{"id":"https://openalex.org/W2945660977","doi":"https://doi.org/10.1109/tcbb.2019.2911069","title":"An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer","display_name":"An Efficient Algorithm for Identifying Mutated Subnetworks Associated with Survival in Cancer","publication_year":2019,"publication_date":"2019-05-21","ids":{"openalex":"https://openalex.org/W2945660977","doi":"https://doi.org/10.1109/tcbb.2019.2911069","mag":"2945660977","pmid":"https://pubmed.ncbi.nlm.nih.gov/30990435"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2911069","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2911069","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5022471155","display_name":"Aisharjya Sarkar","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aisharjya Sarkar","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0001-9469-1022","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059163959","display_name":"Y\u0131lmaz Atay","orcid":"https://orcid.org/0000-0002-3298-3334"},"institutions":[{"id":"https://openalex.org/I137996928","display_name":"Sel\u00e7uk University","ror":"https://ror.org/045hgzm75","country_code":"TR","type":"education","lineage":["https://openalex.org/I137996928"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Yilmaz Atay","raw_affiliation_strings":["Department of Computer Engineering, Selcuk University, Konya, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-3298-3334","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Selcuk University, Konya, Turkey","institution_ids":["https://openalex.org/I137996928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040545337","display_name":"Alana Lorraine Erickson","orcid":"https://orcid.org/0000-0002-5700-7129"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alana Lorraine Erickson","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-5700-7129","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040749243","display_name":"Ivan Arisi","orcid":"https://orcid.org/0000-0002-0536-2508"},"institutions":[{"id":"https://openalex.org/I4210142264","display_name":"European Brain Research Institute","ror":"https://ror.org/03ay27p09","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210142264"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ivan Arisi","raw_affiliation_strings":["European Brain Research Institute, Roma, RM, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Brain Research Institute, Roma, RM, Italy","institution_ids":["https://openalex.org/I4210142264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104385535","display_name":"Cesare Saltini","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cesare Saltini","raw_affiliation_strings":["Department of Medicine, University of Florida, Gainesville, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-4403-8612","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5022471155"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.0859,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.46546433,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"17","issue":"5","first_page":"1582","last_page":"1594"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9896000027656555,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9526000022888184,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/subnetwork","display_name":"Subnetwork","score":0.9589091539382935},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.7166041731834412},{"id":"https://openalex.org/keywords/score","display_name":"Score","score":0.5761605501174927},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5306960940361023},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5235999822616577},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.4821609854698181},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.46251240372657776},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.455265074968338},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.44987526535987854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4008978009223938},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34759247303009033},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2899323105812073},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1822044551372528},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1581707000732422},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.15337979793548584},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1338578462600708},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09085023403167725}],"concepts":[{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.9589091539382935},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.7166041731834412},{"id":"https://openalex.org/C65660741","wikidata":"https://www.wikidata.org/wiki/Q3952743","display_name":"Score","level":2,"score":0.5761605501174927},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5306960940361023},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5235999822616577},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.4821609854698181},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.46251240372657776},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.455265074968338},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.44987526535987854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4008978009223938},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34759247303009033},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2899323105812073},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1822044551372528},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1581707000732422},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.15337979793548584},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1338578462600708},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09085023403167725},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000401","qualifier_name":"mortality","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000401","qualifier_name":"mortality","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000401","qualifier_name":"mortality","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","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},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2911069","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2911069","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30990435","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30990435","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1498528035","https://openalex.org/W1922783847","https://openalex.org/W1930774693","https://openalex.org/W1956871134","https://openalex.org/W1967304777","https://openalex.org/W1986241711","https://openalex.org/W1996729627","https://openalex.org/W2020411245","https://openalex.org/W2020541351","https://openalex.org/W2025183726","https://openalex.org/W2044433401","https://openalex.org/W2048688287","https://openalex.org/W2059300459","https://openalex.org/W2088891952","https://openalex.org/W2096283457","https://openalex.org/W2106391842","https://openalex.org/W2112090702","https://openalex.org/W2114031931","https://openalex.org/W2117632905","https://openalex.org/W2118151336","https://openalex.org/W2123500593","https://openalex.org/W2123696077","https://openalex.org/W2124637492","https://openalex.org/W2158485828","https://openalex.org/W2275877493","https://openalex.org/W2335012284","https://openalex.org/W2336070058","https://openalex.org/W2344657883","https://openalex.org/W2537623931","https://openalex.org/W2611387862","https://openalex.org/W2773456614","https://openalex.org/W2950945059","https://openalex.org/W2963168988","https://openalex.org/W4294216483","https://openalex.org/W4312512934","https://openalex.org/W6703296614"],"related_works":["https://openalex.org/W2060724872","https://openalex.org/W2082094785","https://openalex.org/W2202198356","https://openalex.org/W3087203342","https://openalex.org/W2377184161","https://openalex.org/W228984114","https://openalex.org/W2090026684","https://openalex.org/W2945660977","https://openalex.org/W2588997957","https://openalex.org/W2951296158"],"abstract_inverted_index":{"Protein-protein":[0],"interaction":[1],"(PPI)":[2],"network":[3,68,122],"models":[4],"interconnections":[5],"between":[6,96],"protein-encoding":[7,37],"genes.":[8],"A":[9],"group":[10],"of":[11,41,50,64,154,189,191],"proteins":[12],"that":[13,52,109],"perform":[14],"similar":[15],"functions":[16],"are":[17,159],"often":[18],"connected":[19,71,117],"to":[20,69,88,114,161],"each":[21],"other":[22],"in":[23,36,45,140,147,181,187,197],"the":[24,78,94,116,120,144,162],"PPI":[25,67,121],"network.":[26],"The":[27],"corresponding":[28],"genes":[29,38,174],"form":[30],"pathways":[31,201],"or":[32],"functional":[33],"modules.":[34],"Mutation":[35],"affect":[39],"behavior":[40],"pathways.":[42,55],"This":[43],"results":[44],"initiation,":[46],"progression,":[47],"and":[48,66,134,179,199],"severity":[49],"diseases":[51],"propagates":[53],"through":[54],"In":[56],"this":[57],"work,":[58],"we":[59],"integrate":[60],"mutation,":[61],"survival":[62,95],"information":[63],"patients,":[65],"identify":[70,200],"subnetworks":[72,158],"associated":[73],"with":[74,170,194],"survival.":[75],"We":[76,99,129],"define":[77],"computational":[79],"problem":[80],"using":[81],"a":[82,101],"fitness":[83],"function":[84],"called":[85],"log-rank":[86,127],"statistic":[87,92,153],"score":[89,186],"subnetworks.":[90],"Log-rank":[91,152],"compares":[93],"two":[97],"populations.":[98],"propose":[100],"novel":[102],"method,":[103],"Survival":[104],"Associated":[105],"Mutated":[106],"Subnetwork":[107],"(SAMS)":[108],"adopts":[110],"genetic":[111],"algorithm":[112],"strategy":[113],"find":[115],"subnetwork":[118],"within":[119],"whose":[123],"mutation":[124],"yields":[125],"highest":[126],"statistic.":[128],"test":[130],"on":[131],"real":[132],"cancer":[133,172],"synthetic":[135],"datasets.":[136],"SAMS":[137,155],"generate":[138],"solutions":[139],"negligible":[141],"time":[142],"while":[143],"state-of-art":[145],"method":[146],"literature":[148],"takes":[149],"exponential":[150],"time.":[151],"selected":[156],"mutated":[157],"comparable":[160],"method.":[163],"Our":[164],"result":[165],"genesets":[166],"show":[167],"significant":[168],"overlap":[169],"well-known":[171],"driver":[173],"derived":[175],"from":[176],"curated":[177],"datasets":[178],"studies":[180],"literature,":[182],"display":[183],"high":[184,203],"text-mining":[185],"terms":[188],"number":[190],"citations":[192],"combined":[193],"disease-specific":[195],"keywords":[196],"PubMed,":[198],"having":[202],"biological":[204],"relevance.":[205]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}