diff --git a/.nfs00000000b520555c00000008 b/.nfs00000000b520555c00000008 deleted file mode 100644 index 9d482f6..0000000 --- a/.nfs00000000b520555c00000008 +++ /dev/null @@ -1,630 +0,0 @@ -# ----------------------------------------------------------------------------- -# Site settings -# ----------------------------------------------------------------------------- - -title: blank # the website title (if blank, full name will be used instead) -first_name: Yang -middle_name: -last_name: Xie -email: tvtxieyang@outlook.com -description: > # the ">" symbol means to ignore newlines until "footer_text:" - A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design. - Photos from Unsplash. -footer_text: > - Powered by Jekyll with al-folio theme. - Hosted by GitHub Pages. -keywords: jekyll, jekyll-theme, academic-website, portfolio-website # add your own keywords or leave empty -lang: en # the language of your site (for example: en, fr, cn, ru, etc.) -icon: 🥃 # the emoji used as the favicon (alternatively, provide image name in /assets/img/) - -url: https://Xieeeee.github.io # the base hostname & protocol for your site -baseurl: # the subpath of your site, e.g. /blog/. Leave blank for root -last_updated: false # set to true if you want to display last updated in the footer -impressum_path: # set to path to include impressum link in the footer, use the same path as permalink in a page, helps to conform with EU GDPR -back_to_top: true # set to false to disable the back to top button - -# ----------------------------------------------------------------------------- -# Theme -# ----------------------------------------------------------------------------- - -# repo color theme -repo_theme_light: default # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md -repo_theme_dark: dark # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md -repo_trophies: - enabled: true - theme_light: flat # https://github.com/ryo-ma/github-profile-trophy - theme_dark: gitdimmed # https://github.com/ryo-ma/github-profile-trophy - -# ----------------------------------------------------------------------------- -# RSS Feed -# ----------------------------------------------------------------------------- -# will use title and url fields -# Take a look to https://github.com/jekyll/jekyll-feed for more customization - -rss_icon: true - -# ----------------------------------------------------------------------------- -# Layout -# ----------------------------------------------------------------------------- - -navbar_fixed: true -footer_fixed: true -search_enabled: true -socials_in_search: true - -# Dimensions -max_width: 930px - -# TODO: add layout settings (single page vs. multi-page) - -# ----------------------------------------------------------------------------- -# Open Graph & Schema.org -# ----------------------------------------------------------------------------- -# Display links to the page with a preview object on social media. -# see https://schema.org/docs/faq.html for more information -serve_og_meta: false # Include Open Graph meta tags in the HTML head -serve_schema_org: false # Include Schema.org in the HTML head -og_image: # The site-wide (default for all links) Open Graph preview image - -# ----------------------------------------------------------------------------- -# Social integration -# ----------------------------------------------------------------------------- - -acm_id: # your dl.acm.org/profile/id -blogger_url: # your blogger URL -bluesky_url: # your bluesky URL -dblp_url: # your DBLP profile url -discord_id: # your discord id (18-digit unique numerical identifier) -facebook_id: # your facebook id -flickr_id: # your flickr id -github_username: Xieeeee # your GitHub user name -gitlab_username: # your GitLab user name -ieee_id: # your ieeexplore.ieee.org/author/id -instagram_id: # your instagram id -kaggle_id: # your kaggle id -keybase_username: # your keybase user name -lastfm_id: # your lastfm id -lattes_id: # your ID on Lattes (Brazilian Lattes CV) -linkedin_username: # your LinkedIn user name -mastodon_username: # your mastodon instance+username in the format instance.tld/@username -medium_username: # your Medium username -orcid_id: # your ORCID ID -osf_id: # your OSF ID -pinterest_id: # your pinterest id -publons_id: # your ID on Publons -quora_username: # your Quora username -research_gate_profile: # your profile on ResearchGate -scholar_userid: i_nZvtgAAAAJ # your Google Scholar ID -scopus_id: # your profile on Scopus -semanticscholar_id: # your Semantic Scholar ID -spotify_id: # your spotify id -stackoverflow_id: # your stackoverflow id -telegram_username: # your Telegram user name -unsplash_id: # your unsplash id -wechat_qr: my_wechat.jpg # filename of your wechat qr-code saved as an image (e.g., wechat-qr.png if saved to assets/img/wechat-qr.png) -whatsapp_number: # your WhatsApp number (full phone number in international format. Omit any zeroes, brackets, or dashes when adding the phone number in international format.) -wikidata_id: # your wikidata id -wikipedia_id: # your wikipedia id (Case sensitive) -work_url: # work page URL -x_username: Xieeee4 # your X handle -youtube_id: # your youtube channel id (youtube.com/@) -zotero_username: # your zotero username - -contact_note: > - For questions, protocols, collaboration, or food recommendation in San Diego, please find me at tvtxieyang@outlook.com :) - -# ----------------------------------------------------------------------------- -# Analytics and search engine verification -# ----------------------------------------------------------------------------- - -# For Google Analytics, see https://support.google.com/analytics/answer/10447272?hl=en&ref_topic=14088998&sjid=5129943941510317771-SA#zippy=%2Cgoogle-sites -# and follow the instructions for Google Sites. 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max_related: 5 - -# Giscus comments (RECOMMENDED) -# Follow instructions on https://giscus.app/ to setup for your repo to fill out the information below. -giscus: - repo: # / - repo_id: # leave empty or specify your repo_id (see https://giscus.app/) - category: Comments # name of the category under which discussions will be created - category_id: # leave empty or specify your category_id (see https://giscus.app/) - mapping: title # identify discussions by post title - strict: 1 # use strict identification mode - reactions_enabled: 1 # enable (1) or disable (0) emoji reactions - input_position: bottom # whether to display input form below (bottom) or above (top) the comments - theme: preferred_color_scheme # name of the color scheme (preferred works well with al-folio light/dark mode) - emit_metadata: 0 - lang: en - -# Disqus comments (DEPRECATED) -disqus_shortname: al-folio # put your disqus shortname -# https://help.disqus.com/en/articles/1717111-what-s-a-shortname - -# External sources. -# If you have blog posts published on medium.com or other external sources, -# you can display them in your blog by adding a link to the RSS feed. -external_sources: - 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url: - js: "https://cdn.jsdelivr.net/npm/vega-embed@{{version}}/build/vega-embed.min.js" - js_map: "https://cdn.jsdelivr.net/npm/vega-embed@{{version}}/build/vega-embed.min.js.map" - version: "6.24.0" - vega-lite: - integrity: - js: "sha256-TvBvIS5jUN4BSy009usRjNzjI1qRrHPYv7xVLJyjUyw=" - js_map: "sha256-l2I4D5JC23Ulsu6e3sKVe5AJ+r+DFkzkKnZS8nUGz28=" - url: - js: "https://cdn.jsdelivr.net/npm/vega-lite@{{version}}/build/vega-lite.min.js" - js_map: "https://cdn.jsdelivr.net/npm/vega-lite@{{version}}/build/vega-lite.min.js.map" - version: "5.16.3" - -# ----------------------------------------------------------------------------- -# Get external JSON data -# ----------------------------------------------------------------------------- - -jekyll_get_json: - - data: resume - json: assets/json/resume.json # it can also be an url -jsonresume: - - basics - - work - - education - - publications - - projects - - volunteer - - awards - - certificates - - skills - - languages - - interests - - references diff --git a/_bibliography/papers.bib b/_bibliography/papers.bib index 948f6b6..2616788 100644 --- a/_bibliography/papers.bib +++ b/_bibliography/papers.bib @@ -1,113 +1,61 @@ ---- ---- - -@string{aps = {American Physical Society,}} - -@book{einstein1920relativity, - title={Relativity: the Special and General Theory}, - author={Einstein, Albert}, - year={1920}, - publisher={Methuen & Co Ltd}, - html={relativity.html} -} - -@book{einstein1956investigations, - bibtex_show={true}, - title={Investigations on the Theory of the Brownian Movement}, - author={Einstein, Albert}, - year={1956}, - publisher={Courier Corporation}, - preview={brownian-motion.gif} -} - -@article{einstein1950meaning, - abbr={AJP}, - bibtex_show={true}, - title={The meaning of relativity}, - author={Einstein, Albert and Taub, AH}, - journal={American Journal of Physics}, - volume={18}, - number={6}, - pages={403--404}, - year={1950}, - publisher={American Association of Physics Teachers} -} - -@article{PhysRev.47.777, - abbr={PhysRev}, - title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?}, - author={Einstein, A. and Podolsky, B. and Rosen, N.}, - abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.}, - journal={Phys. Rev.}, - location={New Jersey}, - volume={47}, - issue={10}, - pages={777--780}, - numpages={0}, - year={1935}, - month={May}, - publisher=aps, - doi={10.1103/PhysRev.47.777}, - url={http://link.aps.org/doi/10.1103/PhysRev.47.777}, - html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777}, - pdf={example_pdf.pdf}, - altmetric={248277}, - dimensions={true}, - google_scholar_id={qyhmnyLat1gC}, - video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ}, - additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)}, - selected={true} -} - -@article{einstein1905molekularkinetischen, - title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen}, - author={Einstein, A.}, - journal={Annalen der physik}, - volume={322}, - number={8}, - pages={549--560}, - year={1905}, - publisher={Wiley Online Library} -} - -@article{einstein1905movement, - abbr={Ann. Phys.}, - title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat}, - author={Einstein, A.}, - journal={Ann. Phys.}, - volume={17}, - pages={549--560}, - year={1905} -} - -@article{einstein1905electrodynamics, - title={On the electrodynamics of moving bodies}, - author={Einstein, A.}, - year={1905} -} - -@Article{einstein1905photoelectriceffect, - bibtex_show={true}, - abbr={Ann. Phys.}, - title="{{\"U}ber einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt}", - author={Albert Einstein}, - abstract={This is the abstract text.}, - journal={Ann. Phys.}, - volume={322}, - number={6}, - pages={132--148}, - year={1905}, - doi={10.1002/andp.19053220607}, - award={Albert Einstein receveid the **Nobel Prize in Physics** 1921 *for his services to Theoretical Physics, and especially for his discovery of the law of the photoelectric effect*}, - award_name={Nobel Prize} -} - -@book{przibram1967letters, - bibtex_show={true}, - title={Letters on wave mechanics}, - author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl}, - year={1967}, - publisher={Vision}, - preview={wave-mechanics.gif}, - abbr={Vision} +@article{li2023comparative, + title={A comparative atlas of single-cell chromatin accessibility in the human brain}, + author={Li, Yang Eric and Preissl, Sebastian and Miller, Michael and Johnson, Nicholas D and Wang, Zihan and Jiao, Henry and Zhu, Chenxu and Wang, Zhaoning and Xie, Yang and Poirion, Olivier and others}, + journal={Science}, + volume={382}, + number={6667}, + pages={eadf7044}, + year={2023}, + publisher={American Association for the Advancement of Science} + + link={https://www.science.org/doi/full/10.1126/science.adf7044} +} + +@article{xie2023droplet, + title={Droplet-based single-cell joint profiling of histone modifications and transcriptomes}, + author={Xie, Yang and Zhu, Chenxu and Wang, Zhaoning and Tastemel, Melodi and Chang, Lei and Li, Yang Eric and Ren, Bing}, + journal={Nature Structural \& Molecular Biology}, + volume={30}, + number={10}, + pages={1428--1433}, + year={2023}, + publisher={Nature Publishing Group US New York} + + link={https://www.nature.com/articles/s41594-023-01060-1} +} + +@article{zu2023single, + title={Single-cell analysis of chromatin accessibility in the adult mouse brain}, + author={Zu, Songpeng and Li, Yang Eric and Wang, Kangli and Armand, Ethan J and Mamde, Sainath and Amaral, Maria Luisa and Wang, Yuelai and Chu, Andre and Xie, Yang and Miller, Michael and others}, + journal={Nature}, + volume={624}, + number={7991}, + pages={378--389}, + year={2023}, + publisher={Nature Publishing Group UK London} + + link={https://www.nature.com/articles/s41586-023-06824-9} +} + +@article{zemke2023conserved, + title={Conserved and divergent gene regulatory programs of the mammalian neocortex}, + author={Zemke, Nathan R and Armand, Ethan J and Wang, Wenliang and Lee, Seoyeon and Zhou, Jingtian and Li, Yang Eric and Liu, Hanqing and Tian, Wei and Nery, Joseph R and Castanon, Rosa G and others}, + journal={Nature}, + volume={624}, + number={7991}, + pages={390--402}, + year={2023}, + publisher={Nature Publishing Group UK London} + + link={https://www.nature.com/articles/s41586-023-06819-6} +} + +@article{chang2024droplet, + title={Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells}, + author={Chang, Lei and Xie, Yang and Taylor, Brett and Wang, Zhaoning and Sun, Jiachen and Tan, Tuyet R and Bejar, Rafael and Chen, Clark C and Furnari, Frank B and Hu, Ming and others}, + journal={bioRxiv}, + year={2024}, + publisher={Cold Spring Harbor Laboratory Preprints} + + link={https://www.biorxiv.org/content/10.1101/2024.04.18.590148v1} } diff --git a/_config.yml b/_config.yml index 9d482f6..6064871 100644 --- a/_config.yml +++ b/_config.yml @@ -9,7 +9,6 @@ last_name: Xie email: tvtxieyang@outlook.com description: > # the ">" symbol means to ignore newlines until "footer_text:" A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design. - Photos from Unsplash. footer_text: > Powered by Jekyll with al-folio theme. Hosted by GitHub Pages. diff --git a/_pages/about.md b/_pages/about.md index 3d84b14..8c7948e 100644 --- a/_pages/about.md +++ b/_pages/about.md @@ -19,9 +19,9 @@ Hi there! My name is Yang Xie (谢旸). I am currently a Ph.D. candidate in [Ren Our body is a complex system. Each cell in our body can have different roles and developmental trajetories, even though they usually have the same genes. The diversity is mainly driven by the way genes are turned on and off in specific places and times. This precious regulation process is controlled by different elements in our genome, through various chemical modifications and conformation changes in DNA or associated proteins, all of which make up what we call the epigenome. -During my graduate studies, I focused on developing high-throughput, multi-modal single-cell sequencing techniques to investigate epigenomic diversity in mammalian brains, and study how does the dysregulation contribute to diseases including glioblastoma, a type of malignant brain tumor. +During my graduate studies, I focused on developing high-throughput, multi-modal single-cell sequencing techniques to capture the epigenomic diversity in mammalian brains, and study how does the dysregulation contribute to diseases including glioblastoma, a type of malignant brain tumor. -I completed my BSc in Biological Sciences from Fudan University, China, with Guodong Ren as my undergraduate thesis advisor. Before joing Ren lab, I worked in [O'Shea lab](https://www.salk.edu/scientist/clodagh-oshea/) at Salk Institute, where I studied how DNA folds using electron microscope and live-cell imaging. +I grew up in Shantou, a charming coastal city known for its delicious food. I completed my BSc in Biological Sciences from Fudan University, Shanghai, with Guodong Ren as my undergraduate thesis advisor. Before joing Ren lab, I worked in [O'Shea lab](https://www.salk.edu/scientist/clodagh-oshea/) at Salk Institute, where I studied how DNA folds using electron microscope and live-cell imaging. -Besides research, I enjoy listening to music, exploring different food and cooking. The best part of my weekend is (currently) composed of: Asian pop, contemporary French cuisine, yakiniku, gin, and Hazy IPA. +Besides research, I enjoy listening to music, exploring different food and cooking. The best part of my weekend is (currently) composed of: Fuji Kaze, Yakiniku, Negori, and Hazy IPA. diff --git a/_pages/about_einstein.md b/_pages_unused/about_einstein.md similarity index 100% rename from _pages/about_einstein.md rename to _pages_unused/about_einstein.md diff --git a/_pages/blog.md b/_pages_unused/blog.md similarity index 100% rename from _pages/blog.md rename to _pages_unused/blog.md diff --git a/_pages/cv.md b/_pages_unused/cv.md similarity index 100% rename from _pages/cv.md rename to _pages_unused/cv.md diff --git a/_pages/dropdown.md b/_pages_unused/dropdown.md similarity index 100% rename from _pages/dropdown.md rename to _pages_unused/dropdown.md diff --git a/_pages/news.md b/_pages_unused/news.md similarity index 100% rename from _pages/news.md rename to _pages_unused/news.md diff --git a/_pages_unused/papers.bib b/_pages_unused/papers.bib new file mode 100644 index 0000000..948f6b6 --- /dev/null +++ b/_pages_unused/papers.bib @@ -0,0 +1,113 @@ +--- +--- + +@string{aps = {American Physical Society,}} + +@book{einstein1920relativity, + title={Relativity: the Special and General Theory}, + author={Einstein, Albert}, + year={1920}, + publisher={Methuen & Co Ltd}, + html={relativity.html} +} + +@book{einstein1956investigations, + bibtex_show={true}, + title={Investigations on the Theory of the Brownian Movement}, + author={Einstein, Albert}, + year={1956}, + publisher={Courier Corporation}, + preview={brownian-motion.gif} +} + +@article{einstein1950meaning, + abbr={AJP}, + bibtex_show={true}, + title={The meaning of relativity}, + author={Einstein, Albert and Taub, AH}, + journal={American Journal of Physics}, + volume={18}, + number={6}, + pages={403--404}, + year={1950}, + publisher={American Association of Physics Teachers} +} + +@article{PhysRev.47.777, + abbr={PhysRev}, + title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?}, + author={Einstein, A. and Podolsky, B. and Rosen, N.}, + abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.}, + journal={Phys. Rev.}, + location={New Jersey}, + volume={47}, + issue={10}, + pages={777--780}, + numpages={0}, + year={1935}, + month={May}, + publisher=aps, + doi={10.1103/PhysRev.47.777}, + url={http://link.aps.org/doi/10.1103/PhysRev.47.777}, + html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777}, + pdf={example_pdf.pdf}, + altmetric={248277}, + dimensions={true}, + google_scholar_id={qyhmnyLat1gC}, + video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ}, + additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)}, + selected={true} +} + +@article{einstein1905molekularkinetischen, + title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen}, + author={Einstein, A.}, + journal={Annalen der physik}, + volume={322}, + number={8}, + pages={549--560}, + year={1905}, + publisher={Wiley Online Library} +} + +@article{einstein1905movement, + abbr={Ann. Phys.}, + title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat}, + author={Einstein, A.}, + journal={Ann. Phys.}, + volume={17}, + pages={549--560}, + year={1905} +} + +@article{einstein1905electrodynamics, + title={On the electrodynamics of moving bodies}, + author={Einstein, A.}, + year={1905} +} + +@Article{einstein1905photoelectriceffect, + bibtex_show={true}, + abbr={Ann. Phys.}, + title="{{\"U}ber einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt}", + author={Albert Einstein}, + abstract={This is the abstract text.}, + journal={Ann. Phys.}, + volume={322}, + number={6}, + pages={132--148}, + year={1905}, + doi={10.1002/andp.19053220607}, + award={Albert Einstein receveid the **Nobel Prize in Physics** 1921 *for his services to Theoretical Physics, and especially for his discovery of the law of the photoelectric effect*}, + award_name={Nobel Prize} +} + +@book{przibram1967letters, + bibtex_show={true}, + title={Letters on wave mechanics}, + author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl}, + year={1967}, + publisher={Vision}, + preview={wave-mechanics.gif}, + abbr={Vision} +} diff --git a/_pages/profiles.md b/_pages_unused/profiles.md similarity index 100% rename from _pages/profiles.md rename to _pages_unused/profiles.md diff --git a/_pages/projects.md b/_pages_unused/projects.md similarity index 100% rename from _pages/projects.md rename to _pages_unused/projects.md diff --git a/_pages/repositories.md b/_pages_unused/repositories.md similarity index 100% rename from _pages/repositories.md rename to _pages_unused/repositories.md diff --git a/_pages/teaching.md b/_pages_unused/teaching.md similarity index 100% rename from _pages/teaching.md rename to _pages_unused/teaching.md