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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species
<xref ref-type="fn" rid="FN3"><sup>▿</sup></xref><xref ref-type="fn" rid="FN1">‡</xref><xref ref-type="fn" rid="FN4">#</xref></title><author><name sortKey="Gillespie, Joseph J" sort="Gillespie, Joseph J" uniqKey="Gillespie J" first="Joseph J." last="Gillespie">Joseph J. Gillespie</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland 21201</nlm:aff></affiliation></author><author><name sortKey="Wattam, Alice R" sort="Wattam, Alice R" uniqKey="Wattam A" first="Alice R." last="Wattam">Alice R. Wattam</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Cammer, Stephen A" sort="Cammer, Stephen A" uniqKey="Cammer S" first="Stephen A." last="Cammer">Stephen A. Cammer</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Gabbard, Joseph L" sort="Gabbard, Joseph L" uniqKey="Gabbard J" first="Joseph L." last="Gabbard">Joseph L. Gabbard</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Shukla, Maulik P" sort="Shukla, Maulik P" uniqKey="Shukla M" first="Maulik P." last="Shukla">Maulik P. Shukla</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Dalay, Oral" sort="Dalay, Oral" uniqKey="Dalay O" first="Oral" last="Dalay">Oral Dalay</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Driscoll, Timothy" sort="Driscoll, Timothy" uniqKey="Driscoll T" first="Timothy" last="Driscoll">Timothy Driscoll</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Hix, Deborah" sort="Hix, Deborah" uniqKey="Hix D" first="Deborah" last="Hix">Deborah Hix</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Mane, Shrinivasrao P" sort="Mane, Shrinivasrao P" uniqKey="Mane S" first="Shrinivasrao P." last="Mane">Shrinivasrao P. Mane</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Mao, Chunhong" sort="Mao, Chunhong" uniqKey="Mao C" first="Chunhong" last="Mao">Chunhong Mao</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Nordberg, Eric K" sort="Nordberg, Eric K" uniqKey="Nordberg E" first="Eric K." last="Nordberg">Eric K. Nordberg</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Scott, Mark" sort="Scott, Mark" uniqKey="Scott M" first="Mark" last="Scott">Mark Scott</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Schulman, Julie R" sort="Schulman, Julie R" uniqKey="Schulman J" first="Julie R." last="Schulman">Julie R. Schulman</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Snyder, Eric E" sort="Snyder, Eric E" uniqKey="Snyder E" first="Eric E." last="Snyder">Eric E. Snyder</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">HHS/NIH/NCI SRA International, Inc., Rockville, Maryland 20852-4902</nlm:aff></affiliation></author><author><name sortKey="Sullivan, Daniel E" sort="Sullivan, Daniel E" uniqKey="Sullivan D" first="Daniel E." last="Sullivan">Daniel E. Sullivan</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Wang, Chunxia" sort="Wang, Chunxia" uniqKey="Wang C" first="Chunxia" last="Wang">Chunxia Wang</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Novozymes Biologicals, Inc., Salem, Virginia 24153</nlm:aff></affiliation></author><author><name sortKey="Warren, Andrew" sort="Warren, Andrew" uniqKey="Warren A" first="Andrew" last="Warren">Andrew Warren</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Williams, Kelly P" sort="Williams, Kelly P" uniqKey="Williams K" first="Kelly P." last="Williams">Kelly P. Williams</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Sandia National Laboratories, MS 9291, Livermore, California 94551-0969</nlm:aff></affiliation></author><author><name sortKey="Xue, Tian" sort="Xue, Tian" uniqKey="Xue T" first="Tian" last="Xue">Tian Xue</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Seung Yoo, Hyun" sort="Seung Yoo, Hyun" uniqKey="Seung Yoo H" first="Hyun" last="Seung Yoo">Hyun Seung Yoo</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Zhang, Chengdong" sort="Zhang, Chengdong" uniqKey="Zhang C" first="Chengdong" last="Zhang">Chengdong Zhang</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Zhang, Yan" sort="Zhang, Yan" uniqKey="Zhang Y" first="Yan" last="Zhang">Yan Zhang</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Will, Rebecca" sort="Will, Rebecca" uniqKey="Will R" first="Rebecca" last="Will">Rebecca Will</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Kenyon, Ronald W" sort="Kenyon, Ronald W" uniqKey="Kenyon R" first="Ronald W." last="Kenyon">Ronald W. Kenyon</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Sobral, Bruno W" sort="Sobral, Bruno W" uniqKey="Sobral B" first="Bruno W." last="Sobral">Bruno W. Sobral</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21896772</idno><idno type="pmc">3257917</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257917</idno><idno type="RBID">PMC:3257917</idno><idno type="doi">10.1128/IAI.00207-11</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000689</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species
<xref ref-type="fn" rid="FN3"><sup>▿</sup></xref><xref ref-type="fn" rid="FN1">‡</xref><xref ref-type="fn" rid="FN4">#</xref></title><author><name sortKey="Gillespie, Joseph J" sort="Gillespie, Joseph J" uniqKey="Gillespie J" first="Joseph J." last="Gillespie">Joseph J. Gillespie</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland 21201</nlm:aff></affiliation></author><author><name sortKey="Wattam, Alice R" sort="Wattam, Alice R" uniqKey="Wattam A" first="Alice R." last="Wattam">Alice R. Wattam</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Cammer, Stephen A" sort="Cammer, Stephen A" uniqKey="Cammer S" first="Stephen A." last="Cammer">Stephen A. Cammer</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Gabbard, Joseph L" sort="Gabbard, Joseph L" uniqKey="Gabbard J" first="Joseph L." last="Gabbard">Joseph L. Gabbard</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Shukla, Maulik P" sort="Shukla, Maulik P" uniqKey="Shukla M" first="Maulik P." last="Shukla">Maulik P. Shukla</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Dalay, Oral" sort="Dalay, Oral" uniqKey="Dalay O" first="Oral" last="Dalay">Oral Dalay</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Driscoll, Timothy" sort="Driscoll, Timothy" uniqKey="Driscoll T" first="Timothy" last="Driscoll">Timothy Driscoll</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Hix, Deborah" sort="Hix, Deborah" uniqKey="Hix D" first="Deborah" last="Hix">Deborah Hix</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Mane, Shrinivasrao P" sort="Mane, Shrinivasrao P" uniqKey="Mane S" first="Shrinivasrao P." last="Mane">Shrinivasrao P. Mane</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Mao, Chunhong" sort="Mao, Chunhong" uniqKey="Mao C" first="Chunhong" last="Mao">Chunhong Mao</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Nordberg, Eric K" sort="Nordberg, Eric K" uniqKey="Nordberg E" first="Eric K." last="Nordberg">Eric K. Nordberg</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Scott, Mark" sort="Scott, Mark" uniqKey="Scott M" first="Mark" last="Scott">Mark Scott</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Schulman, Julie R" sort="Schulman, Julie R" uniqKey="Schulman J" first="Julie R." last="Schulman">Julie R. Schulman</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Snyder, Eric E" sort="Snyder, Eric E" uniqKey="Snyder E" first="Eric E." last="Snyder">Eric E. Snyder</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">HHS/NIH/NCI SRA International, Inc., Rockville, Maryland 20852-4902</nlm:aff></affiliation></author><author><name sortKey="Sullivan, Daniel E" sort="Sullivan, Daniel E" uniqKey="Sullivan D" first="Daniel E." last="Sullivan">Daniel E. Sullivan</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Wang, Chunxia" sort="Wang, Chunxia" uniqKey="Wang C" first="Chunxia" last="Wang">Chunxia Wang</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">Novozymes Biologicals, Inc., Salem, Virginia 24153</nlm:aff></affiliation></author><author><name sortKey="Warren, Andrew" sort="Warren, Andrew" uniqKey="Warren A" first="Andrew" last="Warren">Andrew Warren</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Williams, Kelly P" sort="Williams, Kelly P" uniqKey="Williams K" first="Kelly P." last="Williams">Kelly P. Williams</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Sandia National Laboratories, MS 9291, Livermore, California 94551-0969</nlm:aff></affiliation></author><author><name sortKey="Xue, Tian" sort="Xue, Tian" uniqKey="Xue T" first="Tian" last="Xue">Tian Xue</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Seung Yoo, Hyun" sort="Seung Yoo, Hyun" uniqKey="Seung Yoo H" first="Hyun" last="Seung Yoo">Hyun Seung Yoo</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Zhang, Chengdong" sort="Zhang, Chengdong" uniqKey="Zhang C" first="Chengdong" last="Zhang">Chengdong Zhang</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Zhang, Yan" sort="Zhang, Yan" uniqKey="Zhang Y" first="Yan" last="Zhang">Yan Zhang</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Will, Rebecca" sort="Will, Rebecca" uniqKey="Will R" first="Rebecca" last="Will">Rebecca Will</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Kenyon, Ronald W" sort="Kenyon, Ronald W" uniqKey="Kenyon R" first="Ronald W." last="Kenyon">Ronald W. Kenyon</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author><author><name sortKey="Sobral, Bruno W" sort="Sobral, Bruno W" uniqKey="Sobral B" first="Bruno W." last="Sobral">Bruno W. Sobral</name><affiliation><nlm:aff id="aff1">Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</nlm:aff></affiliation></author></analytic><series><title level="j">Infection and Immunity</title><idno type="ISSN">0019-9567</idno><idno type="eISSN">1098-5522</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Funded by the National Institute of Allergy and Infectious Diseases, the <underline>Pat</underline>hosystems <underline>R</underline>esource <underline>I</underline>ntegration <underline>C</underline>enter (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided.</p></div></front></TEI><pmc article-type="review-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Infect Immun</journal-id><journal-id journal-id-type="iso-abbrev">Infect. Immun</journal-id><journal-id journal-id-type="hwp">iai</journal-id><journal-id journal-id-type="pmc">iai</journal-id><journal-id journal-id-type="publisher-id">IAI</journal-id><journal-title-group><journal-title>Infection and Immunity</journal-title></journal-title-group><issn pub-type="ppub">0019-9567</issn><issn pub-type="epub">1098-5522</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21896772</article-id><article-id pub-id-type="pmc">3257917</article-id><article-id pub-id-type="publisher-id">0207-11</article-id><article-id pub-id-type="doi">10.1128/IAI.00207-11</article-id><article-categories><subj-group subj-group-type="heading"><subject>Minireview</subject></subj-group></article-categories><title-group><article-title>PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species
<xref ref-type="fn" rid="FN3"><sup>▿</sup></xref><xref ref-type="fn" rid="FN1">‡</xref><xref ref-type="fn" rid="FN4">#</xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Gillespie</surname><given-names>Joseph J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="author-notes" rid="FN2">†</xref></contrib><contrib contrib-type="author"><name><surname>Wattam</surname><given-names>Alice R.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="FN2">†</xref></contrib><contrib contrib-type="author"><name><surname>Cammer</surname><given-names>Stephen A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="FN2">†</xref></contrib><contrib contrib-type="author"><name><surname>Gabbard</surname><given-names>Joseph L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="FN2">†</xref></contrib><contrib contrib-type="author"><name><surname>Shukla</surname><given-names>Maulik P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="author-notes" rid="FN2">†</xref></contrib><contrib contrib-type="author"><name><surname>Dalay</surname><given-names>Oral</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Driscoll</surname><given-names>Timothy</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hix</surname><given-names>Deborah</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mane</surname><given-names>Shrinivasrao P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mao</surname><given-names>Chunhong</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nordberg</surname><given-names>Eric K.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Scott</surname><given-names>Mark</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Schulman</surname><given-names>Julie R.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Snyder</surname><given-names>Eric E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sullivan</surname><given-names>Daniel E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Chunxia</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Warren</surname><given-names>Andrew</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Williams</surname><given-names>Kelly P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Xue</surname><given-names>Tian</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Seung Yoo</surname><given-names>Hyun</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Chengdong</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Yan</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Will</surname><given-names>Rebecca</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kenyon</surname><given-names>Ronald W.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sobral</surname><given-names>Bruno W.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><aff id="aff1"><label>1</label>Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia 24061</aff><aff id="aff2"><label>2</label>Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland 21201</aff><aff id="aff3"><label>3</label>HHS/NIH/NCI SRA International, Inc., Rockville, Maryland 20852-4902</aff><aff id="aff4"><label>4</label>Novozymes Biologicals, Inc., Salem, Virginia 24153</aff><aff id="aff5"><label>5</label>Sandia National Laboratories, MS 9291, Livermore, California 94551-0969</aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Maurelli</surname><given-names>A. T.</given-names></name><role>Editor</role></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>Corresponding author. Mailing address: <addr-line>Cyberinfrastructure Division, Virginia Bioinformatics Institute, Washington Street, MC 0477, Blacksburg, VA 24061</addr-line>. Phone: <phone>(540) 231-2317</phone>. Fax: <fax>(540) 231-6191</fax>. E-mail: <email>sobral@vbi.vt.edu</email>.</corresp><fn id="FN2" fn-type="equal"><label>†</label><p>These authors contributed equally.</p></fn></author-notes><pub-date pub-type="ppub"><month>11</month><year>2011</year></pub-date><pub-date pub-type="pmc-release"><month>11</month><year>2011</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>79</volume><issue>11</issue><fpage>4286</fpage><lpage>4298</lpage><permissions><copyright-statement>Copyright © 2011, American Society for Microbiology. All Rights Reserved.</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>American Society for Microbiology</copyright-holder><license license-type="open-access"><license-p># The authors have paid a fee to allow immediate free access to this paper.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zii01111004286.pdf"></self-uri><abstract><p>Funded by the National Institute of Allergy and Infectious Diseases, the <underline>Pat</underline>hosystems <underline>R</underline>esource <underline>I</underline>ntegration <underline>C</underline>enter (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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