1<!DOCTYPE html> <html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>Publications | Yuqi Cheng</title> <meta name="author" content="Yuqi Cheng"> <meta name="description" content="List of all publications (* co-first author)."> <link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha256-DF7Zhf293AJxJNTmh5zhoYYIMs2oXitRfBjY+9L//AY=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/css/mdb.min.css" integrity="sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw=" crossorigin="anonymous"> <link defer rel="stylesheet" href="https://unpkg.com/[email protected]/dist/bootstrap-table.min.css"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" integrity="sha256-mUZM63G8m73Mcidfrv5E+Y61y7a12O5mW4ezU3bxqW4=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/css/academicons.min.css" integrity="sha256-i1+4qU2G2860dGGIOJscdC30s9beBXjFfzjWLjBRsBg=" crossorigin="anonymous"> <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/gh/jwarby/jekyll-pygments-themes@master/github.css" media="" id="highlight_theme_light"> <link rel="shortcut icon" href="/assets/img/DNA.png"> <link rel="stylesheet" href="/assets/css/main.css"> <link rel="canonical" href="https://yuqcheng.github.io/publications/"> <link rel="stylesheet" href="https://cdn.jsdelivr.net/gh/jwarby/jekyll-pygments-themes@master/native.css" media="none" id="highlight_theme_dark">
1<script src="/assets/js/theme.js"></script>
1
1<script src="/assets/js/dark_mode.js"></script>
1 </head> <body class="fixed-top-nav "> <header> <nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top"> <div class="container"> <a class="navbar-brand title font-weight-lighter" href="/"><span class="font-weight-bold">Yuqi </span>Cheng</a> <button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar top-bar"></span> <span class="icon-bar middle-bar"></span> <span class="icon-bar bottom-bar"></span> </button> <div class="collapse navbar-collapse text-right" id="navbarNav"> <ul class="navbar-nav ml-auto flex-nowrap"> <li class="nav-item "> <a class="nav-link" href="/">About</a> </li> <li class="nav-item active"> <a class="nav-link" href="/publications/">Publications<span class="sr-only">(current)</span></a> </li> <li class="nav-item "> <a class="nav-link" href="/experience/">Experience</a> </li> <li class="toggle-container"> <button id="light-toggle" title="Change theme"> <i class="fas fa-moon"></i> <i class="fas fa-sun"></i> </button> </li> </ul> </div> </div> </nav> <progress id="progress" value="0"> <div class="progress-container"> <span class="progress-bar"></span> </div> </progress> </header> <div class="container mt-5"> <div class="post"> <header class="post-header"> <h1 class="post-title">Publications</h1> <p class="post-description">List of all publications (* co-first author).</p> </header> <article> <div class="publications"> <h2 class="year">2025</h2> <ol class="bibliography"><li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">EpiPack</abbr></div> <div id="Cheng2025epipack" class="col-sm-8"> <div class="title">Discovering cell types and states from reference atlases with heterogeneous single-cell ATAC-seq features</div> <div class="author"> <em>Yuqi Cheng</em>, and Xiuwei Zhang</div> <div class="periodical"> <em>bioRxiv</em>, 2025 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://www.biorxiv.org/content/10.1101/2025.09.19.677191v1" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right" data-doi="10.1101/2025.09.19.677191"></span> <span class="__dimensions_badge_embed__" data-doi="10.1101/2025.09.19.677191" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">Cheng2025epipack</span><span class="p">,</span> 2 <span class="na">author</span> <span class="p">=</span> <span class="s">{Cheng, Yuqi and Zhang, Xiuwei}</span><span class="p">,</span> 3 <span class="na">title</span> <span class="p">=</span> <span class="s">{Discovering cell types and states from reference atlases with heterogeneous single-cell ATAC-seq features}</span><span class="p">,</span> 4 <span class="na">year</span> <span class="p">=</span> <span class="s">{2025}</span><span class="p">,</span> 5 <span class="na">doi</span> <span class="p">=</span> <span class="s">{10.1101/2025.09.19.677191}</span><span class="p">,</span> 6 <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Cold Spring Harbor Laboratory}</span><span class="p">,</span> 7 <span class="na">journal</span> <span class="p">=</span> <span class="s">{bioRxiv}</span><span class="p">,</span> 8<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> <h2 class="year">2024</h2> <ol class="bibliography"><li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">scNovel</abbr></div> <div id="zheng2024scnovel" class="col-sm-8"> <div class="title">scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics</div> <div class="author"> Chuanyang Zheng, Yixuan Wang, <em>Yuqi Cheng</em>, Xuesong Wang, and <span class="more-authors" title="click to view 3 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '3 more authors' ? 'Hongxin Wei, Irwin King, Yu Li' : '3 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.text(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">3 more authors</span> </div> <div class="periodical"> <em>Briefings in Bioinformatics</em>, 2024 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://academic.oup.com/bib/article/25/3/bbae112/7636757" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right"></span> <span class="__dimensions_badge_embed__" data-pmid="" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">zheng2024scnovel</span><span class="p">,</span> 9 <span class="na">title</span> <span class="p">=</span> <span class="s">{scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics}</span><span class="p">,</span> 10 <span class="na">author</span> <span class="p">=</span> <span class="s">{Zheng, Chuanyang and Wang, Yixuan and Cheng, Yuqi and Wang, Xuesong and Wei, Hongxin and King, Irwin and Li, Yu}</span><span class="p">,</span> 11 <span class="na">
11journal</span> <span class="p">=</span> <span class="s">{Briefings in Bioinformatics}</span><span class="p">,</span> 12 <span class="na">volume</span> <span class="p">=</span> <span class="s">{25}</span><span class="p">,</span> 13 <span class="na">number</span> <span class="p">=</span> <span class="s">{3}</span><span class="p">,</span> 14 <span class="na">pages</span> <span class="p">=</span> <span class="s">{bbae112}</span><span class="p">,</span> 15 <span class="na">year</span> <span class="p">=</span> <span class="s">{2024}</span><span class="p">,</span> 16 <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Oxford University Press}</span><span class="p">,</span> 17<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> <h2 class="year">2023</h2> <ol class="bibliography"><li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">scBalance</abbr></div> <div id="cheng2023scalable" class="col-sm-8"> <div class="title">A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data</div> <div class="author"> <em>Yuqi Cheng</em>, Xingyu Fan, Jianing Zhang, and Yu Li</div> <div class="periodical"> <em>Communications Biology</em>, 2023 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://www.nature.com/articles/s42003-023-04928-6" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right"></span> <span class="__dimensions_badge_embed__" data-pmid="" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">cheng2023scalable</span><span class="p">,</span> 18 <span class="na">title</span> <span class="p">=</span> <span class="s">{A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data}</span><span class="p">,</span> 19 <span class="na">author</span> <span class="p">=</span> <span class="s">{Cheng, Yuqi and Fan, Xingyu and Zhang, Jianing and Li, Yu}</span><span class="p">,</span> 20 <span class="na">journal</span> <span class="p">=</span> <span class="s">{Communications Biology}</span><span class="p">,</span> 21 <span class="na">volume</span> <span class="p">=</span> <span class="s">{6}</span><span class="p">,</span> 22 <span class="na">number</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span> 23 <span class="na">pages</span> <span class="p">=</span> <span class="s">{545}</span><span class="p">,</span> 24 <span class="na">year</span> <span class="p">=</span> <span class="s">{2023}</span><span class="p">,</span> 25 <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Nature Publishing Group UK London}</span><span class="p">,</span> 26<span class="p">}</span></code></pre></figure> </div> </div> </div> </li></ol> <h2 class="year">2022</h2> <ol class="bibliography"> <li> <div class="row"> <div class="col-sm-2 abbr"></div> <div id="chen2022deep" class="col-sm-8"> <div class="title">Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis</div> <div class="author"> Yanshuo Chen, Yixuan Wang, Yuelong Chen, <em>Yuqi Cheng</em>, and <span class="more-authors" title="click to view 6 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '6 more authors' ? 'Yumeng Wei, Yunxiang Li, Jiuming Wang, Yingying Wei, Ting-Fung Chan, Yu Li' : '6 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.text(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">6 more authors</span> </div> <div class="periodical"> <em>Nature Communications</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://www.nature.com/articles/s41467-022-34550-9" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right"></span> <span class="__dimensions_badge_embed__" data-pmid="" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">chen2022deep</span><span class="p">,</span> 27 <span class="na">author</span> <span class="p">=</span> <span class="s">{Chen, Yanshuo and Wang, Yixuan and Chen, Yuelong and Cheng, Yuqi and Wei, Yumeng and Li, Yunxiang and Wang, Jiuming and Wei, Yingying and Chan, Ting-Fung and Li, Yu}</span><span class="p">,</span> 28 <span class="na">
28journal</span> <span class="p">=</span> <span class="s">{Nature Communications}</span><span class="p">,</span> 29 <span class="na">volume</span> <span class="p">=</span> <span class="s">{13}</span><span class="p">,</span> 30 <span class="na">number</span> <span class="p">=</span> <span class="s">{1}</span><span class="p">,</span> 31 <span class="na">pages</span> <span class="p">=</span> <span class="s">{6735}</span><span class="p">,</span> 32 <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span> 33 <span class="na">publisher</span> <span class="p">=</span> <span class="s">{Nature Publishing Group UK London}</span><span class="p">,</span> 34<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> <li> <div class="row"> <div class="col-sm-2 abbr"><abbr class="badge">CLEAR</abbr></div> <div id="han2022self" class="col-sm-8"> <div class="title">Self-supervised contrastive learning for integrative single cell RNA-seq data analysis</div> <div class="author"> Wenkai Han*, <em>Yuqi Cheng*</em>, Jiayang Chen*, Huawen Zhong, and <span class="more-authors" title="click to view 6 more authors" onclick=" var element=$(this); element.attr('title', ''); var more_authors_text=element.text() == '6 more authors' ? 'Zhihang Hu, Siyuan Chen, Licheng Zong, Irwin King, Xin Gao, Yu Li' : '6 more authors'; var cursorPosition=0; var textAdder=setInterval(function(){ element.text(more_authors_text.substring(0, cursorPosition + 1)); if (++cursorPosition == more_authors_text.length){ clearInterval(textAdder); } }, '10'); ">6 more authors</span> </div> <div class="periodical"> <em>Briefings in Bioinformatics</em>, 2022 </div> <div class="periodical"> </div> <div class="links"> <a class="bibtex btn btn-sm z-depth-0" role="button">Bib</a> <a href="https://academic.oup.com/bib/article/23/5/bbac377/6695268" class="btn btn-sm z-depth-0" role="button" rel="external nofollow noopener" target="_blank">HTML</a> </div> <div class="badges"> <span class="altmetric-embed" data-hide-no-mentions="true" data-hide-less-than="15" data-badge-type="2" data-badge-popover="right"></span> <span class="__dimensions_badge_embed__" data-pmid="" data-hide-zero-citations="true" data-style="small_rectangle" data-legend="hover-right" style="margin-bottom: 3px;"></span> </div> <div class="bibtex hidden"> <figure class="highlight"><pre><code class="language-bibtex" data-lang="bibtex"><span class="nc">@article</span><span class="p">{</span><span class="nl">han2022self</span><span class="p">,</span> 35 <span class="na">title</span> <span class="p">=</span> <span class="s">{Self-supervised contrastive learning for integrative single cell RNA-seq data analysis}</span><span class="p">,</span> 36 <span class="na">author</span> <span class="p">=</span> <span class="s">{Han*, Wenkai and Cheng*, Yuqi and Chen*, Jiayang and Zhong, Huawen and Hu, Zhihang and Chen, Siyuan and Zong, Licheng and King, Irwin and Gao, Xin and Li, Yu}</span><span class="p">,</span> 37 <span class="na">journal</span> <span class="p">=</span> <span class="s">{Briefings in Bioinformatics}</span><span class="p">,</span> 38 <span class="na">volume</span> <span class="p">=</span> <span class="s">{23}</span><span class="p">,</span> 39 <span class="na">number</span> <span class="p">=</span> <span class="s">{5}</span><span class="p">,</span> 40 <span class="na">year</span> <span class="p">=</span> <span class="s">{2022}</span><span class="p">,</span> 41<span class="p">}</span></code></pre></figure> </div> </div> </div> </li> </ol> </div> </article> </div> </div> <footer class="fixed-bottom"> <div class="container mt-0"> © Copyright 2025 Yuqi Cheng. </div> </footer>
41<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/jquery.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
41
41<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha256-fgLAgv7fyCGopR/gBNq2iW3ZKIdqIcyshnUULC4vex8=" crossorigin="anonymous"></script>
41
41<script src="https://cdn.jsdelivr.net/npm/[email protected]/js/mdb.min.js" integrity="sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA=" crossorigin="anonymous"></script>
41
41<script defer src="https://cdn.jsdelivr.net/npm/[email protected]/dist/masonry.pkgd.min.js" integrity="sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI=" crossorigin="anonymous"></script>
41
41<script defer src="https://cdn.jsdelivr.net/npm/imagesloaded@4/imagesloaded.pkgd.min.js"></script>
41
41<script defer src="/assets/js/masonry.js" type="text/javascript"></script>
41
41<script defer src="https://cdn.jsdelivr.net/npm/[email protected]/dist/medium-zoom.min.js" integrity="sha256-7PhEpEWEW0XXQ0k6kQrPKwuoIomz8R8IYyuU1Qew4P8=" crossorigin="anonymous"></script>
41
41<script defer src="/assets/js/zoom.js"></script>
41
41<script defer src="https://unpkg.com/[email protected]/dist/bootstrap-table.min.js"></script>
41
41<script src="/assets/js/no_defer.js"></script>
41
41<script defer src="/assets/js/common.js"></script>
41
41<script defer src="/assets/js/copy_code.js" type="text/javascript"></script>
41
41<script async src="https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js"></script>
41
41<script async src="https://badge.dimensions.ai/badge.js"></script>
41
41<script type="text/javascript">window.MathJax={tex:{tags:"ams"}};</script>
41
41<script defer type="text/javascript" id="MathJax-script" src="https://cdn.jsdelivr.net/npm/[email protected]/es5/tex-mml-chtml.js"></script>
41
41<script defer src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
41
41<script type="text/javascript">function progressBarSetup(){"max"in document.createElement("progress")?(initializeProgressElement(),$(document).on("scroll",function(){progressBar.attr({value:getCurrentScrollPosition()})}),$(window).on("resize",initializeProgressElement)):(resizeProgressBar(),$(document).on("scroll",resizeProgressBar),$(window).on("resize",resizeProgressBar))}function getCurrentScrollPosition(){return $(window).scrollTop()}function initializeProgressElement(){let e=$("#navbar").outerHeight(!0);$("body").css({"padding-top":e}),$("progress-container").css({"padding-top":e}),progressBar.css({top:e}),progressBar.attr({max:getDistanceToScroll(),value:getCurrentScrollPosition()})}function getDistanceToScroll(){return $(document).height()-$(window).height()}function resizeProgressBar(){progressBar.css({width:getWidthPercentage()+"%"})}function getWidthPercentage(){return getCurrentScrollPosition()/getDistanceToScroll()*100}const progressBar=$("#progress");window.onload=function(){setTimeout(progressBarSetup,50)};</script>
41 </body> </html>
Line numbers count LF bytes from the start of the resource, as the search results do. Vendor segments are library code the classifier recognised; they are stored but not indexed. Bytes are shown as Latin1 characters, one per byte.