{"id":"https://openalex.org/W2338223499","doi":"https://doi.org/10.1371/journal.pcbi.1004879","title":"Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package","display_name":"Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package","publication_year":2016,"publication_date":"2016-04-20","ids":{"openalex":"https://openalex.org/W2338223499","doi":"https://doi.org/10.1371/journal.pcbi.1004879","mag":"2338223499","pmid":"https://pubmed.ncbi.nlm.nih.gov/27096930"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004879","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004879","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004879&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.1004879&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050761928","display_name":"Nurcan Tun\u00e7ba\u011f","orcid":"https://orcid.org/0000-0002-0389-9459"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nurcan Tuncbag","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084838093","display_name":"Sara J.C. Gosline","orcid":"https://orcid.org/0000-0002-6534-4774"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sara J. C. Gosline","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022792225","display_name":"Amanda J. Kedaigle","orcid":"https://orcid.org/0000-0001-6156-5046"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda Kedaigle","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066829487","display_name":"Anthony R. Soltis","orcid":"https://orcid.org/0000-0002-3394-1275"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony R. Soltis","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083286341","display_name":"Anthony Gitter","orcid":"https://orcid.org/0000-0002-5324-9833"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony Gitter","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043876367","display_name":"Ernest Fraenkel","orcid":"https://orcid.org/0000-0001-9249-8181"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ernest Fraenkel","raw_affiliation_strings":["Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5043876367"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":9.7619,"has_fulltext":true,"cited_by_count":188,"citation_normalized_percentile":{"value":0.98474362,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"12","issue":"4","first_page":"e1004879","last_page":"e1004879"},"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9966999888420105,"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/integrator","display_name":"Integrator","score":0.64707350730896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5814757347106934},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5720304250717163},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5573263168334961},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5026168823242188},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.4828932285308838},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.45675382018089294},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.385902464389801},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36879032850265503},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2844005227088928},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09696829319000244},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08605846762657166},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.07815000414848328}],"concepts":[{"id":"https://openalex.org/C79518650","wikidata":"https://www.wikidata.org/wiki/Q2081431","display_name":"Integrator","level":3,"score":0.64707350730896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5814757347106934},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5720304250717163},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5573263168334961},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5026168823242188},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4828932285308838},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.45675382018089294},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.385902464389801},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36879032850265503},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2844005227088928},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09696829319000244},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08605846762657166},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.07815000414848328},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C2776257435","wikidata":"https://www.wikidata.org/wiki/Q1576430","display_name":"Bandwidth (computing)","level":2,"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":"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":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","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":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1004879","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004879","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004879&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:27096930","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27096930","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:doaj.org/article:c5d51b8fb5d1442194ac100cdca03c12","is_oa":true,"landing_page_url":"https://doaj.org/article/c5d51b8fb5d1442194ac100cdca03c12","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 12, Iss 4, p e1004879 (2016)","raw_type":"article"},{"id":"pmh:oai:open.metu.edu.tr:11511/31590","is_oa":false,"landing_page_url":"https://hdl.handle.net/11511/31590","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4838263","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4838263","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1004879","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004879","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004879&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":[{"score":0.5,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1942221908","display_name":null,"funder_award_id":"NS091046","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2176390815","display_name":null,"funder_award_id":"U01CA184898","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3656437802","display_name":null,"funder_award_id":"0821391","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3675310440","display_name":null,"funder_award_id":"R01GM089903","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6415854368","display_name":null,"funder_award_id":"U54NS091046","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6526793616","display_name":null,"funder_award_id":"U54CA112967","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8305864826","display_name":null,"funder_award_id":"CA112967","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8988934029","display_name":null,"funder_award_id":"DBI-0821391","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2338223499.pdf","grobid_xml":"https://content.openalex.org/works/W2338223499.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W173585903","https://openalex.org/W1200957821","https://openalex.org/W1965804264","https://openalex.org/W1966827022","https://openalex.org/W1973268693","https://openalex.org/W1978177843","https://openalex.org/W1978370150","https://openalex.org/W2003516452","https://openalex.org/W2008051478","https://openalex.org/W2009313526","https://openalex.org/W2010457001","https://openalex.org/W2017138237","https://openalex.org/W2022480285","https://openalex.org/W2038963685","https://openalex.org/W2042778855","https://openalex.org/W2043391289","https://openalex.org/W2043398720","https://openalex.org/W2060232454","https://openalex.org/W2063028213","https://openalex.org/W2076154138","https://openalex.org/W2089691349","https://openalex.org/W2092988184","https://openalex.org/W2095319945","https://openalex.org/W2095867585","https://openalex.org/W2096139934","https://openalex.org/W2099131261","https://openalex.org/W2102265464","https://openalex.org/W2103017472","https://openalex.org/W2103850766","https://openalex.org/W2105924489","https://openalex.org/W2106336008","https://openalex.org/W2111862142","https://openalex.org/W2113654464","https://openalex.org/W2116152510","https://openalex.org/W2117513900","https://openalex.org/W2120826041","https://openalex.org/W2128077939","https://openalex.org/W2128551987","https://openalex.org/W2129422961","https://openalex.org/W2130410032","https://openalex.org/W2130901965","https://openalex.org/W2131579086","https://openalex.org/W2132623845","https://openalex.org/W2134957137","https://openalex.org/W2135030836","https://openalex.org/W2136303131","https://openalex.org/W2137804845","https://openalex.org/W2137896695","https://openalex.org/W2140937045","https://openalex.org/W2141152663","https://openalex.org/W2142410561","https://openalex.org/W2143991512","https://openalex.org/W2147937648","https://openalex.org/W2155993944","https://openalex.org/W2158217645","https://openalex.org/W2158597576","https://openalex.org/W2159675211","https://openalex.org/W2164116506","https://openalex.org/W2165160727","https://openalex.org/W2174632898","https://openalex.org/W2218388869","https://openalex.org/W2247766769"],"related_works":["https://openalex.org/W2366352762","https://openalex.org/W2613964090","https://openalex.org/W2081322886","https://openalex.org/W2380425739","https://openalex.org/W2349324463","https://openalex.org/W1988313539","https://openalex.org/W2027541371","https://openalex.org/W2380535488","https://openalex.org/W2371144154","https://openalex.org/W2029980887"],"abstract_inverted_index":{"High-throughput,":[0],"'omic'":[1,48],"methods":[2],"provide":[3],"sensitive":[4],"measures":[5],"of":[6,29,47,68,70,179,201,204,213],"biological":[7],"responses":[8],"to":[9,20,65,73,97,109,138,154,193,197],"perturbations.":[10],"However,":[11],"inherent":[12,110],"biases":[13],"in":[14,23,88,105,114,222],"high-throughput":[15,205],"assays":[16,96],"make":[17],"it":[18],"difficult":[19],"interpret":[21],"experiments":[22],"which":[24],"more":[25],"than":[26],"one":[27],"type":[28],"data":[30,49,206],"is":[31,177,226],"collected.":[32],"In":[33],"this":[34],"work,":[35],"we":[36],"introduce":[37],"Omics":[38,131,152],"Integrator,":[39],"a":[40,45,66,195],"software":[41,176],"package":[42],"that":[43,78,99,122,186,216],"takes":[44],"variety":[46],"as":[50,207,209],"input":[51],"and":[52,158,184,230],"identifies":[53],"putative":[54],"underlying":[55],"molecular":[56,71,120],"pathways.":[57],"The":[58,175],"approach":[59,117],"applies":[60],"advanced":[61,199],"network":[62,67],"optimization":[63],"algorithms":[64],"thousands":[69],"interactions":[72,215],"find":[74],"high-confidence,":[75],"interpretable":[76],"subnetworks":[77,84,212],"best":[79,217],"explain":[80],"the":[81,106,173,219],"data.":[82,174],"These":[83],"connect":[85,218],"changes":[86,221],"observed":[87,220],"gene":[89],"expression,":[90],"protein":[91,214],"abundance":[92],"or":[93,112,191],"other":[94],"global":[95],"proteins":[98],"may":[100],"not":[101,124,140],"have":[102],"been":[103],"measured":[104],"screens":[107],"due":[108],"bias":[111],"noise":[113],"measurement.":[115],"This":[116],"reveals":[118],"unannotated":[119],"pathways":[121],"would":[123],"be":[125,188],"detectable":[126],"by":[127,172],"searching":[128],"pathway":[129],"databases.":[130],"Integrator":[132,153],"also":[133,145],"provides":[134],"an":[135],"elegant":[136],"framework":[137],"incorporate":[139],"only":[141],"positive":[142],"data,":[143],"but":[144],"negative":[146,149],"evidence.":[147],"Incorporating":[148],"evidence":[150],"allows":[151],"avoid":[155,159],"unexpressed":[156],"genes":[157],"being":[160],"biased":[161],"toward":[162],"highly-studied":[163],"hub":[164],"proteins,":[165],"except":[166],"when":[167],"they":[168],"are":[169],"strongly":[170],"implicated":[171],"comprised":[178],"two":[180],"individual":[181],"tools,":[182],"Garnet":[183],"Forest,":[185],"can":[187],"run":[189],"together":[190],"independently":[192],"allow":[194],"user":[196],"perform":[198],"integration":[200],"multiple":[202],"types":[203],"well":[208],"create":[210],"condition-specific":[211],"various":[223],"datasets.":[224],"It":[225],"available":[227],"at":[228,233],"http://fraenkel.mit.edu/omicsintegrator":[229],"on":[231],"GitHub":[232],"https://github.com/fraenkel-lab/OmicsIntegrator.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":24},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
