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<!DOCTYPE html>
<html lang="en">
<head>
<!-- This is a test comment for Naila. -->
<title>Publications</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link rel="stylesheet" href="https://hive.biochemistry.gwu.edu/prd//gcsslib/bootstrap.min.css" type="text/css">
<link rel="stylesheet" href="https://hive.biochemistry.gwu.edu/prd//gcsslib/global.css" type="text/css">
<link rel="stylesheet" href="https://hive.biochemistry.gwu.edu/prd//gcsslib/googlefonts.css" type="text/css">
</head>
<div vocab="http://schema.org/" typeof="WebPage">
<table style="width:100%;font-size:13px;">
<tr>
<td style="width:100%; vertical-align: top;" colspan="2">
<h3 id="Top">Please cite use of HIVE with:</h3>
</td>
</tr>
<tr style="height: 78px;">
<td style="width: 40px; text-align: right; vertical-align: top; height: 78px;">
<p> </p>
</td>
<td style="vertical-align: top; width:100%; height: 78px;font-size:13px;">
<ol>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle">
<span property="author">Simonyan V and Mazumder R.</span>
<span property="name"> High-performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.</span>
<span property="isPartof" typeof="PublicationIssue">
<span typeof="Periodical">
<span property="name">Genes</span>,
</span>
<time datetime="2014-09-30" property="datePublished">2014 Sep 30</time>;<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">5</span></span>(<span property="issueNumber">4</span>):
</span>
<span property="pageStart">957</span>-<span property="pageEnd">981</span>.
PMID:<a property="sameAs" href="http://www.ncbi.nlm.nih.gov/pubmed/25271953" target="_blank"> 25271953</a>.
</div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle">
<span property="author">Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S, Golikov A, Gulzar N, Karagiannis K, Vinh Nguyen Lam P, Maudru T, Muravitskaja O, Osipova E, Pan Y, Pschenichov A, Rostovtsev A, Santana-Quintero L, Smith K, Thompson EE, Tkachenko V, Torcivia-Rodriguez J, Voskanian A, Wan Q, Wang J, Wu TJ, Wilson C, Mazumder R.</span>
<span property="name"> High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. </span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Database (Oxford)</span>.
<span property="datePublished">2016</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2016</span></span>:baw022. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/26989153" target="_blank">26989153</a></span>.
</div>
</li>
</ol>
</td>
</tr>
<tr>
<td style="width:100%; vertical-align: top;" colspan="2">
<br>
<h3>HIVE Team publications:</h3>
<a href="#Top">Back to Top (Publications)</a> | <a href="#Multimedia">Jump to Multimedia</a> | <a href="#Posters">Jump to Posters</a> | <a href="#Other">Jump to Other Works</a><br><br>
</td>
</tr>
<tr style="height: 13px;">
<td style="width: 40px; text-align: right; vertical-align: top; height: 13px;"> </td>
<td style="width:100%; height: 13px; vertical-align: top;">
<ol>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R</span>.
<span property="name">Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Glycobiology</span>.
<span property="datePublished">August 2022</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> <a href="https://academic.oup.com/glycob/advance-article-abstract/doi/10.1093/glycob/cwac046/6655823" target="_blank">35925813</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Torcivia J, Abdilleh K, Seidl F, Shahzada O, Rodriguez R, Pot D, Mazumder R</span>.
<span property="name">Whole Genome Variant Dataset for Enriching Studies across 18 Different Cancers</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Onco</span>.
<span property="datePublished">June 2022</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2(2):129-144.</span></span> <a href="https://www.mdpi.com/2673-7523/2/2/9" target="_blank">https://doi.org/10.3390/onco2020009</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Dahlin M, Singleton S, David J, Basuchoudhary A, Wickstrom, Mazumder R, Prast-Nielsen S</span>.
<span property="name">Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">eBioMedicine</span>.
<span property="datePublished">June 2022</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">vol: 80.</span></span> <a href="https://www.sciencedirect.com/science/article/pii/S2352396422002420" target="_blank">https://doi.org/10.1016/j.ebiom.2022.104061</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF.</span>
<span property="name">Communicating regulatory high-throughput sequencing data using BioCompute Objects.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Drug Discov Today</span>.
<span property="datePublished">2022 Jan 22</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> PMID: <a property="sameAs" href="https://pubmed.ncbi.nlm.nih.gov/35077912/" target="_blank">35077912</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Wang Z, Hopson L, Singleton S, Yang X, Jogunoori W, Mazumder R, Obias V, Lin P, Nguyen BN, Yao M, Miller L, White J, Rao S, Mishra L.</span>
<span property="name">Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Biochim Biophys Acta Mol Basis Dis</span>.
<span property="datePublished">2021 Oct 1</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">1867(10):166179.</span></span> PMID: <a property="sameAs" href="https://pubmed.ncbi.nlm.nih.gov/34082069/" target="_blank">34082069</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R.</span>
<span property="name">Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy</span>.
<span property="datePublished">2021 Sep 16-18</span>;<a href="http://ceur-ws.org/Vol-3073/paper13.pdf" _target="blank"> ceur-ws.org.</a>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J.</span>
<span property="name">Bioinformatics tools developed to support BioCompute Objects.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Database (Oxford)</span>.
<span property="datePublished">2021 March 31</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> PMID: <a property="sameAs" href="https://pubmed.ncbi.nlm.nih.gov/33784373/" target="_blank">33784373</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Hora B, Gulzar N, Chen Y, Karagiannis K, Cai F, Su C, Smith K, Simonyan V, Shah SA, Ahmed M, Sanchez AM, Stone M, Cohen MS, Denny TN, Mazumder R, Gao F.</span>
<span property="name">Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">mSphere</span>.
<span property="datePublished">2020 Oct 14</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/33055255" target="_blank">33055255</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Hopson L, Singleton S, David J, Basuchoudhary A, Prast-Nielsen S, Klein P, Sen S, Mazumder R.</span>
<span property="name">Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Prog Mol Biol Transl Sci</span>.
<span property="datePublished">2020 Sep 30</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">176:141-178.</span></span> PMID: <a property="sameAs" href="https://pubmed.ncbi.nlm.nih.gov/33814114/" target="_blank">33814114</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Torcivia J, Mazumder R</span>.
<span property="name">Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Briefings in Bioinformatics.</span>
<span property="datePublished">2020 Sep 17</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/32940334" target="_blank">32940334</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R.</span>
<span property="name"> COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Brief Bioinform</span>.
<span property="datePublished">2021 May 20</span>; <a href="https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab191/6278606" _target="blank"> bbab191. doi: 10.1093/bib/bbab191.</a>
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> PMID: <a property="sameAs" href="https://pubmed.ncbi.nlm.nih.gov/34015823/" target="_blank">34015823</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R</span>.
<span property="name">GlyGen data model and processing workflow</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Bioinformatics</span>.
<span property="datePublished">2020</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber"></span></span> PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/32324859" target="_blank">32324859</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Kurnat-Thoma E, Baranova A, Baird P, Brodsky E, Butte AJ, Cheema AK, Cheng F, Dutta S, Grant C, Giordano J, Maitland-van der Zee AH, Fridsma DB, Jarrin R, Kann MG, Keeney J, Loscalzo J, Madhavan G, Maron BA, McBride DK, McKean M, Mun SK, Palmer JC, Patel B, Parakh K, Pariser AR, Pristipino C, Radstake TRDJ, Rajasimha HK, Rouse WB, Rozman D, Saleh A, Schmidt HHHW, Schultz N, Sethi T, Silverman EK, Skopac J, Svab I, Trujillo S, Valentine JE, Verma D, West BJ, Vasudevan S</span>.
<span property="name">Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Syst Med (New Rochelle)</span>.
<span property="datePublished">2020</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">3</span></span>(<span property="issueNumber">1</span>):22-35. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099876/" target="_blank">32226924</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R</span>.
<span property="name">OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">JCO Clin Cancer Inform</span>.
<span property="datePublished">2020</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">4</span></span>:210-220. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/32142370/" target="_blank">32142370</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH</span>.
<span property="name">The GlySpace Alliance: toward a collaborative global glycoinformatics community</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Glycobiology</span>.
<span property="datePublished">2020</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">30</span></span>(<span property="issueNumber">2</span>):70-71. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/31573039/" target="_blank">31573039</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">York WS, Mazumder R, Ranzinger R, et al</span>.
<span property="name">GlyGen: Computational and Informatics Resources for Glycoscience</span>.
<span property="isPartOf" typeof="PublicationIssue">
<span property="name" typeof="Peridical">Glycobiology</span>.
<span property="datePublished">2019.</span> <a property="sameAs" href="https://doi.org/10.1093/glycob/cwz080" target="_blank">https://doi.org/10.1093/glycob/cwz080</a>
PMID: <a property="sameAs" href="http://www.ncbi.nlm.nih.gov/pubmed/31616925" target="_blank">31616925</a>
</span>
</p></div>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">King CH</span>,
<span property="author">Desai H</span>,
<span property="author">Sylvetsky AC</span>,
<span property="author">LoTempio J</span>,
<span property="author">Ayanyan S</span>,
<span property="author">Carrie J</span>,
<span property="author">Crandall K</span>,
<span property="author">Fochtman B</span>,
<span property="author">Gasparyan L</span>,
<span property="author">Gulzar N</span>,
<span property="author">Howell P</span>,
<span property="author">Issa N</span>,
<span property="author">Krampis K</span>,
<span property="author">Mishra L</span>,
<span property="author">Morizono H</span>,
<span property="author">Pisegna JR</span>,
<span property="author">Rao S</span>,
<span property="author">Ren Y</span>,
<span property="author">Simonyan V</span>,
<span property="author">Smith K</span>,
<span property="author">VedBrat S</span>,
<span property="author">Yao M</span>,
<span property="author">Mazumder R.</span>
<span property="name">Baseline human gut microbiota profile in healthy people and standard reporting template</span>.
<span property="isPartOf" typeof="PublicationIssue">
<span property="name" typeof="Peridical">PLOS ONE</span>.
<span property="datePublished">2019.</span>
<a property="sameAs" href="https://0.1371/journal.pone.0206484" target="_blank">https://0.1371/journal.pone.0206484</a>
PMID: <a property="sameAs" href="http://www.ncbi.nlm.nih.gov/pubmed/31509535" target="_blank">31509535</a>
</span>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Fan Y, Hu Y, Yan C, Goldman R, Pan Y, Mazumder R, Dingerdissen H</span>.
<span property="name">Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. Scientific Reports</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">PLoS One</span>.
<span property="datePublished">2018</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">8</span></span>(<span property="issueNumber"></span>):4322. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/29531238" target="_blank">29531238</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Baekdoo Kim, Thahmina Ali, Changsu Dong, Carlos Lijeron, Raja Mazumder, Claudia Wultsch, and Konstantinos Krampis </span>.
<span property="name">miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines </span>.
<span property="isPartOf" typeof="PublicationIssue">
<span property="name" typeof="Peridical">Journal of Computational Biology</span>.
<span property="datePublished">2018.</span>
<a property="sameAs" href="http://doi.org/10.1089/cmb.2018.0218" target="_blank">http://doi.org/10.1089/cmb.2018.0218</a>
</span></p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R</span>.
<span property="name">Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results</span>.
<span property="isPartOf" typeof="PublicationIssue">
<span property="name" typeof="Peridical">PLOS Biology; 16(12): e3000099</span>.
<span property="datePublished">2018.</span>
<a property="sameAs" href="https://doi.org/10.1371/journal.pbio.3000099" target="_blank">https://doi.org/10.1371/journal.pbio.3000099</a>
</span></p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Hu Y, Dingerdissen H, Gupta S, Kahsay R, Shanker V, Wan Q, Yan C, Mazumder R. </span>
<span property="name">Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. </span>
<span property="isPartOf" typeof="PublicationIssue"></span>
<span property="name" typeof="Peridical">Computers in Biology and Medicine 2018; vol: 103 pp: 183-197. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/30384176" target="_blank">30384176</a>.</span></p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Dingerdissen H, Torcivia-Rodriguez J, Hu Y, Chang T-C, Mazumder R, Kahsay R</span>.
<span property="name">BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Nucleic Acids Research</span>.
<span property="datePublished">2017.</span> PMCID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753215" target="_blank">5753215</a>.</span></p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Karagiannis K, Simonyan V, Chumakov K, Mazumder R</span>.
<span property="name">Separation and assembly of deep sequencing data into discrete sub-population genomes</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Nucleic Acids Research</span>.
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">45</span></span>(<span property="issueNumber">19</span>):10989-11003.
<span property="datePublished">2017.</span> PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28977510" target="_blank">28977510</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Chen J, Zaidi S, Rao S, Chen J-S, Phan L, Farci P, Su X, Shetty K, White J, Zamboni F, Wu X, Rashid A, Pattabiraman N, Mazumder R, Horvath A, Wu R-C, Li S, Xiao C, Deng C-X, Wheeler D A, Mishra B, Akbani R, Mishra L</span>.
<span property="name">Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor beta Pathway</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Gastroenterology</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">S0016-5085</span></span>(<span property="issueNumber">17</span>)36144-9. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28918914" target="_blank">28918914</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C</span>.
<span property="name">A new and updated resource for codon usage tables</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">BMC Bioinformatics</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">18</span></span>(<span property="issueNumber">1</span>):391. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28865429" target="_blank">28865429</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Gannavaram S, Torcivia J, Gasparyan L, Kaul A, Ismail N, Simonyan V, Nakhasi HL</span>.
<span property="name">Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Sci Rep</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">7</span></span>(<span property="issueNumber">1</span>):4718. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28680050" target="_blank">28680050</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Simonyan V, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A</span>.
<span property="name">HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Genomics</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">109</span></span>(<span property="issueNumber">3-4</span>):131-140. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28188908" target="_blank">28188908</a></span>.
</p></div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Pan Y, Yan C, Fan Y, Pan Q, Wan Q, Torcivia-Rodriquez J, Mazumder R.</span>
<span property="name">Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids.</span>
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Scientific Reports</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">7</span></span>:42169 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28176830" target="_blank">28176830</a></span>.
</p></div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Gulzar N, Dingerdissen H, Yan C, Mazumder R.</span>
<span property="name"> Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Methods Mol Biol</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">1558</span></span>:159-190. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/28150238" target="_blank">28150238</a></span>.
</p></div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Simonyan V, Goecks J, Mazumder R</span>.
<span property="name">BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">PDA J Pharm Sci Technol</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">71</span></span>(<span property="issueNumber">2</span>):136-146 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/27974626" target="_blank">27974626</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Yan C, Pattabiraman N, Goecks J, Lam P, Nayak A, Pan Y, Torcivia-Rodriquez J, Voskanian A, Wan Q, Mazumder R</span>.
<span property="name">Impact of germline and somatic missense variations on drug binding sites</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Pharmacogenomics J</span>.
<span property="datePublished">2017</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">17</span></span>(<span property="issueNumber">2</span>):128-136 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/26810135" target="_blank">26810135</a></span>.
</p></div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Novatt H, Theisen TC, Massie T, Simonyan V, Voskanian-Kordi A, Renn LA, Rabin RL</span>.
<span property="name">Distinct Patterns of Expression of Transcription Factors in Response to Interferon Beta and Interferon lambda-1</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">J Interferon Cytokine Res</span>.
<span property="datePublished">2016</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">36</span></span>(<span property="issueNumber">10</span>):589-598 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/27447339" target="_blank">27447339</a></span>.
</p></div>
</li>
<li>
<div vocab= "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Poison SW, Wang Y, Wu CH, UniProt Consortium</span>.
<span property="name">Computational clustering for viral reference proteomes</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">Bioinformatics</span>.
<span property="datePublished">2016</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">32</span></span>(<span property="issueNumber">13</span>):2041-3 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/27153712" target="_blank">27153712</a></span>.
</p></div>
</li>
<li>
<div vocab= "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Mahmood AS, Wu TJ, Mazumder R, Vijay-Shanker K</span>.
<span property="name">DiMeX: A text-mining system for mutation-disease association extraction</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Peridical">PLoS One</span>.
<span property="datePublished">2016</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">11</span></span>(<span property="issueNumber">4</span>):e0152725 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/27073839" target="_blank">27073839</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Goldweber S, Theodore J, Torcivia-Rodriquez J, Simonyan V, Mazumder R</span>.
<span property="name">Pubcast and Genecast: Browsing and exploring publications and associated curated content in biology through mobile devices</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical"> IEEE/ACM Trans Comput Biol Bioinform</span>.
<span property="datePublished">2016</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">14</span></span>(<span property="issueNumber">2</span>):498-500 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/27019500" target="_blank">27019500</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Laassri M, Zagorodnyaya T, Plant EP, Petrovskaya S, Bidzhieva B, Ye Z, Simonyan V, Chumakov K</span>.
<span property="name">Deep Sequencing for Evaluation of Genetic Stability of Influenza A/California/07/2009 (H1N1) Vaccine Viruses</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">PLoS One</span>.
<span property="datePublished">2015</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">10</span></span>(<span property="issueNumber">9</span>):e0138650. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/26407068" target="_blank">26407068</a></span>.
</p></div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Sauder CJ, Ngo L, Simonyan V, Cong Y, Zhang C, Link M, Malik T, Rubin SA</span>.
<span property="name">Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Virus Genes</span>.
<span property="datePublished">2015</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">51</span></span>(<span property="issueNumber">1</span>):12-24. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25962759" target="_blank">25962759</a></span>.
</p></div>
</li>
<li>
<div vocab = "http://schema.org/" typeof="ScholarlyArticle"><p>
<span property="author">Wu T-J, Schriml LM, Chen Q-R, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, Mazumder R</span>.
<span property="name">Generating a focused view of Disease Ontology cancer terms for pan-cancer data integration and analysis</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Database (Oxford)</span>.
<span property="datePublished">2015</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2015</span></span>:bav032. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25841438" target="_blank">25841438</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu T-J, Yang C, Zhang H, Mazumder R</span>.
<span property="name">BioXpress: An integrated RNA-seq derived gene expression database for pan-cancer analysis</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Database (Oxford)</span>.
<span property="datePublished">2015</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2015. pii</span></span>: bav019 PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25819073" target="_blank">25819073</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Kumari P, Mazumder R, Simonyan V, Krampis K</span>.
<span property="name">Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly</span>.
<span property="isPartOf" typeof="PublicationIssue"></span>
<span property="name" typeof="Periodical">F1000Research</span>.
<span property="datePublished">2015</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">4</span></span>(<span property="issueNumber">20</span>)
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Abunimer A, Dingerdissen H, Torcivia-Rodriguez J, Vinh Nguyen Lam P, Mazumder R</span>.
<span property="name">Non-synonymous Single-Nucleotide Variations as Cardiovascular System Disease Biomarkers and Their Roles in Bridging Genomic and Proteomic Technologies</span>.
<span property="isPartOf" typeof="PublicationIssue"></span>
<span property="name" typeof="Periodical">Biomarkers in Cardiovascular Disease</span>.
<span property="datePublished">2015</span>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Adhikari S, Chetram MA, Woodrick J, Mitra PS, Manthena PV, Khatkar P, Dakshanamurthy S, Dixon M, Karmahapatra SK, Nuthalapati NK, Gupta S, Narasimhan G, Mazumder R, Loffredo CA, Uren A, Roy R</span>.
<span property="name">Germ-line variants of human N-methylpurine DNA glycosylase show impaired DNA repair activity and facilitate 1,N6 ethenoadenine induced mutations</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">J Biol Chem</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">290</span></span>(<span property="issueNumber">8</span>):4966-80. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25538240" target="_blank">25538240</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Wilson CA and Simonyan V</span>.
<span property="name">FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">PDA J Pharm Sci Technol</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">68</span></span>(<span property="issueNumber">6</span>):626-630. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25475637" target="_blank">25475637</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R</span>.
<span property="name">Census-based rapid and accurate metagenome taxonomic profiling</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">BMC Genomics</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">15</span></span>(<span property="issueNumber">1</span>):918. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25336203" target="_blank">25336203</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R</span>.
<span property="name">Human germline and pan-cancer variomes and their distinct functional profiles</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Nucleic Acids Research</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">42</span></span>(<span property="issueNumber">18</span>):11570-88. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25232094" target="_blank">25232094</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Nayak A, Pattabiraman N, Fadra N, Goldman R, Pond S, Mazumder R</span>.
<span property="name">Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">J Biomol Struct Dyn</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">33</span></span>(<span property="issueNumber">8</span>):1682-94. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/25245635" target="_blank">25245635</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R</span>.
<span property="name">Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Genomics</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">104</span></span>(<span property="issueNumber">1</span>):1-7. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24930720" target="_blank">24930720</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, Simonyan V</span>.
<span property="name">HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">PLOS One</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">9</span></span>(<span property="issueNumber">6</span>):e99033. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24918764" target="_blank">24918764</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R</span>.
<span property="name">A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Biol Direct</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">9</span></span>:9. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24894379" target="_blank">24894379</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Bidzhieva B, Zagorodnyaya T, Karagiannis K, Simonyan V, Laassri M, Chumakov K</span>.
<span property="name">Deep sequencing approach for genetic stability evaluation of influenza A viruses</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">J Virol Methods</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">199</span></span>(<span property="issueNumber">68</span>):75. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24406624" target="_blank">24406624</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Abunimer A, Smith K, Wu T-J, Lam P, Simonyan V, Mazumder R</span>.
<span property="name">Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based variation detection</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Genes</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">5</span></span>(<span property="issueNumber">2</span>):254-69. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24705329" target="_blank">24705329</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Wu T-J, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R</span>.
<span property="name">A framework for organizing cancer related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Database</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2014</span></span>:bau022. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24667251" target="_blank">24667251</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Dabrazhynetskaya A, Soika V, Volokhov D, Simonyan V, Chizhikov V</span>.
<span property="name">Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Genome Announce</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2</span></span>(<span property="issueNumber">2</span>):pii: e00127-14. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24604646" target="_blank">24604646</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Cole C, Krampis K, Karagiannis K, Almeida J, Faison JW, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R</span>.
<span property="name">Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">BMC Bioinformatics</span>.
<span property="datePublished">2014</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">15</span></span>:28. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24467687" target="_blank">24467687</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Mudvari P, Kowsari K, Cole C, Mazumder R, Horvath A</span>.
<span property="name">Extraction of molecular features through exome to transcriptome alignment</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">J Metabol Sys Biol</span>.
<span property="datePublished">2013</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">1</span></span>(<span property="issueNumber">1</span>):7. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/24791251" target="_blank">24791251</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Basuchoudhary A, Simonyan V, Mazumder R</span>.
<span property="name">Community annotation and the evolution of cooperation: How patience matters</span>.
<span property="isPartOf" typeof="PublicationIssue"></span>
<span property="name" typeof="Periodical">Open Bioinformatics Journal</span>.
<span property="datePublished">2013</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">7</span></span>:9-18.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Karagiannis K, Simonyan V, Mazumder R</span>.
<span property="name">SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Genomics Proteomics Bioinformatics</span>.
<span property="datePublished">2013</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">11</span></span>(<span property="issueNumber">2</span>):122-126. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/23618375" target="_blank">23618375</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Lam PV, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, Mazumder R</span>.
<span property="name">Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Genomics Proteomics Bioinformatics</span>.
<span property="datePublished">2013</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">11</span></span>(<span property="issueNumber">2</span>):96-104. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/23459159" target="_blank">23459159</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, Mazumder R</span>.
<span property="name">Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">FEBS J</span>.
<span property="datePublished">2013</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">280</span></span>(<span property="issueNumber">6</span>):1542-1562. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/23350563" target="_blank">23350563</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R</span>.
<span property="name">Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Database (Oxford)</span>.
<span property="datePublished">2012</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">2012</span></span>:bas036. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/23110974" target="_blank">23110974</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE</span>.
<span property="name">RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene phylogenetic analysis and identification of the species of the family Mycoplasmataceae</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">Mol Phylogenet Evol</span>.
<span property="datePublished">2012</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">62</span></span>(<span property="issueNumber">1</span>):515-28. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/22115576" target="_blank">22115576</a></span>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="ScholarlyArticle"><p>
<span property="author">Mazumder R, Morampudi KS, Motwani M, Vasudevan S, Goldman R</span>.
<span property="name">Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes</span>.
<span property="isPartOf" typeof="PublicationIssue"><span property="name" typeof="Periodical">PLoS One</span>.
<span property="datePublished">2012</span>;
<span property="isPartOf" typeof="PublicationVolume"><span property="volumeNumber">7</span></span>(<span property="issueNumber">5</span>):e36212. PMID: <a property="sameAs" href="https://www.ncbi.nlm.nih.gov/pubmed/22586465" target="_blank">22586465</a></span>.
</p></div>
</li>
</ol>
</td>
</tr>
<tr>
<td style="width:100%; vertical-align: top;" colspan="2"><br>
<h3 id="Multimedia">HIVE Team Multimedia:</h3>
<a href="#Top">Back to Top (Publications)</a> | <a href="#Multimedia">Jump to Multimedia</a> | <a href="#Posters">Jump to Posters</a> | <a href="#Other">Jump to Other Works</a><br><br>
</td>
</tr>
<tr style="height: 13px;">
<td style="width: 40px; text-align: right; vertical-align: top; height: 13px;"> </td>
<td style="width: 1428px; height: 13px; vertical-align: top;"><br />
<ol>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">BioCompute Workshop 2022: New tools for building BioCompute Objects on DNAnexus, Seven Bridges, and Galaxy for deposit to an access-controlled BioComputeDB</span></b><br>
Presented by: <span property="author">Charles Hadley King</span>,
<span property="author">Jonathon Keeney</span>,
<span property="author">Dennis Dean</span>,
<span property="author">Omar Serang</span>,
<span property="author">Sam Westreich</span>,
<span property="author">Nicola Soranzo</span><br>
Published <span property="datePublished">Sept 13, 2022</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/DcjhuyfUJz8" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">
Introduction slides: <a href="HTMLROOT/content/media/introKeeney.pdf">Introduction_keeney.pdf </a></span>
BioComputeDB slides: <a href="HTMLROOT/content/media/WorkshopSlides_2022_HK.pdf">BCO Portal and BCODB.pdf </a></span>
DNAnexus slides: <a href="HTMLROOT/content/media/BCO Workshop Slides-DNAnexus.pdf">BCO Workshop Slides-DNAnexus.pdf </a></span>
Seven Bridges slides: <a href="HTMLROOT/content/media/BCO Workshop 2022-SB.pdf">BCO Workshop Slides-SevenBridges.pdf </a></span>
Galaxy slides: <a href="HTMLROOT/content/media/Intro to galaxy.pdf">Intro to Galaxy.pdf </a></span>
</span><br>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name"> Publication of BioCompute Objects (IEEE-2791-2020) from Galaxy Workfloow Invocations</span></b><br>
Presendted by <span property="author">Charles Hadley King</span>
at <span property="superEvent" typeof="Event"><a href="https://galaxyproject.org/events/gcc2021/">2021 Galaxy Community Conference (GCC2021)</a></span><br>
Published <span property="datePublished">July 8th, 2021</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://player.vimeo.com/video/567195992" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">
<a href="https://f1000research.com/posters/10-603" target="_blank">Poster</a>
<a href="https://static.sched.com/hosted_files/gcc2021/5d/abstract46.pdf" target="_blank">Abstract</a>
<a href="https://f1000research.com/slides/10-602" target="_blank">Slides</a>
</span><br>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">HIVE Seminar 2: Analysis of RNA-Seq Data in HIVE</span></b><br>
Presented by: <span property="author">Luis Santos-Quintero</span>,
<span property="author">Jonathon Keeney</span>,
<span property="editor">Raja Mazumder</span><br>
Published <span property="datePublished">June 4th, 2021</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/FRct48SuxFk" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name"> HIVE Seminar 1: Novel Approach for Identification of Defective Viral Genomes using NGS Data </span></b><br>
Featuring <span property="author"> Konstantinos Karagiannis, Ph.D. </span>,
Edited by <span property="editor"> Jonathon Keeney </span><br>
Published <span property="datePublished"> 2/22/2021 </span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/m0-RDLvWzgU" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract"> Defective viral genomes (DVGs) are spontaneously generated by most viruses due to errors in the replication process and cannot replicate in the absence of a non-defective helper virus. Some DVGs are recognized to be important triggers of the antiviral innate immune response, and have therefore gained interest for their potential to alter the attenuation and immunogenicity of vaccines. High-throughput sequencing (HTS) is a powerful way to look for DVGs and has an advantage over conventional methods like RT-PCR, which can detect only primer-specific species, but HTS requires careful data analysis to be applicable.<br>
The DVG-profiler algorithm is a novel approach to accurately detect the DVGs in HTS data as a post sequence alignment process, and is useful for both basic virus research and for monitoring live attenuated vaccines for DVG content.</span><br>
Relevant publications:
<a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216944">10.1371/journal.pone.0216944</a> ;
<a href="https://msphere.asm.org/content/5/5/e00551-20">https://msphere.asm.org/content/5/5/e00551-20</a><br>
Lecture slides: <a href="HTMLROOT/content/media/HIVE_seminar_DVG_KKaragiannis_22_02_2021.pdf">HIVE_seminar_DVG_KKaragiannis_22_02_2021.pdf </a></span>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">Microbiome: VA AI Tech Sprint 2021 | Phase 2 Demo</span></b><br>
Featuring <span property="author">Stephanie Singleton</span>,
Edited by <span property="editor">James Ziegler</span><br>
Published <span property="datePublished">December 8th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/K2S7YrIBN_0" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">Phase 2 Demo.
View our <a href="https://youtu.be/RRm6-kCGegE">MATLAB Prototype Demo</a>.<br>
View our <a href="https://tinyurl.com/phase-2-demo-slides">Phase 2 Demo Slides</a></span>.<br>
This video is a part of the <a href="https://hive.biochemistry.gwu.edu/gfkb">Microbiome Project</a>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">VA AI Tech Sprint Phase 3 Final Demo | GWU HIVE</span></b><br>
Presented by <span property="author">Stephanie Singleton</span>,
<span property="author">James Ziegler</span>,
Edited by <span property="editor">James Ziegler</span><br>
Published <span property="datePublished">April 20th, 2021</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/CgIwy_zfn9g" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">View our <a href="https://tinyurl.com/Final-Demo-Materials">materials</a>.</span><br>
This video is a part of the <a href="https://hive.biochemistry.gwu.edu/gfkb">Microbiome Project</a>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">BioCompute: The Error Domain</span></b><br>
Edited by <span property="editor">James Ziegler</span><br>
Published <span property="datePublished">January 14, 2021</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/k2IZCpMXDCE" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">The Error Domain of a BCO is useful for reporting the accuracy and precision of your analysis pipeline. Find out more by watching this video.</span><br>
This video is a part of the <a href="https://www.biocomputeobject.org">BioCompute Objects Project</a>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">BioCompute: An Introduction to the Project</span></b><br>
Featuring <span property="author">Raja Mazumder</span>,
Edited by <span property="editor">James Ziegler</span><br>
Published <span property="datePublished">December 8th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/S9CrDF4a8bQ" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">If you're new to BioCompute Objects, you've come to the right place. This video discusses the story behind the creation of BioCompute and how the project has become so important to the world of bioinformatics.<br>
BioCompute is a standardized way to communicate an analysis pipeline. BioCompute substantially improves the clarity and reproducibility of analysis and can be packaged with other standards, such as the Common Workflow Language. An analysis that is reported in a way that conforms to the BioCompute specification is called a BioCompute Object (BCO). A BCO provides the structure that dictates what information must be present in a report.</span><br>
This video is a part of the <a href="https://www.biocomputeobject.org">BioCompute Objects Project</a>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">BioCompute: Description Domain Tutorial</span></b><br>
Edited by <span property="editor">James Ziegler</span><br>
Published <span property="datePublished">December 2nd, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/OE_V0LkePu4" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">Want to know more about the Description Domain of a BCO? You've come to the right place. The purpose of the Description Domain is to put the actual steps, process, and information related to executing the experiment.</span><br>
This video is a part of the <a href="https://www.biocomputeobject.org">BioCompute Objects Project</a>.
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name"> Implementation of the IEEE-2791-2020 standard (BioCompute Objects) in Galaxy via workflow invocations</span></b><br>
Presendted by <span property="author">Charles Hadley King</span>
at <span property="superEvent" typeof="Event"><a href="https://bcc2020.github.io/" target="_blank">Bioinformatics Community Conference 2020</a></span><br>
Published <span property="datePublished">July 20th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://player.vimeo.com/video/437704225" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">
<a href="https://static.sched.com/hosted_files/bcc2020/07/BCC2020_abstract_63.pdf" target="_blank">Abstract</a>
</span><br>
</p></div>
</li>
<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">Development of BioCompute Objects for Integration into Galaxy in a Cloud Computing Environment</span></b><br>
Presented by <span property="author">Raja Mazumder</span>,
<span property="author">Jonathon Keeney</span>,
<span property="author">Charles Hadley King</span>, and
<span property="author">Janisha Patel</span>.<br>
Published <span property="datePublished">April 15th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/8pwss1SY8Tg" style="border:0;" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">BioCompute objects allow researchers to describe bioinformatic analyses comprised of any number of algorithmic steps and variables to make computational experimental results clearly understandable and easier to repeat. This project will create a library of BioCompute objects that describe bioinformatic workflows on AWS, which can be accessed and contributed to by users of the widely used bioinformatics platform, Galaxy.</span>
Presented at the <a href="https://www.internet2.edu/vision-initiatives/initiatives/exploring-clouds-acceleration-science/">Exploring Clouds for Acceleration of Science (E-CAS)</a> panel during the <span property="superEvent" typeof="Event">Internet2 Global Summit</span>
<span property="video" typeof="url"><a href="https://youtu.be/8pwss1SY8Tg?list=PLLIsQFBBoJG8EWC0DDwehjCn56mejEtCA" target="_blank" style="color:blue">(Open Video on YouTube)</a></span><br>
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<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">How to Navigate Through Matlab to Perform Machine Learning Analysis on Metagenomics Data</span></b><br>
Presented by <span property="author">Lindsay Hopson</span>,
Edited by <span property="editor">James Ziegler</span>
<br>
Published <span property="datePublished">October 30th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/Q3ZCwV2touQ" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">This video is a step-by-step demonstration of how to navigate through Matlab's Statistics and Machine Learning toolbox to perform machine learning analysis on metagenomics data. By watching this video, one is able to become familiar with basic machine learning concepts to review and ideas to take your own biological data analysis to a new level.</span>
This video is a part of the Microbiome Project's <a href="https://hive.biochemistry.gwu.edu/gfkb">GutFeeling KnowledgeBase</a>
<span property="video" typeof="url"><a href="https://www.youtube.com/watch?v=Q3ZCwV2touQ&t=18s" target="_blank">(Open Video on YouTube)</a></span>
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<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">OncoMX: A Cancer Biomarker Database, Explained</span></b><br>
Presented by <span property="author">OncoMX Team</span>,
Edited by <span property="editor">James Ziegler</span>
<br>
Published <span property="datePublished">November 4th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/h_TZQYzlp04" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">This explainer video shows a few of the features and datasets available in OncoMX, a cancer biomarker database with mutation and expression metadata related to the study of cancer alongside relevant experimental and functional annotations. </span>
This video is a part of the <a href="https://www.oncomx.org">OncoMX Project</a>.
<span property="video" typeof="url"><a href="https://www.youtube.com/watch?v=h_TZQYzlp04" target="_blank">(Open Video on YouTube)</a></span>
</p></div>
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<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">BioCompute Objects: Tree View Tutorial</span></b><br>
Produced by <span property="producer">James Ziegler</span> and
<span property="voice over">Jonathon Keeney</span>
<br>
Published <span property="datePublished">September 21st, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/cs3qCpIdRMw" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">Welcome to the first tutorial video of many in this series! Join us as we discuss JSON Files and Tree View Tools for BioCompute Objects and how powerful these tools are when reporting pipeline steps. </span>
This video is a part of the <a href="https://www.biocomputeobject.org">BioCompute Objects Project</a>.
</p></div>
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<li>
<div vocab="http://schema.org" typeof="VideoObject"><p>
<b><span property="name">OncoMX: COVID-19 Biomarker Knowledgebase</span></b><br>
Presented by <span property="author">Niharika Chandna</span>,
<span property="author">Noyanika Vattathara</span>,
Edited by <span property="editor">James Ziegler</span>
<br>
Published <span property="datePublished">November 20th, 2020</span><br>
<!-- Select the "copy the embed code" from the YouTube video and paste it below -->
<iframe width="420" height="236.25" src="https://www.youtube.com/embed/YJ9kUMusD_k" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br><span property="abstract">Get an overview of COVID-19 Biomarker Knowledge-base project that aims to bring together biomarker data from publications and bioinformatic databases that will assist researchers working on the development of diagnostics or drugs. </span>
This video is a part of the <a href="https://www.oncomx.org">OncoMX Project</a>.
</p></div>
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<br>
<h3 id="Posters">HIVE Team Selected Posters:</h3>
<a href="#Top">Back to Top (Publications)</a> | <a href="#Multimedia">Jump to Multimedia</a> | <a href="#Posters">Jump to Posters</a> | <a href="#Other">Jump to Other Works</a><br><br>
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<ol>
<li>
<p typeof="Event">
<span property="name">Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations</span>,
presented by <span property="performer" typeof="Person">Charles Hadley King</span>
at the <span property="superEvent" typeof="Event"><a href="https://galaxyproject.org/events/gcc2021/">2021 Galaxy Community Conference (GCC2021)</a></span>,
<span property="startDate" content="2015-11-16">July 8th, 2021</span>.
<span property="image" typeof="URL"><a href="https://f1000research.com/posters/10-603" style="color:blue">Link</a></span></p>
</li>
<li>
<p typeof="Event">
<span property="name">HIVE Pathogen Detection Pipeline</span>,
presented by <span property="performer" typeof="Person">Ekaterina Osipova</span>
at the <span property="superEvent" typeof="Event">1st Annual Office of Biostatistics and Epidemiology (OBE) Research Day: Advancing Regulatory Sciences</span>,
<span property="startDate" content="2015-11-16">November 16, 2015</span>,
<span property="location">Silver Spring, MD</span>.
<span property="image" typeof="URL"><a href="HTMLROOT/content/PathogenPoster.pdf" style="color:blue">(view as pdf)</a></span></p>
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<li>
<p>
<span typeof="Event">
<span property="name">Assessing the Immunoglobulin Repertoire by Next-Generation Sequencing using HIVE tools</span>,
presented by HIVE user <span property="performer" typeof="Person">Andrea Siegel</span>
at the <span property="superEvent" typeof="Event">3rd Annual Scientific Computing Day</span>,
<span property="startDate" content="2015-09-08">September 8</span>-
<span property="endDate" content="2015-09-09">9, 2015</span>,
<span property="location">Silver Spring, MD</span>.
<span property="image" typeof="URL"><a href="HTMLROOT/content/Immunoglobulin.pdf" style="color:blue">(view as pdf)</a></span>
</span>