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<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1 maximum-scale=1; minimum-scale=1; user-scalable=no;"> <meta content="Chunyu's personal website." name="description"> <meta name="keywords" content="personal website,github,gh-pages"> <meta name="author" content="Chunyu Ma"> <title>Chunyu's Personal Website</title> <!-- favicon --> <link rel="shortcut icon" href="/static/assets/img/favicon.ico"> <!-- Main CSS --> <link href="/static/assets/app-20180125.min.css" rel="stylesheet"> <link href="/static/css/custom.css" rel="stylesheet"> <!-- Main scripts --> <script src="/static/assets/app-20180125.min.js"></script> <script async defer src="/static/js/github_api.min.js"></script> <script src="/static/assets/i18-20180125.min.js"></script> <!-- Google AdSense --> <!-- <script async src="//pagead2.googlesyndication.com/pagead/js/adsbygoogle.js"></script> <script> (adsbygoogle = window.adsbygoogle || []).push({ google_ad_client: "ca-pub-6196184668650108", enable_page_level_ads: true }); </script> --> </head> <body id="page-top" class="landing-page"> <div class="navbar-wrapper"> <nav class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container i18container"> <div class="navbar-header page-scroll"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="#page-top"><span data-i18n="website.title">Chunyu's Personal Website</span></a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav navbar-right"> <li> <a class="page-scroll" href="#about-me "> <span data-i18n="nav.about_me">About</span> </a> </li> <li> <a class="page-scroll" href="#career "> <span data-i18n="nav.career">Career</span> </a> </li> <li> <a class="page-scroll" href="#skills "> <span data-i18n="nav.skills">Skills</span> </a> </li> <li> <a class="page-scroll" href="#projects "> <span data-i18n="nav.projects">Projects</span> </a> </li> <li> <a class="page-scroll" href="#publications "> <span data-i18n="nav.publications">Publications</span> </a> </li> <li> <a id="set_lang_zh" class="btn btn-sm set_zh" data-locale="zh"> <img src="/static/assets/img/flags/China.png" height="16" width="16"> </a> </li> <li> <a id="set_lang_en" class="btn btn-sm set_en" data-locale="en"> <img src="/static/assets/img/flags/USA.png" height="16" width="16"> </a> </li> </ul> </div> </div> </nav> </div> <div class="intro-header" style="background-image: url(/static/assets/img/intro_header_bg.jpg)"> <div class="container i18container header_container"> <div class="row"> <div class="col-lg-8 col-lg-offset-2 col-md-10 col-md-offset-1 header_div"> <div class="site-heading"> <h1><span data-i18n="header.title">Welcome to My Website</span></h1> <span class="subheading" data-i18n="header.subtitle">「Work hard, Play Hard」</span> </div> </div> </div> </div> </div> <section id="about-me" class="features " style="margin-top: 0;"> <div class="container" id="i18_about_me"> <div class="row m-b-lg"> <div class="col-lg-12 text-center"> <div class="navy-line"></div> <h1><span data-i18n="about_me.about_me">About Me</span></h1> <!-- <p>Donec sed odio dui. Etiam porta sem malesuada magna mollis euismod.</p> --> </div> </div> <div class="row" style="margin-bottom:30px"> <!-- avatar --> <div class="col-xs-12 col-md-4 i18container"> <div class="team-member wow zoomIn"> <img src="/static/assets/img/landing/avatar2.jpg" height="200" width="300" class="img-responsive img-circle" alt=""> <h1 itemprop="name"><span data-i18n="author.last_name">Ma</span> <span class="navy" data-i18n="author.first_name">Chunyu</span></h1> <h3 itemprop="jobTitle"><span data-i18n="author.job_title">PhD. Graduate student</span></h3> <h3><a href="https://www.psu.edu/" target="_blank" itemprop="url"><span itemprop="name" data-i18n="author.organization">Pennsylvania State University</span></a></h3> <ul style="margin-top:20px" class="list-inline social-icon" aria-hidden="true"> <li><a href="https://github.com/chunyuma" target="blank"><i class="aboutme_fa fa fa-github"></i></a></li> <li><a href="https://www.linkedin.com/in/chunyu-ma-419257ba" target="blank"><i class="aboutme_fa fa fa-linkedin"></i></a></li> <li><a href="https://scholar.google.com/citations?hl=en&user=NnUeLicAAAAJ" target="blank"><i class="aboutme_fa fa fa-google"></i></a></li> <li><a href="mailto:[email protected]"><i class="aboutme_fa fa fa-envelope-o"></i></a></li> </ul> </div> </div> <div class="col-xs-12 col-md-8 i18container" itemprop="description"> <div class="row"> <div class="col-sm-12"> <h1 style="font-weight:bold"><span data-i18n="about_me.biography">Biography</span></h1> <div> <p style="text-align:justify;font-size:150%;color:black;"><span data-i18n="about_me.des"></span></p> </div> </div> </div> <div class="row"> <div class="col-sm-5"> <h1 style="font-weight:bold"><span data-i18n="about_me.interests.name">Interests</span></h1> <ul style="font-size:150%"> <li><span data-i18n="about_me.interests.var1"></span></li> <li><span data-i18n="about_me.interests.var2"></span></li> <li><span data-i18n="about_me.interests.var3"></span></li> <li><span data-i18n="about_me.interests.var4"></span></li> <li><span data-i18n="about_me.interests.var5"></span></li> </ul> </div> <div class="col-sm-7"> <h1 style="font-weight:bold"><span data-i18n="about_me.education.name">Education</span></h1> <ul style="font-size:150%" class="fa-ul"> <li><i class="fa-li fa fa-graduation-cap"></i><strong><span data-i18n="about_me.education.var1.degree"></span></strong></li> <li><span data-i18n="about_me.education.var1.school"></span></li> <li><i class="fa-li fa fa-graduation-cap"></i><strong><span data-i18n="about_me.education.var2.degree"></span></strong></li> <li><span data-i18n="about_me.education.var2.school"></span></li> <li><i class="fa-li fa fa-graduation-cap"></i><strong><span data-i18n="about_me.education.var3.degree"></span></strong></li> <li><span data-i18n="about_me.education.var3.school"></span></li> </ul> </div> </div> </div> </div> </div> </section> <section id="career" class="features gray-section timeline" style="margin-top: 0;"> <div class="container" id="i18_career"> <div class="row"> <div class="col-lg-12 text-center"> <div class="navy-line"></div> <h1><span data-i18n="career.my_career">My Career</span></h1> </div> </div> <div class="row features-block"> <div class="col-lg-12"> <div id="vertical-timeline" class="vertical-container light-timeline center-orientation"> <div class="vertical-timeline-block"> <div class="vertical-timeline-icon white-bg wow rotateIn"> <i class="career_fa fa fa-university"></i> </div> <div class="vertical-timeline-content wow rotateInUpRight "> <h2><span style="font-weight:bold;" data-i18n="career.var1.name"></span></h2> <p><span style="font-weight:bold; color:rgb(83, 79, 79);" data-i18n="career.var1.loc"></span></p> <p><span style="color:black;" data-i18n="career.var1.desc"></span></p> <span class="vertical-date"><span style="font-size:110%;" data-i18n="career.var1.date"></span> <br/><span style="font-size:130%; color:#3385FF;" data-i18n="career.var1.job"></span></span> </div> </div> <div class="vertical-timeline-block"> <div class="vertical-timeline-icon white-bg wow rotateIn"> <i class="career_fa fa fa-university"></i> </div> <div class="vertical-timeline-content wow rotateInUpLeft "> <h2><span style="font-weight:bold;" data-i18n="career.var2.name"></span></h2> <p><span style="font-weight:bold; color:rgb(83, 79, 79);" data-i18n="career.var2.loc"></span></p> <p><span style="color:black;" data-i18n="career.var2.desc"></span></p> <span class="vertical-date"><span style="font-size:110%;" data-i18n="career.var2.date"></span> <br/><span style="font-size:130%; color:#3385FF;" data-i18n="career.var2.job"></span></span> </div> </div> <div class="vertical-timeline-block"> <div class="vertical-timeline-icon white-bg wow rotateIn"> <i class="career_fa fa fa-flask"></i> </div> <div class="vertical-timeline-content wow rotateInUpRight "> <h2><span style="font-weight:bold;" data-i18n="career.var3.name"></span></h2> <p><span style="font-weight:bold; color:rgb(83, 79, 79);" data-i18n="career.var3.loc"></span></p> <p><span style="color:black;" data-i18n="career.var3.desc"></span></p> <span class="vertical-date"><span style="font-size:110%;" data-i18n="career.var3.date"></span> <br/><span style="font-size:130%; color:#3385FF;" data-i18n="career.var3.job"></span></span> </div> </div> <div class="vertical-timeline-block"> <div class="vertical-timeline-icon white-bg wow rotateIn"> <i class="career_fa fa fa-university"></i> </div> <div class="vertical-timeline-content wow rotateInUpLeft "> <h2><span style="font-weight:bold;" data-i18n="career.var4.name"></span></h2> <p><span style="font-weight:bold; color:rgb(83, 79, 79);" data-i18n="career.var4.loc"></span></p> <p><span style="color:black;" data-i18n="career.var4.desc"></span></p> <span class="vertical-date"><span style="font-size:110%;" data-i18n="career.var4.date"></span> <br/><span style="font-size:130%; color:#3385FF;" data-i18n="career.var4.job"></span></span> </div> </div> <div class="vertical-timeline-block"> <div class="vertical-timeline-icon white-bg wow rotateIn"> <i class="career_fa fa fa-building"></i> </div> <div class="vertical-timeline-content wow rotateInUpRight "> <h2><span style="font-weight:bold;" data-i18n="career.var5.name"></span></h2> <p><span style="font-weight:bold; color:rgb(83, 79, 79);" data-i18n="career.var5.loc"></span></p> <p><span style="color:black;" data-i18n="career.var5.desc"></span></p> <span class="vertical-date"><span style="font-size:110%;" data-i18n="career.var5.date"></span> <br/><span style="font-size:130%; color:#3385FF;" data-i18n="career.var5.job"></span></span> </div> </div> </div> </div> </div> </div> </section> <section id="skills" class="features team" style="margin-top: 0;"> <div class="container"> <div class="row"> <div class="col-lg-12 text-center" id="i18_skills"> <div class="navy-line"></div> <h1><span data-i18n="skills.my_skills">My Skills</span></h1> </div> </div> <div style="margin-top:0;text-align:center;" class="row features-block"> <div class="col-lg-2"></div> <div class="wow zoomIn col-lg-8"> <canvas id="cs" height="500" width="500"></canvas> </div> <div class="col-lg-2"></div> <script> var ctx = document.getElementById("cs"); var data = { labels: "Machine Learing, Python, R, C, SHELL, Linux, MongoDB, Neo4j, HTML/CSS/JavaScript".split(","), datasets: [{ label: "Ability", backgroundColor: "rgba(179,181,198,0.2)", borderColor: "#3385FF", pointBackgroundColor: "#3385FF", pointBorderColor: "#fff", pointHoverBackgroundColor: "#3385FF", pointHoverBorderColor: "#3385FF", data: [90, 100, 80, 70, 90, 90, 70, 70, 60] }] }; var myRadarChart = new Chart(ctx, { type: 'radar', data: data, options: { scale: { responsive: true, ticks: {min: 0, max: 100}, lineArc: false, pointLabels: { fontSize: 15, fontStyle: "bold" }, }, legend: { display: false }, } }); </script> </div> </div> </section> <section id="projects" class="features gray-section project" style="margin-top: 0;"> <div class="container" id="i18_projects"> <div class="row m-b-lg"> <div class="col-lg-12 text-center"> <div class="navy-line"></div> <h1><span data-i18n="projects.my_projects">My Projects</span></h1> </div> </div> <div class="row"> <div class="projec_idv col-sm-6 wow fadeInLeft "> <div class="team-member"> <img src="/static/assets/img/landing/featsnp.png" class="img-responsive img-circle img-small" alt=""> <h4><a href="http://featsnp.org" target="_blank"><span class="navy" data-i18n="projects.var1.name"></span></a></h4> <p><span style="color:black" data-i18n="projects.var1.desc"></span></p> </div> </div> <div class="projec_idv col-sm-6 wow fadeInRight "> <div class="team-member"> <img src="/static/assets/img/landing/xmspanda.png" class="img-responsive img-circle img-small" alt=""> <h4><a href="https://github.com/kuppal2/xmsPANDA" target="_blank"><span class="navy" data-i18n="projects.var2.name"></span></a></h4> <p><span style="color:black" data-i18n="projects.var2.desc"></span></p> </div> </div> <div class="projec_idv col-sm-6 wow fadeInLeft "> <div class="team-member"> <img src="/static/assets/img/landing/xmwas.png" class="img-responsive img-circle img-small" alt=""> <h4><a href="https://kuppal.shinyapps.io/xmwas" target="_blank"><span class="navy" data-i18n="projects.var3.name"></span></a></h4> <p><span style="color:black" data-i18n="projects.var3.desc"></span></p> </div> </div> <div class="projec_idv col-sm-6 wow fadeInRight "> <div class="team-member"> <img src="/static/assets/img/landing/PyCDB.png" class="img-responsive img-circle img-small" alt=""> <h4><a href="https://kuppal.shinyapps.io/pycdb" target="_blank"><span class="navy" data-i18n="projects.var4.name"></span></a></h4> <p><span style="color:black" data-i18n="projects.var4.desc"></span></p> </div> </div> <div class="projec_idv col-sm-6 wow fadeInLeft col-sm-offset-3 "> <div class="team-member"> <img src="/static/assets/img/landing/ncats_translator.png" class="img-responsive img-circle img-small" alt=""> <h4><a href="https://github.com/RTXteam/RTX" target="_blank"><span class="navy" data-i18n="projects.var5.name"></span></a></h4> <p><span style="color:black" data-i18n="projects.var5.desc"></span></p> </div> </div> </div> </div> <br> </section> <section id="publications" class="features " style="margin-top: 0;"> <div class="container i18container" id="i18_publications"> <div class="row"> <div class="col-lg-12 text-center"> <div class="navy-line"></div> <h1><span data-i18n="publications.my_publications">My Publications (Selected)</span></h1> </div> </div> <div class="col-xs-12 col-md-12"> <ul class="fa-ul"> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample</span></h1> <h2 style="font-size: 12px;">David Koslicki, Stephen White, <span style="font-weight: bold;">Chunyu Ma</span>, Alexei Novikov</h2> <h2 style="font-size: 12px;">Published on <em>Bioinformatics</em>, 2024 Feb 01</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://academic.oup.com/bioinformatics/article/40/2/btae047/7588873" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>KGML-xDTD: A Knowledge Graph-based Machine Learning Framework for Drug Treatment Prediction and Mechanism Description</span></h1> <h2 style="font-size: 12px;"><span style="font-weight: bold;">Chunyu Ma</span>, Zhihan Zhou, Han Liu, David Koslicki</h2> <h2 style="font-size: 12px;">Published on <em>GigaScience</em>, 2023 Aug 21</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad057/7246583" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>ARAX: a graph-based modular reasoning tool for translational biomedicine</span></h1> <h2 style="font-size: 12px;">Amy K Glen, <span style="font-weight: bold;">Chunyu Ma</span>, Luis Mendoza, Finn Womack, EC Wood, Meghamala Sinha, Liliana Acevedo, Lindsey G Kvarfordt, Ross C Peene, Shaopeng Liu, Andrew S Hoffman, Jared C Roach, Eric W Deutsch, Stephen A Ramsey, David Koslicki</h2> <h2 style="font-size: 12px;">Published on <em>Bioinformatics</em>, 2023 Feb 08</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://academic.oup.com/bioinformatics/article/39/3/btad082/7031241" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine</span></h1> <h2 style="font-size: 12px;">E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, <span style="font-weight: bold;">Chunyu Ma</span>, Veronica Flores, Meghamala Sinha, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey</h2> <h2 style="font-size: 12px;">Published on <em>BMC bioinformatics</em>, 2022 Sep 29</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://link.springer.com/article/10.1186/s12859-022-04932-3" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>Plasma Metabolomics of Intermediate and Neovascular Age-Related Macular Degeneration Patients</span></h1> <h2 style="font-size: 12px;">Sabrina L Mitchell, <span style="font-weight: bold;">Chunyu Ma</span>, William K Scott, Anita Agarwal, Margaret A Pericak-Vance, Jonathan L Haines, Dean P Jones, Karan Uppal, Milam A Brantley Jr</h2> <h2 style="font-size: 12px;">Published on <em>Cells</em>, 2021 Nov 12</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://www.mdpi.com/2073-4409/10/11/3141" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>Addressing the batch effect issue for LC/MS metabolomics data in data preprocessing</span></h1> <h2 style="font-size: 12px;">Qin Liu, Douglas Walker, Karan Uppal, Zihe Liu, <span style="font-weight: bold;">Chunyu Ma</span>, ViLinh Tran, Shuzhao Li, Dean P Jones, Tianwei Yu</h2> <h2 style="font-size: 12px;">Published on <em>Scientific reports</em>, 2020 Aug 17</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://www.nature.com/articles/s41598-020-70850-0" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>Reference Standardization for Quantification and Harmonization of Large-Scale Metabolomics</span></h1> <h2 style="font-size: 12px;">Ken H Liu, Mary Nellis, Karan Uppal, <span style="font-weight: bold;">Chunyu Ma</span>, ViLinh Tran, Yongliang Liang, Douglas I Walker, Dean P Jones</h2> <h2 style="font-size: 12px;">Published on <em>Analytical Chemistry</em>, 2020 Jun 03</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.0c00338" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs</span></h1> <h2 style="font-size: 12px;"><span style="font-weight: bold;">Chunyu Ma</span>, Pamela Madden, Paul Gontarz, Ting Wang and Bo Zhang</h2> <h2 style="font-size: 12px;">Published on <em>Frontiers in Genetics</em>, 2019 Apr 2</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.00262/full" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals</span></h1> <h2 style="font-size: 12px;">Kristine K Dennis, Karan Uppal, Ken H Liu, <span style="font-weight: bold;">Chunyu Ma</span>, Bill Liang, Young-Mi Go, Dean P Jones</h2> <h2 style="font-size: 12px;">Published on <em>Database</em>, 2019 Jul 02</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://academic.oup.com/database/article/doi/10.1093/database/baz083/5527149" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>Striatal neurons directly converted from Huntington's disease patient fibroblasts recapitulate age-associated disease phenotypes</span></h1> <h2 style="font-size: 12px;">Matheus B. Victor, Michelle Richner, Hannah E. Olsen, Seong Won Lee, Alejandro M. Monteys, <span style="font-weight: bold;">Chunyu Ma</span>, Christine J. Huh, Bo Zhang, Beverly L. Davidson, X. William Yang & Andrew S. Yoo</h2> <h2 style="font-size: 12px;">Published on <em>Nature Neuroscience</em>, 2018 Feb 05</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://www.nature.com/articles/s41593-018-0075-7" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>xMWAS: a data-driven integration and differential network analysis tool</span></h1> <h2 style="font-size: 12px;">Karan Uppal, <span style="font-weight: bold;">Chunyu Ma</span>, Young-Mi Go, Dean P Jones</h2> <h2 style="font-size: 12px;">Published on <em>Bioinformatics</em>, 2018 Jun 15</h2> <button type="button" class="btn btn-outline-primary my-btn"><a href="https://academic.oup.com/bioinformatics/article-abstract/34/4/701/4562327" target="_blank">More Details</a></button> </li> <li style="margin-top: 20px;"> <h1 style="font-size: 20px; font-weight:bold;"><i class="fa-li fa fa-file-text-o pub-icon" aria-hidden="true"></i><span>Reciprocal genomic evolution in the ant-fungus agricultural symbiosis</span></h1> <h2 style="font-size: 12px;">Sanne Nygaard, Haofu Hu, Cai Li, Morten Schiøtt, Zhensheng Chen, Zhikai Yang, Qiaolin Xie, <span style="font-weight: bold;">Chunyu Ma</span>, Yuan Deng, Rebecca B. 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