{"id":"https://openalex.org/W1992443735","doi":"https://doi.org/10.1371/journal.pcbi.1002816","title":"Chapter 2: Data-Driven View of Disease Biology","display_name":"Chapter 2: Data-Driven View of Disease Biology","publication_year":2012,"publication_date":"2012-12-27","ids":{"openalex":"https://openalex.org/W1992443735","doi":"https://doi.org/10.1371/journal.pcbi.1002816","mag":"1992443735","pmid":"https://pubmed.ncbi.nlm.nih.gov/23300408"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002816","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002816","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002816&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002816&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050692257","display_name":"Casey S. Greene","orcid":"https://orcid.org/0000-0001-8713-9213"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Casey S. Greene","raw_affiliation_strings":["Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025250742","display_name":"Olga G. Troyanskaya","orcid":"https://orcid.org/0000-0002-5676-5737"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Olga G. Troyanskaya","raw_affiliation_strings":["Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America","Princeton Institute for Computational Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America","institution_ids":["https://openalex.org/I20089843"]},{"raw_affiliation_string":"Princeton Institute for Computational Science and Engineering","institution_ids":["https://openalex.org/I20089843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025250742"],"corresponding_institution_ids":["https://openalex.org/I20089843"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8062,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.70490911,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"8","issue":"12","first_page":"e1002816","last_page":"e1002816"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.998199999332428,"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":0.9948999881744385,"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/human-disease","display_name":"Human disease","score":0.624015212059021},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5578363537788391},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5407017469406128},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.537597119808197},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4914015531539917},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.48692238330841064},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.44066011905670166},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.35379835963249207},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34144890308380127},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18803361058235168},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1078450083732605}],"concepts":[{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.624015212059021},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5578363537788391},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5407017469406128},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.537597119808197},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4914015531539917},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.48692238330841064},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.44066011905670166},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.35379835963249207},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34144890308380127},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18803361058235168},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1078450083732605},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1002816","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002816","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002816&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:23300408","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23300408","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1002816","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002816","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:dc6ed742a518497f9c40cc67bd314bd0","is_oa":true,"landing_page_url":"https://doaj.org/article/dc6ed742a518497f9c40cc67bd314bd0","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 8, Iss 12, p e1002816 (2012)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3531282","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3531282","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002816","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002816","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002816&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1011064577","display_name":null,"funder_award_id":"P50 GM071508","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2271306371","display_name":null,"funder_award_id":"GM071508","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2994491871","display_name":null,"funder_award_id":"GM071508","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5288662233","display_name":null,"funder_award_id":"GM071966","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5910422865","display_name":null,"funder_award_id":"P50 GM071508","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7105370156","display_name":null,"funder_award_id":"R01 GM071966","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7588032409","display_name":"CAREER: An Integrated Approach to the Study of Biological Process Specific Networks","funder_award_id":"0546275","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7844601725","display_name":null,"funder_award_id":"GM071966","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7928206049","display_name":null,"funder_award_id":"T32 HG003284","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1992443735.pdf","grobid_xml":"https://content.openalex.org/works/W1992443735.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1546962148","https://openalex.org/W1929792927","https://openalex.org/W1967057818","https://openalex.org/W1969941684","https://openalex.org/W1971045545","https://openalex.org/W1985213868","https://openalex.org/W1994127362","https://openalex.org/W2013207687","https://openalex.org/W2019926860","https://openalex.org/W2020541351","https://openalex.org/W2043329626","https://openalex.org/W2046618236","https://openalex.org/W2057419867","https://openalex.org/W2066874799","https://openalex.org/W2090098862","https://openalex.org/W2095956310","https://openalex.org/W2097255042","https://openalex.org/W2101674614","https://openalex.org/W2103017472","https://openalex.org/W2105712639","https://openalex.org/W2118259897","https://openalex.org/W2119043225","https://openalex.org/W2123280311","https://openalex.org/W2124649441","https://openalex.org/W2125118217","https://openalex.org/W2132582966","https://openalex.org/W2132992030","https://openalex.org/W2134672568","https://openalex.org/W2134783591","https://openalex.org/W2136549265","https://openalex.org/W2144087703","https://openalex.org/W2145506897","https://openalex.org/W2146188765","https://openalex.org/W2148851475","https://openalex.org/W2150646520","https://openalex.org/W2152360905","https://openalex.org/W2152896172","https://openalex.org/W2153577994","https://openalex.org/W2159482845","https://openalex.org/W2161811833","https://openalex.org/W2163149540","https://openalex.org/W2164683872","https://openalex.org/W4255855797","https://openalex.org/W4294216483","https://openalex.org/W6675471023"],"related_works":["https://openalex.org/W1969895229","https://openalex.org/W2108497208","https://openalex.org/W3143099716","https://openalex.org/W1984654525","https://openalex.org/W2210302816","https://openalex.org/W95537919","https://openalex.org/W2132924928","https://openalex.org/W2316091998","https://openalex.org/W2394962248","https://openalex.org/W1038530937"],"abstract_inverted_index":{"Modern":[0],"experimental":[1],"strategies":[2],"often":[3,18],"generate":[4],"genome-scale":[5,58],"measurements":[6,59],"of":[7,28,41,67,72,96,116,119],"human":[8,29,120],"tissues":[9],"or":[10,53],"cell":[11],"lines":[12],"in":[13],"various":[14],"physiological":[15],"states.":[16],"Investigators":[17],"use":[19],"these":[20,102],"datasets":[21,43],"individually":[22],"to":[23,44,83],"help":[24],"elucidate":[25],"molecular":[26],"mechanisms":[27],"diseases.":[30],"Here":[31],"we":[32],"discuss":[33,75],"approaches":[34,62],"that":[35,47,111],"effectively":[36],"weight":[37],"and":[38,56,69,94],"integrate":[39],"hundreds":[40],"heterogeneous":[42],"gene-gene":[45],"networks":[46],"focus":[48],"on":[49],"a":[50,64,70],"specific":[51],"process":[52],"disease.":[54,121],"Diverse":[55],"systematic":[57],"provide":[60],"such":[61,77,97],"both":[63],"great":[65],"deal":[66],"power":[68],"number":[71],"challenges.":[73],"We":[74,86],"some":[76],"challenges":[78],"as":[79,81],"well":[80],"methods":[82,105],"address":[84],"them.":[85],"also":[87],"raise":[88],"important":[89],"considerations":[90],"for":[91],"the":[92,117],"assessment":[93],"evaluation":[95],"approaches.":[98],"When":[99],"carefully":[100],"applied,":[101],"integrative":[103],"data-driven":[104],"can":[106,112],"make":[107],"novel":[108],"high-quality":[109],"predictions":[110],"transform":[113],"our":[114],"understanding":[115],"molecular-basis":[118]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
