{"id":"https://openalex.org/W2018586580","doi":"https://doi.org/10.1147/jrd.2011.2163276","title":"Modeling mutations of influenza virus with IBM Blue Gene","display_name":"Modeling mutations of influenza virus with IBM Blue Gene","publication_year":2011,"publication_date":"2011-09-01","ids":{"openalex":"https://openalex.org/W2018586580","doi":"https://doi.org/10.1147/jrd.2011.2163276","mag":"2018586580"},"language":"en","primary_location":{"id":"doi:10.1147/jrd.2011.2163276","is_oa":false,"landing_page_url":"https://doi.org/10.1147/jrd.2011.2163276","pdf_url":null,"source":{"id":"https://openalex.org/S4210219925","display_name":"IBM Journal of Research and Development","issn_l":"0018-8646","issn":["0018-8646","2151-8556"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320652","host_organization_name":"IBM","host_organization_lineage":["https://openalex.org/P4310320652"],"host_organization_lineage_names":["IBM"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IBM Journal of Research and Development","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108561039","display_name":"Zhen Xia","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Z. Xia","raw_affiliation_strings":["Department of Biomedical Engineering, The University of Texas at Austin, Austin , TX, USA","Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX;"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, The University of Texas at Austin, Austin , TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064335115","display_name":"Payel Das","orcid":"https://orcid.org/0000-0002-7288-0516"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]},{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Das","raw_affiliation_strings":["IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#"],"affiliations":[{"raw_affiliation_string":"IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I4210114115"]},{"raw_affiliation_string":"IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034869508","display_name":"Thanhthao Huynh","orcid":"https://orcid.org/0000-0002-9171-3537"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]},{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Huynh","raw_affiliation_strings":["IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#"],"affiliations":[{"raw_affiliation_string":"IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I4210114115"]},{"raw_affiliation_string":"IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022453482","display_name":"Ajay K. Royyuru","orcid":"https://orcid.org/0000-0003-4440-4755"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]},{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. K. Royyuru","raw_affiliation_strings":["IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#"],"affiliations":[{"raw_affiliation_string":"IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I4210114115"]},{"raw_affiliation_string":"IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078014032","display_name":"Ruhong Zhou","orcid":"https://orcid.org/0000-0001-8624-5591"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]},{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Zhou","raw_affiliation_strings":["IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#"],"affiliations":[{"raw_affiliation_string":"IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I4210114115"]},{"raw_affiliation_string":"IBM Research, Division Thomas J. Watson Research Center, Yorktown Heights, NY#TAB#","institution_ids":["https://openalex.org/I1341412227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5108561039"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":null,"apc_paid":null,"fwci":0.1956,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.58339403,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"55","issue":"5","first_page":"7:1","last_page":"7:11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9768999814987183,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ibm","display_name":"IBM","score":0.7636221647262573},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.7108058929443359},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.5834230780601501},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5651717185974121},{"id":"https://openalex.org/keywords/influenza-a-virus","display_name":"Influenza A virus","score":0.48149383068084717},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4581959843635559},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.38928645849227905},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33316245675086975},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14618957042694092}],"concepts":[{"id":"https://openalex.org/C70388272","wikidata":"https://www.wikidata.org/wiki/Q5968558","display_name":"IBM","level":2,"score":0.7636221647262573},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.7108058929443359},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.5834230780601501},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5651717185974121},{"id":"https://openalex.org/C2777546802","wikidata":"https://www.wikidata.org/wiki/Q834390","display_name":"Influenza A virus","level":3,"score":0.48149383068084717},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4581959843635559},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.38928645849227905},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33316245675086975},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14618957042694092},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1147/jrd.2011.2163276","is_oa":false,"landing_page_url":"https://doi.org/10.1147/jrd.2011.2163276","pdf_url":null,"source":{"id":"https://openalex.org/S4210219925","display_name":"IBM Journal of Research and Development","issn_l":"0018-8646","issn":["0018-8646","2151-8556"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320652","host_organization_name":"IBM","host_organization_lineage":["https://openalex.org/P4310320652"],"host_organization_lineage_names":["IBM"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IBM Journal of Research and Development","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8700000047683716,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307762","display_name":"International Business Machines Corporation","ror":"https://ror.org/05hh8d621"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1974185791","https://openalex.org/W1974694453","https://openalex.org/W1979158913","https://openalex.org/W1983051226","https://openalex.org/W1988533731","https://openalex.org/W1990627326","https://openalex.org/W1992452843","https://openalex.org/W1993610826","https://openalex.org/W1997343899","https://openalex.org/W1998561673","https://openalex.org/W2001903814","https://openalex.org/W2011779648","https://openalex.org/W2022879191","https://openalex.org/W2024553805","https://openalex.org/W2026391844","https://openalex.org/W2030216750","https://openalex.org/W2031908280","https://openalex.org/W2032946695","https://openalex.org/W2037652551","https://openalex.org/W2043429268","https://openalex.org/W2044054342","https://openalex.org/W2044525257","https://openalex.org/W2046378278","https://openalex.org/W2049105549","https://openalex.org/W2049740179","https://openalex.org/W2056213072","https://openalex.org/W2061277189","https://openalex.org/W2062119305","https://openalex.org/W2066218699","https://openalex.org/W2066787645","https://openalex.org/W2067284235","https://openalex.org/W2068944150","https://openalex.org/W2075468840","https://openalex.org/W2078149659","https://openalex.org/W2078889580","https://openalex.org/W2099487753","https://openalex.org/W2099933160","https://openalex.org/W2102335249","https://openalex.org/W2102406806","https://openalex.org/W2102640727","https://openalex.org/W2109539263","https://openalex.org/W2112934045","https://openalex.org/W2114289644","https://openalex.org/W2120113718","https://openalex.org/W2121378139","https://openalex.org/W2124448263","https://openalex.org/W2129375624","https://openalex.org/W2131492616","https://openalex.org/W2133585817","https://openalex.org/W2138928225","https://openalex.org/W2144718643","https://openalex.org/W2146982119","https://openalex.org/W2148712714","https://openalex.org/W2155761127","https://openalex.org/W2158892874","https://openalex.org/W2159367911","https://openalex.org/W2160364329","https://openalex.org/W3022728992","https://openalex.org/W3099289621"],"related_works":["https://openalex.org/W2016551366","https://openalex.org/W2188759708","https://openalex.org/W2138564085","https://openalex.org/W2123163123","https://openalex.org/W4386371748","https://openalex.org/W2147145791","https://openalex.org/W2162191803","https://openalex.org/W4389981580","https://openalex.org/W2023372797","https://openalex.org/W2682601159"],"abstract_inverted_index":{"Outbreaks":[0],"of":[1,13,23,29,217],"influenza":[2,30,89,219],"cause":[3,71],"considerable":[4],"public":[5],"health":[6],"concerns":[7],"and":[8,67,137,184,222],"pose":[9],"a":[10,14,103,113,145,179,204,214],"potential":[11],"threat":[12],"global":[15],"pandemic.":[16],"In":[17],"this":[18],"paper,":[19],"we":[20,142],"describe":[21],"some":[22],"our":[24],"recent":[25,172],"work":[26],"on":[27,134,149],"modeling":[28],"virus":[31,201,220],"with":[32,171],"an":[33],"IBM":[34],"Blue":[35],"Gene\u00ae":[36],"supercomputer.":[37],"The":[38],"goal":[39],"is":[40],"to":[41,53,76,81,95,97,111,117,129,196,202],"predict":[42,118],"which":[43,60,68,108],"mutations":[44,61,69],"[on":[45],"the":[46,56,99,131,135,154,189,200,207,218],"viral":[47],"glycoprotein":[48],"hemagglutinin":[49],"(HA)]":[50],"are":[51],"likely":[52],"occur":[54],"in":[55,168,206],"next":[57],"flu":[58],"season,":[59],"might":[62,70],"escape":[63],"antibody":[64],"(Ab)":[65],"neutralization,":[66],"its":[72],"receptor":[73,223],"binding":[74,156,192,224],"specificity":[75,193],"switch":[77,188],"(e.g.,":[78],"from":[79,93,194],"avian":[80,195],"human).":[82],"We":[83,121,175],"have":[84],"analyzed":[85],"more":[86],"than":[87],"4,000":[88],"A/H3N2":[90],"HA":[91,151,191],"sequences":[92],"1968":[94],"2010":[96],"model":[98],"evolutionary":[100],"path":[101],"using":[102],"weighted":[104],"mutual":[105],"information":[106],"method,":[107],"allows":[109],"us":[110],"build":[112],"site":[114],"transition":[115],"network":[116],"antigenic":[119],"drifts.":[120],"then":[122],"used":[123],"large-scale":[124],"free":[125],"energy":[126],"perturbation":[127],"calculations":[128],"study":[130],"mutation-induced":[132],"effects":[133],"antigen\u2013Ab":[136],"antigen\u2013receptor":[138],"bindings.":[139],"For":[140],"example,":[141],"found":[143,177],"that":[144,178],"single":[146],"mutation":[147],"T131I":[148],"H3N2":[150],"can":[152],"decrease":[153],"HA\u2013Ab":[155],"affinity":[157],"by":[158],"5.2":[159],"<formula":[160],"formulatype=\"inline\"":[161],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[162],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">":[163],"<tex":[164],"Notation=\"TeX\">$\\pm$</tex></formula>":[165],"0.9":[166],"kcal/mol,":[167],"excellent":[169],"agreement":[170],"experimental":[173],"results.":[174],"also":[176,212],"double":[180],"mutation,":[181],"i.e.,":[182],"V135S":[183],"A138S,":[185],"could":[186],"potentially":[187],"H5N1":[190],"human,":[197],"thus":[198],"allowing":[199],"gain":[203],"foothold":[205],"human":[208],"population.":[209],"Detailed":[210],"analyses":[211],"reveal":[213],"molecular":[215],"picture":[216],"Ab":[221],"mechanisms.":[225]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
