{"id":"https://openalex.org/W2171255489","doi":"https://doi.org/10.1093/bioinformatics/btt713","title":"BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks","display_name":"BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks","publication_year":2013,"publication_date":"2013-12-11","ids":{"openalex":"https://openalex.org/W2171255489","doi":"https://doi.org/10.1093/bioinformatics/btt713","mag":"2171255489","pmid":"https://pubmed.ncbi.nlm.nih.gov/24336414"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt713","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt713","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009958002","display_name":"Ferhat Alkan","orcid":"https://orcid.org/0000-0001-6709-9605"},"institutions":[{"id":"https://openalex.org/I132286405","display_name":"Kadir Has University","ror":"https://ror.org/03zzckc47","country_code":"TR","type":"education","lineage":["https://openalex.org/I132286405"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Ferhat Alkan","raw_affiliation_strings":["Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083, Turkey","institution_ids":["https://openalex.org/I132286405"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066274617","display_name":"Cesim Erten","orcid":"https://orcid.org/0000-0002-8149-7113"},"institutions":[{"id":"https://openalex.org/I132286405","display_name":"Kadir Has University","ror":"https://ror.org/03zzckc47","country_code":"TR","type":"education","lineage":["https://openalex.org/I132286405"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Cesim Erten","raw_affiliation_strings":["Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083, Turkey","institution_ids":["https://openalex.org/I132286405"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009958002"],"corresponding_institution_ids":["https://openalex.org/I132286405"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.3364,"has_fulltext":false,"cited_by_count":85,"citation_normalized_percentile":{"value":0.8901655,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"30","issue":"4","first_page":"531","last_page":"539"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9789999723434448,"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":0.9789999723434448,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.005400000140070915,"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":0.0017000000225380063,"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/merge","display_name":"Merge (version control)","score":0.8715510368347168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7333153486251831},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5833941102027893},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.48393040895462036},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.44336387515068054},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4351559579372406},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.41811466217041016},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.19578817486763},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14767780900001526},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11818984150886536},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.10442441701889038}],"concepts":[{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.8715510368347168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7333153486251831},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5833941102027893},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.48393040895462036},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.44336387515068054},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4351559579372406},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.41811466217041016},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.19578817486763},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14767780900001526},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11818984150886536},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.10442441701889038},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":"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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btt713","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt713","pdf_url":null,"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:24336414","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24336414","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W118615843","https://openalex.org/W1596411313","https://openalex.org/W1659605498","https://openalex.org/W1967820990","https://openalex.org/W1976511318","https://openalex.org/W1990144966","https://openalex.org/W1994101847","https://openalex.org/W2003516452","https://openalex.org/W2023096047","https://openalex.org/W2028111526","https://openalex.org/W2028793292","https://openalex.org/W2037442572","https://openalex.org/W2039616005","https://openalex.org/W2091931698","https://openalex.org/W2096428977","https://openalex.org/W2103017472","https://openalex.org/W2109715166","https://openalex.org/W2120973253","https://openalex.org/W2122863289","https://openalex.org/W2127957894","https://openalex.org/W2130687290","https://openalex.org/W2137648512","https://openalex.org/W2139879863","https://openalex.org/W2153929049","https://openalex.org/W2156153879","https://openalex.org/W2167222948","https://openalex.org/W2168474259","https://openalex.org/W2171081680","https://openalex.org/W2171108134","https://openalex.org/W2916767477","https://openalex.org/W2917375902","https://openalex.org/W2917431650","https://openalex.org/W2920957129","https://openalex.org/W4210430020","https://openalex.org/W4210777595","https://openalex.org/W6604748481","https://openalex.org/W6657558948","https://openalex.org/W6819574719"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W4385510321","https://openalex.org/W2101315668","https://openalex.org/W15348386","https://openalex.org/W2314128295","https://openalex.org/W1509942269","https://openalex.org/W4287026692","https://openalex.org/W2770735656","https://openalex.org/W2077895977"],"abstract_inverted_index":{"MOTIVATION:":[0],"Global":[1],"many-to-many":[2,139],"alignment":[3,140],"of":[4,20,36,47,52,71,91,102,117,136,141,156,201,207],"biological":[5,14,21,183],"networks":[6,56,145],"has":[7],"been":[8],"a":[9,18,133,162],"central":[10,85],"problem":[11],"in":[12,63,67,77,88,121,205,228],"comparative":[13],"network":[15],"studies.":[16],"Given":[17],"set":[19],"interaction":[22,38,144],"networks,":[23,39],"the":[24,34,69,115,118,122,128,137,153,157,174,187,194,198,202,217,234],"informal":[25,86,149],"goal":[26],"is":[27,94,100,213],"to":[28,44,95],"group":[29],"together":[30],"related":[31],"nodes.":[32],"For":[33],"case":[35],"protein-protein":[37,143],"such":[40,53],"groups":[41],"are":[42,125,236],"expected":[43],"form":[45],"clusters":[46,54,90],"functionally":[48],"orthologous":[49,92],"proteins.":[50],"Construction":[51],"for":[55,173],"from":[57],"different":[58],"species":[59],"may":[60],"prove":[61],"useful":[62],"determining":[64],"evolutionary":[65],"relationships,":[66],"predicting":[68],"functions":[70,75],"proteins":[72,93,119],"with":[73,80,104],"unknown":[74],"and":[76,113,169,210,233],"verifying":[78],"those":[79],"estimated":[81],"functions.":[82],"RESULTS:":[83],"A":[84],"objective":[87],"constructing":[89],"guarantee":[96],"that":[97,114,146,186],"each":[98],"cluster":[99,124],"composed":[101],"members":[103],"high":[105],"homological":[106],"similarity,":[107],"usually":[108],"determined":[109],"via":[110],"sequence":[111],"similarities,":[112],"interactions":[116],"involved":[120],"same":[123],"conserved":[126],"across":[127],"input":[129],"networks.":[130],"We":[131,151,160,176],"provide":[132,161],"formal":[134],"definition":[135],"global":[138],"multiple":[142],"captures":[147],"this":[148],"objective.":[150],"show":[152],"computational":[154,199],"intractability":[155],"suggested":[158],"definition.":[159],"heuristic":[163],"method":[164],"based":[165,181],"on":[166,182],"backbone":[167],"extraction":[168],"merge":[170],"strategy":[171],"(BEAMS)":[172],"problem.":[175],"finally":[177],"show,":[178],"through":[179],"experiments":[180],"significance":[184],"tests,":[185],"proposed":[188],"BEAMS":[189,203],"algorithm":[190,204],"performs":[191],"better":[192],"than":[193,216],"state-of-the-art":[195],"approaches.":[196],"Furthermore,":[197],"burden":[200],"terms":[206],"execution":[208],"speed":[209],"memory":[211],"requirements":[212],"more":[214],"reasonable":[215],"competing":[218],"algorithms.":[219],"AVAILABILITY":[220],"AND":[221],"IMPLEMENTATION:":[222],"Supplementary":[223],"material":[224],"including":[225],"code":[226],"implementations":[227],"LEDA":[229],"C++,":[230],"experimental":[231],"data":[232],"results":[235],"available":[237],"at":[238],"http://webprs.khas.edu.tr/~cesim/BEAMS.tar.gz.":[239]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
