{"id":"https://openalex.org/W2746067691","doi":"https://doi.org/10.1145/3107411.3107461","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":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2746067691","doi":"https://doi.org/10.1145/3107411.3107461","mag":"2746067691"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107461","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107461","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-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/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":true,"raw_author_name":"Amanda J. Kedaigle","raw_affiliation_strings":["Massachusetts Institute of Technology, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5022792225"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":null,"apc_paid":null,"fwci":0.1063,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.48274702,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"640","last_page":"640"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9944000244140625,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9846000075340271,"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":0.7857757806777954},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6239322423934937},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.603176474571228},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5707442164421082},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4993288516998291},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.45510920882225037},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4304898679256439},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39132803678512573},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3224439024925232},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2644891142845154},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.07588338851928711}],"concepts":[{"id":"https://openalex.org/C79518650","wikidata":"https://www.wikidata.org/wiki/Q2081431","display_name":"Integrator","level":3,"score":0.7857757806777954},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6239322423934937},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.603176474571228},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5707442164421082},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4993288516998291},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.45510920882225037},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4304898679256439},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39132803678512573},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3224439024925232},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2644891142845154},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.07588338851928711},{"id":"https://openalex.org/C2776257435","wikidata":"https://www.wikidata.org/wiki/Q1576430","display_name":"Bandwidth (computing)","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107461","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107461","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.41999998688697815,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4210989272","https://openalex.org/W4206945140","https://openalex.org/W4386628104","https://openalex.org/W3149361930","https://openalex.org/W2509687359","https://openalex.org/W4212865750","https://openalex.org/W2362023034"],"abstract_inverted_index":{"High-throughput":[0],"'omic'":[1,67],"methods":[2],"reveal":[3],"many":[4],"aspects":[5],"of":[6,21,30,66,88,90],"cellular":[7,25],"state":[8],"and":[9,45,71,130,161,169],"biological":[10,173],"responses":[11],"to":[12,40,85,93,110,126,165],"perturbations.":[13],"However,":[14],"no":[15],"single":[16],"data":[17,34,43,68,156],"type":[18],"is":[19,37],"capable":[20],"fully":[22],"representing":[23],"the":[24,28,47,58,101,145,180],"activity.":[26],"Beyond":[27],"list":[29],"molecules":[31,51],"from":[32,158],"each":[33],"type,":[35],"there":[36],"a":[38,64,86],"necessity":[39],"consider":[41],"multiple":[42],"jointly":[44],"reconstruct":[46],"relations":[48],"between":[49],"these":[50],"with":[52],"personalized":[53],"network-based":[54],"approaches.":[55],"We":[56],"introduced":[57],"Omics":[59,103,124],"Integrator":[60,104,125],"software":[61],"that":[62,98],"integrates":[63],"variety":[65],"as":[69],"input":[70],"identifies":[72],"putative":[73],"underlying":[74],"molecular":[75,91],"pathways.":[76],"The":[77,147],"approach":[78],"applies":[79],"an":[80,107],"advanced":[81],"network":[82,87],"optimization":[83],"algorithm":[84],"thousands":[89],"interactions":[92],"find":[94],"high-confidence,":[95],"interpretable":[96],"subnetworks":[97],"best":[99],"explain":[100],"data.":[102,146],"also":[105,117],"provides":[106],"elegant":[108],"framework":[109],"incorporate":[111],"not":[112],"only":[113],"positive":[114],"data,":[115],"but":[116],"negative":[118,121],"evidence.":[119],"Incorporating":[120],"evidence":[122],"allows":[123],"avoid":[127,131],"unexpressed":[128],"genes":[129],"being":[132],"biased":[133],"toward":[134],"highly-studied":[135],"hub":[136],"proteins,":[137],"except":[138],"when":[139],"they":[140],"are":[141],"strongly":[142],"implicated":[143],"by":[144],"tool":[148],"has":[149],"been":[150],"applied":[151],"in":[152,179],"several":[153],"examples,":[154],"including":[155],"derived":[157],"Huntington's":[159],"Disease":[160],"glioblastoma":[162],"multiforme":[163],"models,":[164],"identify":[166],"novel":[167],"pathways":[168],"nodes":[170],"through":[171],"which":[172],"perturbations":[174],"like":[175],"disease":[176],"cause":[177],"changes":[178],"cell.":[181]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}