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<!--DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"--><!Doctype html> <html><!-- InstanceBegin template="/Templates/index.dwt" codeOutsideHTMLIsLocked="false" --><head><!-- InstanceBeginEditable name="doctitle" --><title>Welcome to He Group Webpage</title><!-- InstanceEndEditable --> <!--meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"--><!--link rel="shortcut icon" href="/favicon.ico" /--><!--link href="../styleMain.css" rel="stylesheet" type="text/css"--> <meta charset="utf-8"> <link rel="stylesheet" href="styleMain.css"> <!-- script src=“javascriptfile.js"></script --> <!-- InstanceBeginEditable name="head" --><script language="JavaScript" type="text/JavaScript"> var desc = new Array(); var name = new Array(); name["VIOLIN"] = "VIOLIN: Vaccine Investigation and Online Information Network"; desc["VIOLIN"] = "VIOLIN is a web-based vaccine database and analysis system"; name["CRCView"] = "CRCView"; desc["CRCView"] = "CRCView is a web-based microarray data analysis and visualization system"; name["GenoMesh"] = "GenoMesh"; desc["GenoMesh"] = "CRCView is a web-based, genome-wide literature mining system"; name["MARIMBA"] = "MARIMBA: Molecular Annotation Resource for Integrating Microarrays with Bayesian Analysis"; desc["MARIMBA"] = "MARIMBA is a web-based Bayesian network system for analysis of gene expression data"; name["miniTUBA"] = "miniTUBA:Medical Inference by Network Integration of Temporal Data Using Bayesian Analysis"; desc["miniTUBA"] = "miniTUBA is a web-based dynamic Bayesian network system for analysis of gene expression data"; name["BBP"] = "BBP: Brucella Bioinformatics Portal"; desc["BBP"] = "BBP is a web-based Brucella resource portal and analysis system"; name["PHIDIAS"] = "PHIDIAS: Pathogen-host Interaction and Data Analysis System"; desc["PHIDIAS"] = "PHIDIAS is a web-based pathogen-host interaction database and analysis system"; name["VO"] = "VO: Vaccine Ontology"; desc["VO"] = "The VO project is a community-based effort to develop the Vaccine Ontology (VO)"; name["OntoFox"] = "OntoFox"; desc["OntoFox"] = "A web server that supports ontology reuse";</script><style type="text/css"><!--.smallContent strong em { color: #800000;}--></style><!-- InstanceEndEditable --><style type="text/css"><!--.style3 {font-size: 14px}--></style></head> <body><table align="center" cellpadding="0" cellspacing="0" width="900px" style="border:1px solid #999966"> <tr> <td><table bgcolor="#ffcc33" border="0" cellpadding="0" cellspacing="0" width="900px"> <tr class="content"> <td><img src="images/pixel.gif" alt="pixel image" height="5" width="1"></td> </tr> </table> <table bgcolor="#003366" border="0" cellpadding="5" cellspacing="0" width="900px"> <tr> <td width="130" height="90" align="center" valign="middle"> </td> <td width="420" align="center" valign="middle" class="emhead"><a href="/index.php"><img src="images/HeGroup.gif" alt="He Group" width="188" border="0"></a></td> <td align="center" valign="middle" width="140"> </td> </tr> </table> <table bgcolor="#003366" border="0" cellpadding="3" cellspacing="0" width="900px"> <form name="webSearch" action="searchWeb.php" method="POST" target="_blank"> <tr> <td align="center" valign="middle" bgcolor="#ffcc33"> <a href="index.php" class="topnav">Home</a><span class="temphead">|</span><a href="aboutUs/aboutUs.html" class="topnav">People</a><span class="temphead">|</span><a href="projects.html" class="topnav">Projects</a><span class="temphead">|</span><a href="publications.html" class="topnav">Publications</a><span class="temphead">|</span><a href="faqs.php" class="topnav">FAQs</a><span class="temphead">|</span><a href="links.html" class="topnav">Links</a><span class="temphead">|</span><a href="news.php" class="topnav">News</a><span class="temphead">|</span><a href="contacts/index.php" class="topnav">Contact Us</a></td> </tr> </form> </table> <table width="900px" border="0" cellpadding="5" cellspacing="0" bgcolor="#ffffcc"> <tr> <td valign="top" style="height:400px;"><!-- InstanceBeginEditable name="Main" --> <table width="860" align="center"> <tr> <td> <p align="center" class="mainhead"><i>Welcome to hegroup.org!</i></p> <p><br/> Welcome to the home page of <a href="aboutUs/Oliver.html">Dr. Yongqun "Oliver" He</a>'s laboratory research group at the University of Michigan Medical School, Ann Arbor, MI, USA! </p> <p>Our group has now focused on computational medicine and bioinformatics research, with primary research interests in the areas of microbiology, vaccinology, nephrology, ontology, literature mining, and machine learning. Our primary scientific research domains are microbiology, vaccinology, and nephrology. Our primary technical research domains are ontology, semantic web, literature mining, and machine learning. These technical domains are all closely related to artificial intelligence (AI), so we do AI research! We are also interested in applying our technologies to other interesting areas as well. </p> <p><em><strong>News:</strong></em> Currently we are recruiting a <a href="https://careers.umich.edu/job_detail/227896/software-developer-bioinformatician"><em>Software Developer / Bioinformatician</em></a>. Welcome to forward or apply! </p> <p>A brief introduction of our research is provided below: </p> <p><strong>(1) Development and applications of community-based ontologies. </strong>Ontologies have emerged to become critical to biomedical data and knowledge integration, sharing and validation, as well as new knowledge discovery. A major field of AI is <a href="https://en.wikipedia.org/wiki/Knowledge_representation_and_reasoning">knowledge representation and reasoning</a> (KR², KR&R), for which ontology is a part of the story and critical. </p> <p>We have initiated and led the development of many community-based ontologies such as the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387853/">Cell Line Ontology</a> (CLO), <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024438/">Ontology of Biological and Clinical Statistics</a> (OBCS), and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937947/"> Ontology of Host-Microbiome Interactions</a> (OHMI). Dr. He is also an active developer of the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851331/">Ontology for Biomedical Investigations</a> (OBI), which is collaboratively developed by over 20 communities, and Dr. He is the representation of the vaccine community. </p> <p>To support the Kidney Precision Medicine Project (<a href="http://kpmp.org/">KPMP</a>), We have actively involved in the community-based development of the <a href="http://ceur-ws.org/Vol-2285/ICBO_2018_paper_28.pdf">Kidney Tissue Atlas Ontology</a> (KTAO) and <a href="https://github.com/OPMI/opmi">Ontology of Precision Medicine Investigation</a> (OPMI). </p> <p> <p>To face the challenge of the pandemic COVID-19, Dr. He has co-initiated the development of the community-driven <a href="https://github.com/CIDO-ontology/cido">Coronavirus Infectious Disease Ontology</a> (CIDO, see <a href="https://www.nature.com/articles/s41597-020-0523-6">the CIDO paper in <em>Scientifc Data</em></a>). As a first effort to develop the CIDO, we manually collected from the literature over 100 chemical drugs or biological antibodies against pathological human coronaviruses, mapped as many as possible these drugs to existing ontologies, and analyzed them using ontology and bioinformatics methods. The preprint paper about this anti-coronavirus drug study is availabl by clicking <a href="https://www.preprints.org/manuscript/202003.0413/v1">here</a>. We have also applied the Vaccine Ontology (VO) and CIDO to model, represent, and analyze COVID-19 vaccines, and are currently developing a <a href="https://violinet.org/cov19vaxkb">COVID-19 vaccine knowledgebase (Cov19VaxKB)</a>. As described below, we applied our own reverse vaccinology and mechine learning methods to <a href="https://www.frontiersin.org/articles/10.3389/fimmu.2020.01581/full">predict COVID-19 vaccine antigens</a>. Dr. He has also been selected as a faculty member to serve on the President's and Provost's <a href="https://record.umich.edu/articles/sixteen-faculty-members-named-to-covid-19-council/">COVID-19 Faculty Council</a> in the University of Michigan.</p> <p>These ontologies can be used in many applications, including standardized data and knowledge representation, sharing, integration, and advanced analysis. We can also apply ontology to different informatics methods such as literature mining and machine learning. <!-- p align="center"><strong><em>News:</em></strong> Welcome to attend <a href="https://github.com/CIDO-ontology/WCO/">WCO-2020 (Workshop on COVID-19 Ontologies)</a> on Oct 23 and 30, 2020! </p --> <p>As a major social activity, Oliver hosted and co-chaired the 2022 International Conference on Biomedical Ontology (<a href="https://icbo-conference.github.io/icbo2022/">ICBO-2022</a>) in September 2022 at the University of Michigan, Ann Arbor, MI, USA.</p> <p><strong>(2) Development of Ontoanimal tools to support interoperable ontology development and applications. </strong> <p>We have developed many widely used ontology tools (e.g., <a href="https://ontobee.org/">Ontobee</a>, <a href="http://ontofox.hegroup.org/">Ontofox</a>, <a href="http://ontodog.hegroup.org">Ontodog</a>, and <a href="http://ontorat.hegroup.org">Ontorat</a>), collectively names “Ontoanimal” tools. Each tool has specific functions; together, these tools are able to extract ontology subsets, provide ontology community views, generate and edit ontology terms, query and visualize ontology terms, provide statistics of ontologies, and compare ontologies. </p> <p>We have also initiated the proposal of the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765662/">eXtensible ontology development (XOD) principles</a> and methods to support ontology interoperability. </p> With the XOD and our Ontoanimal tools, ontology development is no longer boring and has become more fun and useful! <p><strong> (3) Vaccine informatics, host-pathogen interactions, and vaccine/drug design and safety analysis.</strong></p> <p>We study <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134834/">Vaccine Informatics</a>, a branch of vaccinology that Dr. He and his colleagues have advertised and pioneered as referenced here: <a href="https://doi.org/10.1155%2F2010%2F218590"><em>doi: 10.1155/2010/218590</em></a>. We developed <a href="https://violinet.org/">VIOLIN</a>, the most comprehensive vaccine database and analysis system. The <a href="https://violinet.org/vaccineontology/index.php">Vaccine Ontology (VO)</a> has become a community effort for standard representation of vaccines, vaccine components, vaccination, and host responses to vaccines. We have also developed <a href="https://violinet.org/vaxign">Vaxign</a> and <a href="https://violinet.org/vaxign2">Vaxign2</a>, the first web-based publically available vaccine target design tool based on bioinformatics analysis of genome sequences using the strategy of reverse vaccinology. We have also developed <a href="https://violinet.org/vaxign/vaxign-ml">Vaxign-ML</a>, a supervised machine learning model to support vaccine design. We have also used these tools to <a href="https://www.frontiersin.org/articles/10.3389/fimmu.2020.01581/full">predict COVID-19 vaccine candidates</a>. </p> <p align="center"> <strong><em>News:</em></strong> On August 19, 2022, Dr. Oliver He and his collaborators were awarded a 5-year NIH U24 grant entitled <br/>"VIOLIN 2.0: Vaccine Information and Ontology LInked kNowledgebase" (<a href="https://reporter.nih.gov/project-details/10506013">U24AI171008</a>). Congratulations! </p> <p> We study host-pathogen interactions. We developed <a href="https://phidias.us/">PHIDIAS</a>, the most comprehesenive host-pathogen interaction database focusing on human and animal pathogens. As part of PHIDIAS, we have developed <a href="https://phidias.us/victors/">Victors</a>, a comprehensive knowledge base of more than 3,000 virulence factors in >120 human and animal pathogens. We have also developed an <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324020/">Ontology of Host-Pathogen Interactions</a> (OHPI) to logically represent the virulence factors and their interactions with the hosts.</p> <p>We are interested in vaccine and drug safety study. We have led the development of the community-based <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120740/">Ontology of Adverse Events </a>(OAE), and applied it to <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=yongqun+he%2C+Adverse+Events">study vaccine and drug adverse events</a>. </p> <p><strong>(4) Systematic ontology and bioinformatics analysis of biological interaction networks. </strong></p> <p>We hypothesized that ontology supports literature mining and analysis of biological interaction networks. As a result, we developed the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362819/">Interaction Network Ontology</a> (INO) and applied it to enhance literature mining performance. We are also collaborating with our collaborators, including Drs. <a href="https://und.edu/directory/jung.hur">Junguk Hur</a> and <a href="https://www.cmpe.boun.edu.tr/~ozgur/">Arzugan Özgür,</a> to apply ontology for more advanced literature mining. </p> <p>Bayesian network (BN) can model linear, nonlinear, combinatorial, and stochastic relationships among variables across multiple levels of biological organizations. We have developed new BN algorithms and tools for analysis of gene interaction networks using high throughput gene expression data. </p> <p>In a 2014 paper (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815432/">He, 2014</a>) and then a 2016 paper (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957564/">He, 2016</a>), Dr. He proposed a new <span lang="en-US"><span dir="ltr">“<a href="https://hegroup.org/onenettheory.html">OneNet Theory of Life</a>”. The OneNet theory states that </span></span><em> the whole process of a life of an organism is a single complex and dynamic network (called “OneNet”)</em>. </p> Dr. He also proposes OneNet tenets to characterize different aspects of the OneNet life. Ontologies and ontology-based bioinformatics tools, such as those introduced above, can be used to integratively represent and study such OneNet theory and OneNet knowledge of different organisms.</p> <p><strong>(5) Wet-lab (not active now): Host-<em>Brucella</em> interaction and protective vaccine immune mechanisms. </strong> <p> Dr. Oliver He has strong backgrounds in wet-lab microbiology and immunology research. In his M.S. wet-lab research (1993-1996), he developed a new ELISA method, applied the method for <a href="http://www.cnki.com.cn/Article/CJFD1998-XMSY801.011.htm">epidemiological survey of avian reticuloendotheliosis virus</a> (REV, a RNA virus) outbreak in China, and for the first time found its wide existance in North China. <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=(He+Y)+AND+(Schurig+G)+AND+1996%3A2002%5Bdp%5D">His Ph.D. thesis research </a> (advisor: Dr. <a href="https://vtx.vt.edu/content/vtx_vt_edu/en/articles/2013/01/011113-vetmed-schurigstepsdown.html">Gerhardt G. Schurig</a>) focused on vaccine development and immune mechanism against brucellosis, a zoonotic bacterial disease caused by <em>Brucella</em>. After Dr. He joined the University of Michigan in 2005, we continued the <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=(He+Y)+AND+Brucella+AND+2005%3A2020%5Bdp%5D"><em>Brucella</em> vaccine research in He lab</a>. One major finding out of our wet-lab studies is the identification of a unique caspase-2-mediated proinflammatory cell death mechanism, which was first observed in our laboratory in macrophages infected with <em>Brucella</em> cattle vaccine RB51 and other rough <em>Brucella</em> strains (but not virulent wild type <em>Brucella</em> strains) (References: <a href="http://www.ncbi.nlm.nih.gov/pubmed/16926395"><em>He et al, 2006</em></a>, <a href="https://pubmed.ncbi.nlm.nih.gov/19714247/"><em>Chen and He, 2009</em></a>, <a href="https://pubmed.ncbi.nlm.nih.gov/21464087/"><em>Chen et al, 2011</em></a>, <a href="https://pubmed.ncbi.nlm.nih.gov/22927979/"><em>Li and He, 2012</em></a>, <a href="https://pubmed.ncbi.nlm.nih.gov/24350060/"><em>Bronner et al, 2013</em></a>, and <a href="https://pubmed.ncbi.nlm.nih.gov/26341399/"><em>Bronner et al, 2015</em></a>). Our research has also made <em>Brucella</em> a good model system to study caspase-2 related roles and pathways. </p> <p>More details about our projects can be found <a href="../projects.html">here</a>. </p> <p>Your <a href="contacts/index.php">suggestions, comments, and collaborations</a> are welcome. Thank you! </p> </td> </tr> </table><script type="text/javascript" src="inc/boxover.js"></script> <!-- InstanceEndEditable --> </td> </tr> </table> <table bgcolor="#ffcc33" border="0" cellpadding="0" cellspacing="0" width="900px"> <tr> <td height="25" align="center"><a href="https://www.ontobee.org/" class="footerlink">Ontobee</a><span class="subhead">|</span><a href="https://ontofox.hegroup.org" class="footerlink">Ontofox</a><span class="subhead">|</span><a href="https://github.com/OAE-ontology/OAE" class="footerlink">OAE</a><span class="subhead">|</span><a href="https://violinet.org/vaccineontology" class="footerlink">VO</a><span class="subhead">|</span><a href="http://genomesh.hegroup.org" class="footerlink">Genomesh</a><span class="subhead">|</span><a href="https://www.ignet.org" class="footerlink">Ignet</a><span class="subhead">|</span><a href="http://minituba.hegroup.org" class="footerlink">miniTUBA</a><span class="subhead">|</span><a href="https://www.phidias.us" class="footerlink">PHIDIAS</a><span class="subhead">|</span><a href="https://violinet.org" class="footerlink">VIOLIN</a></td> </tr> </table> </td> </tr> <tr> <td><table border="0" cellpadding="8" cellspacing="0" width="100%"> <tr> <td valign="top" bgcolor="#ffffcc" style="padding-left:22px;">He Group <br> University of Michigan Medical School<br> Ann Arbor, MI 48109</td> <td width="175" align="center" valign="middle" bgcolor="#ffffcc" class="smallcontent"><a href="http://www.umich.edu" target="_blank"><img src="images/wordmark_m_web.jpg" alt="U of M" width="166" height="20" border="0"></a></td> <td width="100" align="center" valign="middle" bgcolor="#ffffcc" class="smallcontent" style="padding-right:22px;"><a href="http://www.umich.edu" target="_blank"></a><a href="http://www3.niaid.nih.gov/"><img src="images/niaid.gif" alt="NIAID" width="45" height="45" border="0"></a><span class="style3"><a href="http://www3.niaid.nih.gov/">NIAID</a></span></td> </tr> </table></td> </tr></table><script type="text/javascript">var gaJsHost = (("https:" == document.location.protocol) ? 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