{"id":"https://openalex.org/W2301370215","doi":"https://doi.org/10.1093/bioinformatics/btw007","title":"Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions","display_name":"Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions","publication_year":2016,"publication_date":"2016-01-21","ids":{"openalex":"https://openalex.org/W2301370215","doi":"https://doi.org/10.1093/bioinformatics/btw007","mag":"2301370215","pmid":"https://pubmed.ncbi.nlm.nih.gov/26801959"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/10/1509/24342924/btw007.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/10/1509/24342924/btw007.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009560042","display_name":"Zhen Niu","orcid":"https://orcid.org/0000-0002-4263-8884"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhen Niu","raw_affiliation_strings":["1 Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, WI 53706, USA","2 Wisconsin Institute for Discovery, University of Wisconsin\u2013Madison, Madison, WI 53715, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, WI 53706, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"2 Wisconsin Institute for Discovery, University of Wisconsin\u2013Madison, Madison, WI 53715, USA","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088715947","display_name":"Deborah Chasman","orcid":"https://orcid.org/0000-0002-7324-0131"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deborah Chasman","raw_affiliation_strings":["2 Wisconsin Institute for Discovery, University of Wisconsin\u2013Madison, Madison, WI 53715, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Wisconsin Institute for Discovery, University of Wisconsin\u2013Madison, Madison, WI 53715, USA","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033752290","display_name":"Amie J. Eisfeld","orcid":"https://orcid.org/0000-0003-2231-3107"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amie J. Eisfeld","raw_affiliation_strings":["3 Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2013Madison, Madison, WI, 53711, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2013Madison, Madison, WI, 53711, USA","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076363097","display_name":"Yoshihiro Kawaoka","orcid":"https://orcid.org/0000-0001-5061-8296"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I161296585","display_name":"Tokyo University of Science","ror":"https://ror.org/05sj3n476","country_code":"JP","type":"education","lineage":["https://openalex.org/I161296585"]}],"countries":["JP","US"],"is_corresponding":false,"raw_author_name":"Yoshihiro Kawaoka","raw_affiliation_strings":["3 Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2013Madison, Madison, WI, 53711, USA","4 Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin\u2013Madison, Madison, WI, 53711, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"4 Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I161296585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082616445","display_name":"Sushmita Roy","orcid":"https://orcid.org/0000-0002-3694-1705"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sushmita Roy","raw_affiliation_strings":["1 Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, WI 53706, USA","2 Wisconsin Institute for Discovery, University of Wisconsin\u2013Madison, Madison, WI 53715, USA","5 Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, WI 53792, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Sciences, University of Wisconsin\u2013Madison, Madison, WI 53706, USA","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"2 Wisconsin Institute for Discovery, University of Wisconsin\u2013Madison, Madison, WI 53715, USA","institution_ids":["https://openalex.org/I2802999273","https://openalex.org/I135310074"]},{"raw_affiliation_string":"5 Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, WI 53792, USA","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5082616445"],"corresponding_institution_ids":["https://openalex.org/I135310074","https://openalex.org/I2802999273"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5222,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.70846799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"32","issue":"10","first_page":"1509","last_page":"1517"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.42910000681877136,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.42910000681877136,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.16859999299049377,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.0771000012755394,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6892814636230469},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5998688340187073},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.529737114906311},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.48318734765052795},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44730302691459656},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4431873559951782},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.4360884428024292},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4343678057193756},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.29173049330711365},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.20319366455078125}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6892814636230469},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5998688340187073},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.529737114906311},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.48318734765052795},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44730302691459656},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4431873559951782},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4360884428024292},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4343678057193756},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29173049330711365},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.20319366455078125},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D032921","descriptor_name":"Consensus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/10/1509/24342924/btw007.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26801959","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26801959","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:4775831","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860402","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/10/1509","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/10/1509","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/10/1509/24342924/btw007.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1548779692","https://openalex.org/W1578737958","https://openalex.org/W1997536991","https://openalex.org/W1998015722","https://openalex.org/W2003988251","https://openalex.org/W2010457001","https://openalex.org/W2011226251","https://openalex.org/W2019163875","https://openalex.org/W2028133290","https://openalex.org/W2043698583","https://openalex.org/W2049762266","https://openalex.org/W2058904528","https://openalex.org/W2065180801","https://openalex.org/W2070924692","https://openalex.org/W2074410038","https://openalex.org/W2078950112","https://openalex.org/W2084833542","https://openalex.org/W2087430129","https://openalex.org/W2102158416","https://openalex.org/W2102878257","https://openalex.org/W2108502868","https://openalex.org/W2116376819","https://openalex.org/W2129265801","https://openalex.org/W2131649910","https://openalex.org/W2131848047","https://openalex.org/W2132914434","https://openalex.org/W2141599838","https://openalex.org/W2142011660","https://openalex.org/W2142823706","https://openalex.org/W2151417892","https://openalex.org/W2158128075","https://openalex.org/W2160103276","https://openalex.org/W2167190345","https://openalex.org/W2176433868","https://openalex.org/W2294414050","https://openalex.org/W2792874300","https://openalex.org/W2913340405","https://openalex.org/W2963664118","https://openalex.org/W6675424377","https://openalex.org/W6676223633"],"related_works":["https://openalex.org/W2804364458","https://openalex.org/W2117112636","https://openalex.org/W4298130764","https://openalex.org/W2132641928","https://openalex.org/W4310225030","https://openalex.org/W2090259340","https://openalex.org/W2001981265","https://openalex.org/W2086525401","https://openalex.org/W2083665254","https://openalex.org/W2393816671"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"the":[2,16,70],"shared":[3,67],"and":[4,51,66,145,186,200,205],"pathogen-specific":[5,140],"components":[6,68],"of":[7,18,20,29,38,69,113,150,159,207,212],"host":[8,41,122,208],"transcriptional":[9,42,154],"regulatory":[10,71],"programs":[11],"is":[12,76,221],"important":[13,74],"for":[14,106,181],"understanding":[15],"principles":[17],"regulation":[19],"immune":[21,183],"response.":[22],"Recent":[23],"efforts":[24],"in":[25,34],"systems":[26],"biology":[27],"studies":[28],"infectious":[30],"diseases":[31],"have":[32],"resulted":[33],"a":[35,60,110,114,157,192],"large":[36],"collection":[37],"datasets":[39],"measuring":[40],"response":[43,123,155,209],"to":[44,49,63,77,87,118,143,152,156,172,196,210],"various":[45],"pathogens.":[46],"Computational":[47],"methods":[48],"identify":[50,64,78,197],"compare":[52],"gene":[53,81,201],"expression":[54,82],"modules":[55,83,124],"across":[56],"different":[57,213],"infections":[58,126],"offer":[59],"powerful":[61],"way":[62],"strain-specific":[65,121],"program.":[72],"An":[73],"challenge":[75],"statistically":[79],"robust":[80],"as":[84,86],"well":[85],"reliably":[88],"detect":[89],"genes":[90,138],"that":[91,163],"change":[92],"their":[93],"module":[94],"memberships":[95],"between":[96],"infections.":[97],"RESULTS:":[98],"We":[99],"present":[100],"MULCCH":[101,134,151,176,190],"(MULti-task":[102],"spectral":[103],"Consensus":[104],"Clustering":[105],"Hierarchically":[107],"related":[108],"tasks),":[109],"consensus":[111],"extension":[112],"multi-task":[115],"clustering":[116,147],"algorithm":[117],"infer":[119],"high-confidence":[120],"under":[125],"from":[127],"multiple":[128],"virus":[129],"strains.":[130],"On":[131],"simulated":[132],"data,":[133],"more":[135],"accurately":[136],"identifies":[137,166],"exhibiting":[139],"patterns":[141],"compared":[142,171],"non-consensus":[144,173],"nonmulti-task":[146],"approaches.":[148],"Application":[149],"mammalian":[153],"panel":[158],"influenza":[160],"viruses":[161,211],"showed":[162],"our":[164],"method":[165],"clusters":[167,178],"with":[168],"greater":[169],"coherence":[170],"methods.":[174],"Further,":[175],"derived":[177],"are":[179,231],"enriched":[180],"several":[182],"system-related":[184],"processes":[185],"regulators.":[187],"In":[188],"summary,":[189],"provides":[191],"reliable":[193],"module-based":[194],"approach":[195],"molecular":[198],"pathways":[199],"sets":[202],"characterizing":[203],"commonality":[204],"specificity":[206],"pathogenicities.":[214],"AVAILABILITY":[215],"AND":[216],"IMPLEMENTATION:":[217],"The":[218],"source":[219],"code":[220],"available":[222,232],"at":[223,233],"https://bitbucket.org/roygroup/mulcch":[224],"CONTACT:":[225],"sroy@biostat.wisc.edu":[226],"SUPPLEMENTARY":[227],"INFORMATION:":[228],"Supplementary":[229],"data":[230],"Bioinformatics":[234],"online.":[235]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}