflow.com](http://www.cssflow.com/snippets/sliding-tags){:target="_blank"}
|
||||||
|
* By [Michael Lanyon](https://github.com/lanyonm){:target="_blank"} at [lanyonm.github.io](https://github.com/lanyonm/lanyonm.github.io){:target="_blank"}
|
||||||
|
* Bibliography:
|
||||||
|
* [Zot/Bib/Web](https://github.com/davidswelt/zot_bib_web){:target="_blank"} by [David Reitter](https://github.com/davidswelt){:target="_blank"} for *jekyll* page layout and css
|
||||||
|
* [Zotero Reference Manager API](https://www.zotero.org){:target="_blank"} for bibliography management
|
||||||
|
* [BibBase.org](http://bibbase.org){:target="_blank"} for external linking over `http`
|
||||||
44
pages/publications.md
Normal file
44
pages/publications.md
Normal file
|
|
@ -0,0 +1,44 @@
|
||||||
|
---
|
||||||
|
layout: publ
|
||||||
|
category: mypubs
|
||||||
|
permalink: /about/publications/
|
||||||
|
title: "Sample Publications"
|
||||||
|
published: true
|
||||||
|
description: "Sample publication page"
|
||||||
|
tags:
|
||||||
|
- papers
|
||||||
|
- articles
|
||||||
|
- research
|
||||||
|
comments: true
|
||||||
|
modified: "2016-02-13"
|
||||||
|
bibtex: "/files/mypubs.bib"
|
||||||
|
#bibtex: "http://foo-alternate.com/files/mypubs.bib"
|
||||||
|
show_meta: true
|
||||||
|
noindex: false
|
||||||
|
nofollow: true
|
||||||
|
sitemap:
|
||||||
|
priority: 0.5
|
||||||
|
changefreq: 'monthly'
|
||||||
|
lastmod: 2016-02-13
|
||||||
|
style: |
|
||||||
|
.container {
|
||||||
|
max-width: 48rem;
|
||||||
|
}
|
||||||
|
---
|
||||||
|
|
||||||
|
{% comment %}
|
||||||
|
<!-- bibbase.org should work with following code unless you are hosting domain over https. -->
|
||||||
|
|
||||||
|
{% if page.bibtex %}
|
||||||
|
{% if page.bibtex contains 'http' %}
|
||||||
|
{% assign domain = '' %}
|
||||||
|
{% else %}
|
||||||
|
{% assign domain = site.url %}
|
||||||
|
{% endif %}
|
||||||
|
{% capture biburl %}{{ domain }}{{ page.bibtex }}{% endcapture %}
|
||||||
|
<script src="http://bibbase.org/show?bib={{ biburl | cgi_escape }}&jsonp=1&authorFirst=1"></script>
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
|
{% endcomment %}
|
||||||
|
|
||||||
|
If category is *mypubs*, then html content from bibtex file at `_includes/mypubs.html` will be shown below.
|
||||||
100
pages/readme.md
Normal file
100
pages/readme.md
Normal file
|
|
@ -0,0 +1,100 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
permalink: /readme/
|
||||||
|
title: "README - How to set up lanyon-plus jekyll theme"
|
||||||
|
description: "README for setting up lanyon-plus jekyll theme on github pages or custom domain having static website"
|
||||||
|
---
|
||||||
|
{% raw %}
|
||||||
|
## lanyon-plus
|
||||||
|
|
||||||
|
### Based on Jekyll theme: [Lanyon](http://lanyon.getpoole.com) by [Mark Otto](https://github.com/mdo)
|
||||||
|
|
||||||
|
* add-ons by [Samir B. Amin](https://sbamin.com)
|
||||||
|
* License: Open sourced under the [MIT license](LICENSE.md).
|
||||||
|
|
||||||
|
### Required edits:
|
||||||
|
|
||||||
|
#### _config.yml
|
||||||
|
|
||||||
|
* Edit lines where text string `foo` is present with relevant information.
|
||||||
|
* Add relevant author and owner information
|
||||||
|
* For proper sidebar, meta info below post title, and footer bar, add at least twitter, google plus info under `owner` and `sidebar` section.
|
||||||
|
* Uncomment and add relevant user names/keys to enable features, e.g., google analytics, disqus comments, twitter widget, google custom search.
|
||||||
|
|
||||||
|
#### CNAME
|
||||||
|
|
||||||
|
* Read [Using a custom domain with GitHub Pages](https://help.github.com/articles/using-a-custom-domain-with-github-pages/) for set-up details.
|
||||||
|
* If you are hosting website on domain other than `github.io`, rename `CNAME.sample` file to `CNAME`, and add your custom domain name, e.g., `example.com` (only one domain is allowed), otherwise remove `CNAME` file if you want to host at default `github.io`.
|
||||||
|
* If you are hosting website on `github.io`, replace `example.com` with `https://<github-username>.github.io/<repository_name>` (for project site) or `https://<github-username>.github.io` (for user site) under `site.url` and `site.urlimg` in `_config.yml` and `_prose.yml` file.
|
||||||
|
|
||||||
|
#### .travis.yml
|
||||||
|
* See more at [https://travis-ci.org/getting_started](https://travis-ci.org/getting_started)
|
||||||
|
|
||||||
|
#### _prose.yml
|
||||||
|
|
||||||
|
* [https://github.com/prose/prose/wiki/Getting-Started](https://github.com/prose/prose/wiki/Getting-Started)
|
||||||
|
* Edit `example.com` with your domain name.
|
||||||
|
* You may edit names for custom categories.
|
||||||
|
|
||||||
|
#### robots.txt
|
||||||
|
|
||||||
|
* replace `example.com` with your valid url.
|
||||||
|
* Edit search engine inclusion/exclusion if desired.
|
||||||
|
|
||||||
|
#### page specific edits
|
||||||
|
|
||||||
|
* `_data/socialmedia.html`
|
||||||
|
* Replace user `foo` with appropriate username
|
||||||
|
|
||||||
|
* `_includes/`
|
||||||
|
* Check if file paths for appropriate urls have valid css files, scripts, icons, and images in `head.html` and `head_minimal.html`, else comment html tags which are not being used.
|
||||||
|
* Also, check if variables (twitter, google plus, linkedin, google analytics key and disqus username, etc.) are specified in `_config.yml` located under root path.
|
||||||
|
* You may edit `meta_info.html`, `footer.html` and similar include files to add/remove elements in page meta bar, footer, etc.
|
||||||
|
* For publications page, `mypubs.html` and `myaoi.html` are trimmed outputs from [zot_bib_web](https://github.com/davidswelt/zot_bib_web). Github pages can not dynamically build these pages. Alternately, you may export `bib` format for publications under `/files/` directory which can be parsed dynamically using [bibbase.org](http://bibbase.org)
|
||||||
|
* `_includes/footer.html`: Edit copyright information as needed.
|
||||||
|
* `_layouts`
|
||||||
|
* To add/remove/reorder page/post contents, edit `default.html` plus `page.html` or `post.html`.
|
||||||
|
* `_posts`
|
||||||
|
* Live blog posts goes here with markdown formatted post. File name format must have following date-title format `yyyy-mm-dd-title.md` for jekyll to render blog post correctly.
|
||||||
|
* YAML sample header shows all available options. Minimal required elements are: layout, title and date. Date tag overrides date given in post file name.
|
||||||
|
* `blog/index.html`
|
||||||
|
* Edit blog title and description.
|
||||||
|
* `images/`
|
||||||
|
* Under `icons` directory, keep appropriate sized favicons and thumbnails as specified in `_includes/head.html` and `_includes/head_minimal.html`
|
||||||
|
* Also, keep `favicon.png` and `favicon.ico` in root directory.
|
||||||
|
* Final, `images/icons/` should have following images with exact filenames and image size as specified in respective filenames. These images can be generated using online *favicon generator*. Replace `foo` with your site title or other name if desired.
|
||||||
|
|
||||||
|
~~~
|
||||||
|
example.com/images/icons/apple-touch-icon-precomposed.png
|
||||||
|
example.com/images/icons/apple-touch-icon-72x72-precomposed.png
|
||||||
|
example.com/images/icons/apple-touch-icon-114x114-precomposed.png
|
||||||
|
example.com/images/icons/apple-touch-icon-144x144-precomposed.png
|
||||||
|
example.com/images/icons/apple-touch-icon-180x180.png
|
||||||
|
example.com/images/icons/android-icon-192x192.png
|
||||||
|
~~~
|
||||||
|
|
||||||
|
* `pages/about.md`
|
||||||
|
* YAML variable `imagefeature` shoud have image path relative to `images/` directory, i.e., `foo.png` will link to `example.com/images/foo.png`
|
||||||
|
* Specify `site.owner.avatar` and `site.owner.twitter` along with other variables in `_config.yml`
|
||||||
|
* `syspages/`:
|
||||||
|
* Edit page title and description in YAML front matter.
|
||||||
|
* For web search to work, specify [Google Custom Search Engine](https://cse.google.com) API key for `google_search` variable.
|
||||||
|
* Tag generation is experimental and dynamic size for tag box may need to be adjusted if you have more than 100 posts with one or two frequently occurring tags.
|
||||||
|
* All `{% for ... %}...{% endfor %}` loop operations will increase site build time, and remove such features (tags, meta info, related posts, etc.) under `_includes`, `_layouts` and `syspages` if required.
|
||||||
|
* `pages/contact.md`
|
||||||
|
* Edit page title and description.
|
||||||
|
* Edit address, driving direction url, etc.
|
||||||
|
* `pages/cv.md`
|
||||||
|
* Edit `_config.yml` to add twitter, google plus, linkedin, google scholar, ORCID profile info under owner heading.
|
||||||
|
* Add pdf at `{{ site.url }}/cv/cv.pdf`
|
||||||
|
* `pages/publications.md`
|
||||||
|
* Add your publications at `/files/mypubs.bib` and `_includes/mypubs.html`. See above under `_includes` for more.
|
||||||
|
* `pages/disclosure.md`
|
||||||
|
* Appreciated if you keep relevant credits in disclosure page.
|
||||||
|
* `humans.txt`
|
||||||
|
* Replace `foo` with your name.
|
||||||
|
* `rfeed.xml`
|
||||||
|
* Not required unless you are cross-posting about R language on blog aggregation site(s).
|
||||||
|
|
||||||
|
END
|
||||||
|
{% endraw %}
|
||||||
1
public/css/addon.css
Normal file
1
public/css/addon.css
Normal file
|
|
@ -0,0 +1 @@
|
||||||
|
/*CSS pending minification*/
|
||||||
131
public/css/iconmoon.css
Normal file
131
public/css/iconmoon.css
Normal file
|
|
@ -0,0 +1,131 @@
|
||||||
|
@font-face {
|
||||||
|
font-family: 'icomoon';
|
||||||
|
src: url('../fonts/icomoon.eot?o6nkuq');
|
||||||
|
src: url('../fonts/icomoon.eot?o6nkuq#iefix') format('embedded-opentype'),
|
||||||
|
url('../fonts/icomoon.ttf?o6nkuq') format('truetype'),
|
||||||
|
url('../fonts/icomoon.woff?o6nkuq') format('woff'),
|
||||||
|
url('../fonts/icomoon.svg?o6nkuq#icomoon') format('svg');
|
||||||
|
font-weight: normal;
|
||||||
|
font-style: normal;
|
||||||
|
}
|
||||||
|
|
||||||
|
.headicons {
|
||||||
|
display: inline-block;
|
||||||
|
margin-left: 20px;
|
||||||
|
}
|
||||||
|
|
||||||
|
.masthead-title .headicons a {
|
||||||
|
color: #505050;
|
||||||
|
text-decoration: none;
|
||||||
|
}
|
||||||
|
|
||||||
|
i.iconm {
|
||||||
|
/* use !important to prevent issues with browser extensions that change fonts */
|
||||||
|
font-family: 'icomoon' !important;
|
||||||
|
speak: none;
|
||||||
|
font-style: normal;
|
||||||
|
font-weight: normal;
|
||||||
|
font-variant: normal;
|
||||||
|
text-transform: none;
|
||||||
|
line-height: 1;
|
||||||
|
padding: 0px 4px 0px 4px;
|
||||||
|
|
||||||
|
/* Better Font Rendering =========== */
|
||||||
|
-webkit-font-smoothing: antialiased;
|
||||||
|
-moz-osx-font-smoothing: grayscale;
|
||||||
|
}
|
||||||
|
|
||||||
|
i.iconside {
|
||||||
|
/* use !important to prevent issues with browser extensions that change fonts */
|
||||||
|
font-family: 'icomoon' !important;
|
||||||
|
speak: none;
|
||||||
|
font-style: normal;
|
||||||
|
font-weight: normal;
|
||||||
|
font-size: 1.0rem;
|
||||||
|
font-variant: normal;
|
||||||
|
text-transform: none;
|
||||||
|
line-height: 1;
|
||||||
|
|
||||||
|
/* Better Font Rendering =========== */
|
||||||
|
-webkit-font-smoothing: antialiased;
|
||||||
|
-moz-osx-font-smoothing: grayscale;
|
||||||
|
}
|
||||||
|
|
||||||
|
.iconm {
|
||||||
|
-o-transition:.5s;
|
||||||
|
-ms-transition:.5s;
|
||||||
|
-moz-transition:.5s;
|
||||||
|
-webkit-transition:.5s;
|
||||||
|
transition: .5s;
|
||||||
|
background-color: #ffffff;
|
||||||
|
}
|
||||||
|
|
||||||
|
.iconm:hover {
|
||||||
|
background-color: #999999;
|
||||||
|
border-radius: 30px;
|
||||||
|
color: white;
|
||||||
|
}
|
||||||
|
|
||||||
|
.iconm-home:before {
|
||||||
|
content: "\e900";
|
||||||
|
}
|
||||||
|
.iconm-pencil2:before {
|
||||||
|
content: "\e906";
|
||||||
|
}
|
||||||
|
.iconm-quill:before {
|
||||||
|
content: "\e907";
|
||||||
|
}
|
||||||
|
.iconm-blog:before {
|
||||||
|
content: "\e909";
|
||||||
|
}
|
||||||
|
.iconm-profile:before {
|
||||||
|
content: "\e923";
|
||||||
|
}
|
||||||
|
.iconm-envelop:before {
|
||||||
|
content: "\e945";
|
||||||
|
}
|
||||||
|
.iconm-location:before {
|
||||||
|
content: "\e947";
|
||||||
|
}
|
||||||
|
.iconm-compass2:before {
|
||||||
|
content: "\e94a";
|
||||||
|
}
|
||||||
|
|
||||||
|
.iconm-user:before {
|
||||||
|
content: "\e971";
|
||||||
|
}
|
||||||
|
.iconm-user-tie:before {
|
||||||
|
content: "\e976";
|
||||||
|
}
|
||||||
|
.iconm-embed2:before {
|
||||||
|
content: "\ea80";
|
||||||
|
}
|
||||||
|
.iconm-terminal:before {
|
||||||
|
content: "\ea81";
|
||||||
|
}
|
||||||
|
.iconm-google-plus:before {
|
||||||
|
content: "\ea88";
|
||||||
|
}
|
||||||
|
.iconm-twitter:before {
|
||||||
|
content: "\ea91";
|
||||||
|
}
|
||||||
|
.iconm-feed2:before {
|
||||||
|
content: "\ea94";
|
||||||
|
}
|
||||||
|
.iconm-github2:before {
|
||||||
|
content: "\eab2";
|
||||||
|
}
|
||||||
|
.iconm-wordpress:before {
|
||||||
|
content: "\eab6";
|
||||||
|
}
|
||||||
|
.iconm-linkedin2:before {
|
||||||
|
content: "\eac9";
|
||||||
|
}
|
||||||
|
.iconm-file-pdf:before {
|
||||||
|
content: "\eada";
|
||||||
|
}
|
||||||
|
.iconm-html5:before {
|
||||||
|
content: "\eadf";
|
||||||
|
}
|
||||||
|
|
||||||
|
/*END*/
|
||||||
123
public/css/publ.css
Normal file
123
public/css/publ.css
Normal file
|
|
@ -0,0 +1,123 @@
|
||||||
|
/* The bibliography */
|
||||||
|
div.bibliography
|
||||||
|
{
|
||||||
|
font-family: "PT Serif", Georgia, "Times New Roman", serif;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Collection titles */
|
||||||
|
div.bibliography h1, div.bibliography h2, div.bibliography h3, div.bibliography h4
|
||||||
|
{
|
||||||
|
font-family: "PT Sans", Helvetica, Arial, sans-serif;
|
||||||
|
font-weight:1000;
|
||||||
|
color:DarkSlateGray ;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* The entire bibliographic item */
|
||||||
|
div.bib-item {
|
||||||
|
}
|
||||||
|
div.full-bib-section div.bib-item {
|
||||||
|
margin-bottom:25px;
|
||||||
|
}
|
||||||
|
/* the short format (selected works) */
|
||||||
|
div.short-bib-section div.bib-item {
|
||||||
|
margin-bottom:5px;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* The actual BibTeX record (when visible) */
|
||||||
|
div.bib {
|
||||||
|
font-family:Menlo,Courier,monospaced;
|
||||||
|
color: #9A9A9A;
|
||||||
|
padding-left:30px;
|
||||||
|
padding-bottom:10px;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Text "bib" or "abstract" */
|
||||||
|
|
||||||
|
/* Text "bib" or "abstract" */
|
||||||
|
.blink a {
|
||||||
|
font-family:Arial,sans-serif;
|
||||||
|
font-variant: small-caps;
|
||||||
|
clear: both;
|
||||||
|
padding:0;
|
||||||
|
margin:0;
|
||||||
|
}
|
||||||
|
div.full-bib-section .blink a {
|
||||||
|
margin-bottom:-30px;
|
||||||
|
}
|
||||||
|
div.short-bib-section .blink {
|
||||||
|
display:inline-block; /* needed to make margin-top work (collapsed margins) */
|
||||||
|
margin-top:-5px;
|
||||||
|
margin-bottom:10px;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* The actual abstract (when visible) */
|
||||||
|
div.abstract {
|
||||||
|
color:black;
|
||||||
|
padding-left:30px;
|
||||||
|
padding-bottom:10px;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Document titles */
|
||||||
|
.doctitle {
|
||||||
|
font-weight:700;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Document titles linking to a PDF or somewhere else */
|
||||||
|
a.doctitle:link,a.doctitle:visited,a.doctitle,a.doctitle:hover,a.doctitle.active {
|
||||||
|
color:#3090D4;
|
||||||
|
font-weight:700;
|
||||||
|
text-decoration:none; /* do not underline */
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Document titles where shorted, e.g. "selected works" */
|
||||||
|
.doctitle-short {
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Display publication titles in their own lines.
|
||||||
|
Remove to disable. */
|
||||||
|
a.doctitle,span.doctitle {
|
||||||
|
display:block;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* Search box */
|
||||||
|
#pubSearchButton {
|
||||||
|
/* border: 0 solid #d4d0ba; */
|
||||||
|
font-family: inherit;
|
||||||
|
padding: 0;
|
||||||
|
}
|
||||||
|
#pubSearchBox {
|
||||||
|
position:absolute;
|
||||||
|
right:10px; top:100px;
|
||||||
|
display:block;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* Categories at top of the bibliography */
|
||||||
|
.bib-cat {
|
||||||
|
display: inline;
|
||||||
|
list-style: none;
|
||||||
|
text-indent: 0;
|
||||||
|
margin: 0; padding: 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
.bib-cat li {
|
||||||
|
display: inline;
|
||||||
|
}
|
||||||
|
.bib-cat li:after {
|
||||||
|
content: " | ";
|
||||||
|
}
|
||||||
|
.bib-cat li:last-child:after {
|
||||||
|
content: ""
|
||||||
|
}
|
||||||
|
|
||||||
|
@media print {
|
||||||
|
div.full-bib-section .blink {
|
||||||
|
display: none;
|
||||||
|
}
|
||||||
|
a.doctitle:link:after {
|
||||||
|
display: none;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/*END*/
|
||||||
1
public/css/style.min.css
vendored
Normal file
1
public/css/style.min.css
vendored
Normal file
File diff suppressed because one or more lines are too long
BIN
public/fonts/icomoon.eot
Normal file
BIN
public/fonts/icomoon.eot
Normal file
Binary file not shown.
30
public/fonts/icomoon.svg
Normal file
30
public/fonts/icomoon.svg
Normal file
|
|
@ -0,0 +1,30 @@
|
||||||
|
<?xml version="1.0" standalone="no"?>
|
||||||
|
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd" >
|
||||||
|
<svg xmlns="http://www.w3.org/2000/svg">
|
||||||
|
<metadata>Generated by IcoMoon</metadata>
|
||||||
|
<defs>
|
||||||
|
<font id="icomoon" horiz-adv-x="1024">
|
||||||
|
<font-face units-per-em="1024" ascent="960" descent="-64" />
|
||||||
|
<missing-glyph horiz-adv-x="1024" />
|
||||||
|
<glyph unicode=" " horiz-adv-x="512" d="" />
|
||||||
|
<glyph unicode="" glyph-name="home" d="M1024 369.556l-512 397.426-512-397.428v162.038l512 397.426 512-397.428zM896 384v-384h-256v256h-256v-256h-256v384l384 288z" />
|
||||||
|
<glyph unicode="" glyph-name="pencil2" d="M384 320l128 64 448 448-64 64-448-448-64-128zM289.3 92.902c-31.632 66.728-65.666 100.762-132.396 132.394l99.096 272.792 128 77.912 384 384h-192l-384-384-192-640 640 192 384 384v192l-384-384-77.912-128z" />
|
||||||
|
<glyph unicode="" glyph-name="quill" d="M0-64c128 384 463 1024 1024 1024-263-211-384-704-576-704s-192 0-192 0l-192-320h-64z" />
|
||||||
|
<glyph unicode="" glyph-name="blog" d="M384 960v-96c73.482 0 144.712-14.37 211.716-42.71 64.768-27.394 122.958-66.632 172.948-116.624s89.228-108.18 116.624-172.948c28.342-67.004 42.712-138.238 42.712-211.718h96c0 353.46-286.54 640-640 640zM384 768v-96c94.022 0 182.418-36.614 248.9-103.098 66.486-66.484 103.1-154.878 103.1-248.902h96c0 247.422-200.576 448-448 448zM480 576l-64-64-224-64-192-416 25.374-25.374 232.804 232.804c-1.412 5.286-2.178 10.84-2.178 16.57 0 35.346 28.654 64 64 64s64-28.654 64-64-28.654-64-64-64c-5.732 0-11.282 0.764-16.568 2.178l-232.804-232.804 25.372-25.374 416 192 64 224 64 64-160 160z" />
|
||||||
|
<glyph unicode="" glyph-name="profile" d="M864 960h-768c-52.8 0-96-43.2-96-96v-832c0-52.8 43.2-96 96-96h768c52.8 0 96 43.2 96 96v832c0 52.8-43.2 96-96 96zM832 64h-704v768h704v-768zM256 384h448v-64h-448zM256 256h448v-64h-448zM320 672c0 53.019 42.981 96 96 96s96-42.981 96-96c0-53.019-42.981-96-96-96s-96 42.981-96 96zM480 576h-128c-52.8 0-96-28.8-96-64v-64h320v64c0 35.2-43.2 64-96 64z" />
|
||||||
|
<glyph unicode="" glyph-name="envelop" d="M928 832h-832c-52.8 0-96-43.2-96-96v-640c0-52.8 43.2-96 96-96h832c52.8 0 96 43.2 96 96v640c0 52.8-43.2 96-96 96zM398.74 409.628l-270.74-210.892v501.642l270.74-290.75zM176.38 704h671.24l-335.62-252-335.62 252zM409.288 398.302l102.712-110.302 102.71 110.302 210.554-270.302h-626.528l210.552 270.302zM625.26 409.628l270.74 290.75v-501.642l-270.74 210.892z" />
|
||||||
|
<glyph unicode="" glyph-name="location" d="M512 960c-176.732 0-320-143.268-320-320 0-320 320-704 320-704s320 384 320 704c0 176.732-143.27 320-320 320zM512 448c-106.040 0-192 85.96-192 192s85.96 192 192 192 192-85.96 192-192-85.96-192-192-192z" />
|
||||||
|
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<glyph unicode="" glyph-name="wordpress" d="M128 448.008c0-148.026 88.322-275.968 216.43-336.578l-183.178 488.784c-21.308-46.508-33.252-97.982-33.252-152.206zM771.228 466.872c0 46.234-17.054 78.236-31.654 103.142-19.458 30.82-37.72 56.894-37.72 87.716 0 34.374 26.766 66.376 64.486 66.376 1.704 0 3.32-0.204 4.976-0.302-68.316 60.97-159.34 98.196-259.308 98.196-134.16 0-252.186-67.046-320.844-168.568 9.010-0.282 17.506-0.454 24.712-0.454 40.154 0 102.34 4.752 102.34 4.752 20.69 1.182 23.132-28.434 2.458-30.822 0 0-20.81-2.368-43.952-3.55l139.834-405.106 84.044 245.456-59.822 159.65c-20.688 1.184-40.278 3.55-40.278 3.55-20.702 1.192-18.272 32.002 2.438 30.822 0 0 63.4-4.752 101.134-4.752 40.146 0 102.35 4.752 102.35 4.752 20.702 1.182 23.14-28.434 2.446-30.822 0 0-20.834-2.372-43.948-3.55l138.78-402.018 38.312 124.632c16.58 51.75 29.216 88.9 29.216 120.9zM518.742 415.296l-115.226-326.058c34.416-9.858 70.794-15.238 108.488-15.238 44.716 0 87.604 7.518 127.518 21.2-1.018 1.602-1.974 3.304-2.75 5.154l-118.030 314.942zM848.962 627.428c1.652-11.91 2.588-24.686 2.588-38.458 0-37.93-7.292-80.596-29.202-133.95l-117.286-330.272c114.162 64.828 190.938 185.288 190.938 323.258 0 65.030-17.060 126.16-47.038 179.422zM512 960c-282.77 0-512-229.23-512-512s229.23-512 512-512 512 229.23 512 512-229.23 512-512 512zM512 0c-247.424 0-448 200.576-448 448s200.576 448 448 448 448-200.576 448-448-200.576-448-448-448z" />
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<glyph unicode="" glyph-name="linkedin2" d="M384 576h177.106v-90.782h2.532c24.64 44.194 84.958 90.782 174.842 90.782 186.946 0 221.52-116.376 221.52-267.734v-308.266h-184.61v273.278c0 65.184-1.334 149.026-96.028 149.026-96.148 0-110.82-70.986-110.82-144.292v-278.012h-184.542v576zM64 576h192v-576h-192v576zM256 736c0-53.019-42.981-96-96-96s-96 42.981-96 96c0 53.019 42.981 96 96 96s96-42.981 96-96z" />
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<glyph unicode="" glyph-name="file-pdf" d="M842.012 370.52c-13.648 13.446-43.914 20.566-89.972 21.172-31.178 0.344-68.702-2.402-108.17-7.928-17.674 10.198-35.892 21.294-50.188 34.658-38.462 35.916-70.568 85.772-90.576 140.594 1.304 5.12 2.414 9.62 3.448 14.212 0 0 21.666 123.060 15.932 164.666-0.792 5.706-1.276 7.362-2.808 11.796l-1.882 4.834c-5.894 13.592-17.448 27.994-35.564 27.208l-10.916 0.344c-20.202 0-36.664-10.332-40.986-25.774-13.138-48.434 0.418-120.892 24.98-214.738l-6.288-15.286c-17.588-42.876-39.63-86.060-59.078-124.158l-2.528-4.954c-20.46-40.040-39.026-74.028-55.856-102.822l-17.376-9.188c-1.264-0.668-31.044-16.418-38.028-20.644-59.256-35.38-98.524-75.542-105.038-107.416-2.072-10.17-0.53-23.186 10.014-29.212l16.806-8.458c7.292-3.652 14.978-5.502 22.854-5.502 42.206 0 91.202 52.572 158.698 170.366 77.93 25.37 166.652 46.458 244.412 58.090 59.258-33.368 132.142-56.544 178.142-56.544 8.168 0 15.212 0.78 20.932 2.294 8.822 2.336 16.258 7.368 20.792 14.194 8.926 13.432 10.734 31.932 8.312 50.876-0.72 5.622-5.21 12.574-10.068 17.32zM211.646 145.952c7.698 21.042 38.16 62.644 83.206 99.556 2.832 2.296 9.808 8.832 16.194 14.902-47.104-75.124-78.648-105.066-99.4-114.458zM478.434 760.314c13.566 0 21.284-34.194 21.924-66.254s-6.858-54.56-16.158-71.208c-7.702 24.648-11.426 63.5-11.426 88.904 0 0-0.566 48.558 5.66 48.558v0zM398.852 322.506c9.45 16.916 19.282 34.756 29.33 53.678 24.492 46.316 39.958 82.556 51.478 112.346 22.91-41.684 51.444-77.12 84.984-105.512 4.186-3.542 8.62-7.102 13.276-10.65-68.21-13.496-127.164-29.91-179.068-49.862v0zM828.902 326.348c-4.152-2.598-16.052-4.1-23.708-4.1-24.708 0-55.272 11.294-98.126 29.666 16.468 1.218 31.562 1.838 45.102 1.838 24.782 0 32.12 0.108 56.35-6.072 24.228-6.18 24.538-18.734 20.382-21.332v0zM917.806 730.924c-22.21 30.292-53.174 65.7-87.178 99.704s-69.412 64.964-99.704 87.178c-51.574 37.82-76.592 42.194-90.924 42.194h-496c-44.112 0-80-35.888-80-80v-864c0-44.112 35.886-80 80-80h736c44.112 0 80 35.888 80 80v624c0 14.332-4.372 39.35-42.194 90.924v0zM785.374 785.374c30.7-30.7 54.8-58.398 72.58-81.374h-153.954v153.946c22.982-17.78 50.678-41.878 81.374-72.572v0zM896 16c0-8.672-7.328-16-16-16h-736c-8.672 0-16 7.328-16 16v864c0 8.672 7.328 16 16 16 0 0 495.956 0.002 496 0v-224c0-17.672 14.324-32 32-32h224v-624z" />
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|
<glyph unicode="" glyph-name="html5" d="M60.538 960l82.144-921.63 368.756-102.37 369.724 102.524 82.3 921.476h-902.924zM784.63 658.572h-432.54l10.302-115.75h411.968l-31.042-347.010-231.844-64.254-231.572 64.254-15.83 177.512h113.494l8.048-90.232 125.862-33.916 0.278 0.078 125.934 33.992 13.070 146.55h-391.74l-30.494 341.8h566.214l-10.108-113.024z" />
|
||||||
|
</font></defs></svg>
|
||||||
|
After Width: | Height: | Size: 14 KiB |
BIN
public/fonts/icomoon.ttf
Normal file
BIN
public/fonts/icomoon.ttf
Normal file
Binary file not shown.
BIN
public/fonts/icomoon.woff
Normal file
BIN
public/fonts/icomoon.woff
Normal file
Binary file not shown.
6
public/js/jquery.min.js
vendored
Normal file
6
public/js/jquery.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
31
rfeed.xml
Normal file
31
rfeed.xml
Normal file
|
|
@ -0,0 +1,31 @@
|
||||||
|
---
|
||||||
|
layout: null
|
||||||
|
---
|
||||||
|
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||||
|
<channel>
|
||||||
|
<title>{{ site.title | xml_escape }}</title>
|
||||||
|
<description>{{ site.description | xml_escape }}</description>
|
||||||
|
<link>{{ site.url }}{{ site.baseurl }}/</link>
|
||||||
|
<atom:link href="{{ "/rfeed.xml" | prepend: site.baseurl | prepend: site.url }}" rel="self" type="application/rss+xml" />
|
||||||
|
<updated>{{ site.time | date_to_xmlschema }}</updated>
|
||||||
|
<id>{{ site.url }}</id>
|
||||||
|
<author>
|
||||||
|
<name>{{ site.owner.name }}</name>
|
||||||
|
</author>
|
||||||
|
{% for post in site.tags.R limit:10 %}
|
||||||
|
<item>
|
||||||
|
<title>{{ post.title | xml_escape }}</title>
|
||||||
|
{% if post.summaryfeed and post.excerpt %}
|
||||||
|
<description>{{ post.excerpt | xml_escape }}</description>
|
||||||
|
{% else %}
|
||||||
|
<description>{{ post.content | xml_escape }}</description>
|
||||||
|
{% endif %}
|
||||||
|
<pubDate>{{ post.date | date: "%a, %d %b %Y %H:%M:%S %z" }}</pubDate>
|
||||||
|
<link>{{ post.url | prepend: site.baseurl | prepend: site.url }}</link>
|
||||||
|
<guid isPermaLink="true">{{ post.url | prepend: site.baseurl | prepend: site.url }}</guid>
|
||||||
|
</item>
|
||||||
|
{% endfor %}
|
||||||
|
</channel>
|
||||||
|
</rss>
|
||||||
58
robots.txt
Normal file
58
robots.txt
Normal file
|
|
@ -0,0 +1,58 @@
|
||||||
|
User-agent: Googlebot
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: Googlebot-Image
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: Twitterbot
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: Bingbot
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: DuckDuckBot
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: ia_archiver
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: Applebot
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: facebookexternalhit
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: Facebot
|
||||||
|
Disallow: /assets/
|
||||||
|
Disallow: /CNAME
|
||||||
|
Disallow: /*.md$
|
||||||
|
Disallow: /files/
|
||||||
|
|
||||||
|
User-agent: *
|
||||||
|
Disallow: /
|
||||||
|
|
||||||
|
Sitemap: https://example.com/sitemap.xml
|
||||||
54
sitemap.xml
Normal file
54
sitemap.xml
Normal file
|
|
@ -0,0 +1,54 @@
|
||||||
|
---
|
||||||
|
layout: null
|
||||||
|
---
|
||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
|
||||||
|
{% for post in site.posts %}
|
||||||
|
{% unless post.published == false %}
|
||||||
|
<url>
|
||||||
|
<loc>{{ site.url }}{{ post.url }}</loc>
|
||||||
|
{% if post.sitemap.lastmod %}
|
||||||
|
<lastmod>{{ post.sitemap.lastmod | date: "%Y-%m-%d" }}</lastmod>
|
||||||
|
{% elsif post.date %}
|
||||||
|
<lastmod>{{ post.date | date_to_xmlschema }}</lastmod>
|
||||||
|
{% else %}
|
||||||
|
<lastmod>{{ site.time | date_to_xmlschema }}</lastmod>
|
||||||
|
{% endif %}
|
||||||
|
{% if post.sitemap.changefreq %}
|
||||||
|
<changefreq>{{ post.sitemap.changefreq }}</changefreq>
|
||||||
|
{% else %}
|
||||||
|
<changefreq>monthly</changefreq>
|
||||||
|
{% endif %}
|
||||||
|
{% if post.sitemap.priority %}
|
||||||
|
<priority>{{ post.sitemap.priority }}</priority>
|
||||||
|
{% else %}
|
||||||
|
<priority>0.5</priority>
|
||||||
|
{% endif %}
|
||||||
|
</url>
|
||||||
|
{% endunless %}
|
||||||
|
{% endfor %}
|
||||||
|
{% for page in site.pages %}
|
||||||
|
{% unless page.sitemap == false %}
|
||||||
|
<url>
|
||||||
|
<loc>{{ site.url }}{{ page.url | remove: "index.html" }}</loc>
|
||||||
|
{% if page.sitemap.lastmod %}
|
||||||
|
<lastmod>{{ page.sitemap.lastmod | date: "%Y-%m-%d" }}</lastmod>
|
||||||
|
{% elsif page.date %}
|
||||||
|
<lastmod>{{ page.date | date_to_xmlschema }}</lastmod>
|
||||||
|
{% else %}
|
||||||
|
<lastmod>{{ site.time | date_to_xmlschema }}</lastmod>
|
||||||
|
{% endif %}
|
||||||
|
{% if page.sitemap.changefreq %}
|
||||||
|
<changefreq>{{ page.sitemap.changefreq }}</changefreq>
|
||||||
|
{% else %}
|
||||||
|
<changefreq>monthly</changefreq>
|
||||||
|
{% endif %}
|
||||||
|
{% if page.sitemap.priority %}
|
||||||
|
<priority>{{ page.sitemap.priority }}</priority>
|
||||||
|
{% else %}
|
||||||
|
<priority>0.3</priority>
|
||||||
|
{% endif %}
|
||||||
|
</url>
|
||||||
|
{% endunless %}
|
||||||
|
{% endfor %}
|
||||||
|
</urlset>
|
||||||
35
syspages/404.md
Normal file
35
syspages/404.md
Normal file
|
|
@ -0,0 +1,35 @@
|
||||||
|
---
|
||||||
|
layout: default_minimal
|
||||||
|
title: "404: Page not found"
|
||||||
|
description: "Error 404: Requested page not found"
|
||||||
|
permalink: /404.html
|
||||||
|
sitemap: false
|
||||||
|
noindex: true
|
||||||
|
nofollow: true
|
||||||
|
category: base
|
||||||
|
---
|
||||||
|
|
||||||
|
<p>Sorry! The page you were trying to view does not exist.</p>
|
||||||
|
<p>Perhaps you may have error while typing web address. If not, you may tweet me to fix missing link. Thanks!</p>
|
||||||
|
<div class="text-center">
|
||||||
|
<a href="https://twitter.com/share" class="twitter-share-button" data-via="{{ site.owner.twitter }}" data-size="large" data-dnt="true">Tweet</a>
|
||||||
|
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore(js,fjs);}}(document, 'script', 'twitter-wjs');</script>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
{:.text-center}
|
||||||
|
You may also visit [tags]({{ site.url }}/tags) or [archive]({{ site.url }}/archive) page to browse website contents.
|
||||||
|
|
||||||
|
<hr class="gh">
|
||||||
|
|
||||||
|
{% if site.google_search %}
|
||||||
|
<div id="searchbox2" style="margin:0 auto; display: table;">
|
||||||
|
<div class="searchcont2">
|
||||||
|
<!-- span class="searchicon2"><i class="fa fa-search fa-2x"></i></span -->
|
||||||
|
<form role="search" method="get" action="{{ site.url }}/cse/">
|
||||||
|
<input id="searchString2" name="searchString2"
|
||||||
|
placeholder=" Search" type="text">
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
{% endif %}
|
||||||
|
|
||||||
26
syspages/archive.md
Normal file
26
syspages/archive.md
Normal file
|
|
@ -0,0 +1,26 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
title: Archive
|
||||||
|
description: "Archive"
|
||||||
|
permalink: /archive/
|
||||||
|
category: base
|
||||||
|
---
|
||||||
|
|
||||||
|
<section id="archive">
|
||||||
|
<h3>This year's posts</h3>
|
||||||
|
{%for post in site.posts %}
|
||||||
|
{% unless post.next %}
|
||||||
|
<ul class="post-list">
|
||||||
|
{% else %}
|
||||||
|
{% capture year %}{{ post.date | date: '%Y' }}{% endcapture %}
|
||||||
|
{% capture nyear %}{{ post.next.date | date: '%Y' }}{% endcapture %}
|
||||||
|
{% if year != nyear %}
|
||||||
|
</ul>
|
||||||
|
<h3>{{ post.date | date: '%Y' }}</h3>
|
||||||
|
<ul class="post-list">
|
||||||
|
{% endif %}
|
||||||
|
{% endunless %}
|
||||||
|
<li><a href="{{ site.url }}{{ post.url }}">{{ post.title }}<span class="entry-date"><time datetime="{{ post.date | date_to_xmlschema }}">{{ post.date | date: "%b %d, %Y" }}</time></span></a></li>
|
||||||
|
{% endfor %}
|
||||||
|
</ul>
|
||||||
|
</section>
|
||||||
52
syspages/cse.md
Normal file
52
syspages/cse.md
Normal file
|
|
@ -0,0 +1,52 @@
|
||||||
|
---
|
||||||
|
layout: default_minimal
|
||||||
|
title: "Search"
|
||||||
|
description: "Search"
|
||||||
|
permalink: /cse/
|
||||||
|
sitemap: false
|
||||||
|
noindex: true
|
||||||
|
nofollow: true
|
||||||
|
category: base
|
||||||
|
---
|
||||||
|
{:.text-center}
|
||||||
|
You may also visit [tags]({{ site.url }}/tags) or [archive]({{ site.url }}/archive) page to browse website contents.
|
||||||
|
|
||||||
|
{:.text-center}
|
||||||
|
<a href="javascript:goBack()" class="social-icons" title="Return to previous page"><i class="fa fa-arrow-circle-left fa-2x"></i></a>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
function goBack() {
|
||||||
|
window.history.back();
|
||||||
|
}
|
||||||
|
</script>
|
||||||
|
|
||||||
|
{% if site.google_search %}
|
||||||
|
<hr class="gh">
|
||||||
|
|
||||||
|
<div id="searchbox2" align="center">
|
||||||
|
<div class="searchcont2">
|
||||||
|
<!-- span class="searchicon2"><i class="fa fa-search fa-2x"></i></span -->
|
||||||
|
<form role="search" method="get" action="{{ site.url }}/cse/">
|
||||||
|
<input id="searchString2" name="searchString2"
|
||||||
|
placeholder=" Search" type="text">
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
|
||||||
|
<script>
|
||||||
|
(function() {
|
||||||
|
var cx = '{{ site.google_search }}';
|
||||||
|
var gcse = document.createElement('script');
|
||||||
|
gcse.type = 'text/javascript';
|
||||||
|
gcse.async = true;
|
||||||
|
gcse.src = (document.location.protocol == 'https:' ? 'https:' : 'http:') +
|
||||||
|
'//cse.google.com/cse.js?cx=' + cx;
|
||||||
|
var s = document.getElementsByTagName('script')[0];
|
||||||
|
s.parentNode.insertBefore(gcse, s);
|
||||||
|
})();
|
||||||
|
</script>
|
||||||
|
<gcse:searchresults-only queryParameterName="searchString2" enableAutoComplete="true" autoCompleteMatchType='any' autoCompleteMaxCompletions="5" autoCompleteMaxPromotions="1"></gcse:searchresults-only>
|
||||||
|
<!-- <gcse:searchbox-only resultsUrl="{{ site.url }}/cse/" queryParameterName="searchString"></gcse:searchbox-only> -->
|
||||||
|
{% else %}
|
||||||
|
This page will serve search results if Google Custom Search key is set in `_config.yml`
|
||||||
|
{% endif %}
|
||||||
26
syspages/featured.md
Normal file
26
syspages/featured.md
Normal file
|
|
@ -0,0 +1,26 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
title: Featured Posts
|
||||||
|
description: "Featured posts"
|
||||||
|
permalink: /featured/
|
||||||
|
sitemap: false
|
||||||
|
noindex: true
|
||||||
|
category: base
|
||||||
|
---
|
||||||
|
<hr class="gh">
|
||||||
|
<div class="posts">
|
||||||
|
{% for post in site.categories.featured %}
|
||||||
|
<div class="post">
|
||||||
|
<h1 class="post-title">
|
||||||
|
<a href="{{ site.url }}{{ post.url }}">
|
||||||
|
{{ post.title }}
|
||||||
|
</a>
|
||||||
|
</h1>
|
||||||
|
|
||||||
|
{% if post.modified.size > 2 %}<span class="post-date indexpg" itemprop="dateModified" content="{{ post.modified | date: "%Y-%m-%d" }}"><i class="fa fa-edit" title="Last updated"> {{ post.modified | date_to_string }}</i></span>{% else %}<span class="post-date indexpg" itemprop="datePublished" content="{{ post.date | date: "%Y-%m-%d" }}"><i class="fa fa-calendar" title="Date published"> {{ post.date | date_to_string }}</i></span>{% endif %}
|
||||||
|
|
||||||
|
{% if post.description.size > 140 %}{{ post.description | markdownify | remove: '<p>' | remove: '</p>' }}{% else %}{{ post.excerpt | markdownify | remove: '<p>' | remove: '</p>' }}{% endif %} <a href="{{ site.url }}{{ post.url }}" title="Read more"><strong>Read more...</strong></a>
|
||||||
|
</div>
|
||||||
|
{% unless forloop.last %}<hr class="transp">{% endunless %}
|
||||||
|
{% endfor %}
|
||||||
|
</div>
|
||||||
8
syspages/news.md
Normal file
8
syspages/news.md
Normal file
|
|
@ -0,0 +1,8 @@
|
||||||
|
---
|
||||||
|
title: "Redirecting to Blog"
|
||||||
|
layout: redirect
|
||||||
|
sitemap: false
|
||||||
|
permalink: /news/
|
||||||
|
redirect_to: /blog/
|
||||||
|
#teaser: SYSTEM GENERATED PAGE FOR PAGE REDIRECT FUNCTION. DO NOT EDIT/RENAME/REMOVE THIS PAGE.
|
||||||
|
---
|
||||||
8
syspages/pubs_redir.md
Normal file
8
syspages/pubs_redir.md
Normal file
|
|
@ -0,0 +1,8 @@
|
||||||
|
---
|
||||||
|
title: "Redirecting to About/Publications"
|
||||||
|
layout: redirect
|
||||||
|
sitemap: false
|
||||||
|
permalink: /publications/
|
||||||
|
redirect_to: /about/publications/
|
||||||
|
#teaser: SYSTEM GENERATED PAGE FOR PAGE REDIRECT FUNCTION. DO NOT EDIT/RENAME/REMOVE THIS PAGE.
|
||||||
|
---
|
||||||
8
syspages/resume.md
Normal file
8
syspages/resume.md
Normal file
|
|
@ -0,0 +1,8 @@
|
||||||
|
---
|
||||||
|
title: "Redirecting to Curriculum Vitae page"
|
||||||
|
layout: redirect
|
||||||
|
sitemap: true
|
||||||
|
permalink: /resume/
|
||||||
|
redirect_to: /cv/
|
||||||
|
#teaser: SYSTEM GENERATED PAGE FOR PAGE REDIRECT FUNCTION. DO NOT EDIT/RENAME/REMOVE THIS PAGE.
|
||||||
|
---
|
||||||
24
syspages/search.md
Normal file
24
syspages/search.md
Normal file
|
|
@ -0,0 +1,24 @@
|
||||||
|
---
|
||||||
|
layout: default_minimal
|
||||||
|
title: "Search"
|
||||||
|
description: "Search"
|
||||||
|
permalink: /search/
|
||||||
|
sitemap: false
|
||||||
|
noindex: true
|
||||||
|
nofollow: true
|
||||||
|
category: base
|
||||||
|
---
|
||||||
|
|
||||||
|
{% if site.google_search %}
|
||||||
|
<div id="searchbox2" style="margin:0 auto; display: table;">
|
||||||
|
<div class="searchcont2">
|
||||||
|
<!-- span class="searchicon2"><i class="fa fa-search fa-2x"></i></span -->
|
||||||
|
<form role="search" method="get" action="{{ site.url }}/cse/">
|
||||||
|
<input id="searchString2" name="searchString2"
|
||||||
|
placeholder=" Search" type="text">
|
||||||
|
</form>
|
||||||
|
</div>
|
||||||
|
</div>
|
||||||
|
{% else %}
|
||||||
|
Google Custom Search key is not set in `_config.yml`
|
||||||
|
{% endif %}
|
||||||
39
syspages/tags.md
Normal file
39
syspages/tags.md
Normal file
|
|
@ -0,0 +1,39 @@
|
||||||
|
---
|
||||||
|
layout: page
|
||||||
|
title: "Tag Cloud"
|
||||||
|
permalink: "/tags/"
|
||||||
|
description: "Browse website by tag based index"
|
||||||
|
comments: false
|
||||||
|
sitemap: false
|
||||||
|
category: base
|
||||||
|
---
|
||||||
|
|
||||||
|
{:.text-center}
|
||||||
|
## <i class="fa fa-paperclip" title="Featured"></i> <a href="{{ site.url }}/featured">Featured Posts</a>
|
||||||
|
|
||||||
|
<hr class="style17" style="margin:1.0rem 0;">
|
||||||
|
|
||||||
|
{% comment %}
|
||||||
|
Tag generation is experimental and dynamic size for tag box may need to be adjusted if you have more than 100 posts with one or two frequently occurring tags. Also,all for loop operations will increase site build time.
|
||||||
|
{% endcomment %}
|
||||||
|
|
||||||
|
{% capture site_tags %}{% for tag in site.tags %}{{ tag | first }}{% unless forloop.last %},{% endunless %}{% endfor %}{% endcapture %}
|
||||||
|
{% assign tags_list = site_tags | split:',' | sort %}
|
||||||
|
|
||||||
|
<ul class="slidetags">
|
||||||
|
{% for item in (0..site.tags.size) %}{% unless forloop.last %}
|
||||||
|
{% capture this_word %}{{ tags_list[item] | strip_newlines }}{% endcapture %}
|
||||||
|
<li style="font-size:{{ site.tags[this_word].size | times: 100 | divided_by: site.tags.size | plus: 70 }}%"><a href="#{{ this_word }}">{{ this_word }} <span>{{ site.tags[this_word].size }}</span></a></li>
|
||||||
|
{% endunless %}{% endfor %}
|
||||||
|
</ul>
|
||||||
|
|
||||||
|
{% for item in (0..site.tags.size) %}{% unless forloop.last %}
|
||||||
|
{% capture this_word %}{{ tags_list[item] | strip_newlines }}{% endcapture %}
|
||||||
|
<h2 id="{{ this_word }}">{{ this_word }}</h2>
|
||||||
|
<ul class="post-list">
|
||||||
|
{% for post in site.tags[this_word] %}{% if post.title != null %}
|
||||||
|
<li><a href="{{ site.url }}{{ post.url }}">{{ post.title }}<span class="entry-date"><time datetime="{{ post.date | date_to_xmlschema }}">{{ post.date | date: "%b %d, %Y" }}</time></span></a></li>
|
||||||
|
{% endif %}{% endfor %}
|
||||||
|
</ul>
|
||||||
|
{% endunless %}{% endfor %}
|
||||||
|
|
||||||
Loading…
Reference in a new issue