{"id":"https://openalex.org/W2096428977","doi":"https://doi.org/10.1093/bioinformatics/btt235","title":"CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways","display_name":"CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways","publication_year":2013,"publication_date":"2013-06-19","ids":{"openalex":"https://openalex.org/W2096428977","doi":"https://doi.org/10.1093/bioinformatics/btt235","mag":"2096428977","pmid":"https://pubmed.ncbi.nlm.nih.gov/23812978"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt235","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt235","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i145/18535839/btt235.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i145/18535839/btt235.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034244056","display_name":"Gamze Abaka","orcid":null},"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":"Gamze Abaka","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":"middle","author":{"id":"https://openalex.org/A5044320290","display_name":"T\u00fcrker B\u0131\u0301y\u0131\u0301ko\u011flu","orcid":null},"institutions":[{"id":"https://openalex.org/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"T\u00fcrker B\u0131y\u0131ko\u011flu","raw_affiliation_strings":["1Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083 and 2Department of Mathematics, Izmir Institute of Technology, Izmir 35430, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083 and 2Department of Mathematics, Izmir Institute of Technology, Izmir 35430, Turkey","institution_ids":["https://openalex.org/I120217413"]}]},{"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/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]},{"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 and","1Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083 and 2Department of Mathematics, Izmir Institute of Technology, Izmir 35430, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083 and","institution_ids":["https://openalex.org/I132286405"]},{"raw_affiliation_string":"1Department of Computer Engineering, Kadir Has University, Cibali, Istanbul 34083 and 2Department of Mathematics, Izmir Institute of Technology, Izmir 35430, Turkey","institution_ids":["https://openalex.org/I120217413"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7481,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.72111372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"29","issue":"13","first_page":"i145","last_page":"i153"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.784600019454956,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.784600019454956,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.13199999928474426,"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":0.015699999406933784,"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/computer-science","display_name":"Computer science","score":0.6705608367919922},{"id":"https://openalex.org/keywords/pathway-analysis","display_name":"Pathway analysis","score":0.5789099335670471},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46824944019317627},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.46489256620407104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16483351588249207},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11723101139068604},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06745722889900208}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6705608367919922},{"id":"https://openalex.org/C2779230013","wikidata":"https://www.wikidata.org/wiki/Q25303877","display_name":"Pathway analysis","level":4,"score":0.5789099335670471},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46824944019317627},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.46489256620407104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16483351588249207},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11723101139068604},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06745722889900208},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btt235","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt235","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i145/18535839/btt235.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23812978","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23812978","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":null},{"id":"pmh:oai:europepmc.org:2688169","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3694646","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:gcris.iyte.edu.tr:11147/5283","is_oa":true,"landing_page_url":"https://hdl.handle.net/11147/5283","pdf_url":null,"source":{"id":"https://openalex.org/S4306400894","display_name":"\u0130YTE (\u0130ZM\u0130R Y\u00dcKSEK TEKNOLOJ\u0130 ENST\u0130T\u00dcS\u00dc)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I120217413","host_organization_name":"Izmir Institute of Technology","host_organization_lineage":["https://openalex.org/I120217413"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:openaccess.iyte.edu.tr:11147/5283","is_oa":true,"landing_page_url":"http://hdl.handle.net/11147/5283","pdf_url":null,"source":{"id":"https://openalex.org/S4377196445","display_name":"IYTE GCRIS Database (Izmir Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I120217413","host_organization_name":"Izmir Institute of Technology","host_organization_lineage":["https://openalex.org/I120217413"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:openaccess.iyte.edu.tr:8080:11147/5283","is_oa":true,"landing_page_url":"http://doi.org/10.1093/bioinformatics/btt235","pdf_url":null,"source":{"id":"https://openalex.org/S4306400894","display_name":"\u0130YTE (\u0130ZM\u0130R Y\u00dcKSEK TEKNOLOJ\u0130 ENST\u0130T\u00dcS\u00dc)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I120217413","host_organization_name":"Izmir Institute of Technology","host_organization_lineage":["https://openalex.org/I120217413"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3694646","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3694646","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt235","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt235","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/i145/18535839/btt235.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096428977.pdf","grobid_xml":"https://content.openalex.org/works/W2096428977.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W118615843","https://openalex.org/W1510054038","https://openalex.org/W1541075805","https://openalex.org/W1761820742","https://openalex.org/W1970737407","https://openalex.org/W1976511318","https://openalex.org/W1984209790","https://openalex.org/W1998767819","https://openalex.org/W2008690976","https://openalex.org/W2011039300","https://openalex.org/W2028111526","https://openalex.org/W2075735883","https://openalex.org/W2100438221","https://openalex.org/W2106275553","https://openalex.org/W2119497586","https://openalex.org/W2121773288","https://openalex.org/W2122961704","https://openalex.org/W2128601422","https://openalex.org/W2135445920","https://openalex.org/W2136316164","https://openalex.org/W2137648512","https://openalex.org/W2139559590","https://openalex.org/W2144589197","https://openalex.org/W2153929049","https://openalex.org/W2156153879","https://openalex.org/W2160648174","https://openalex.org/W2167065750","https://openalex.org/W2167222948","https://openalex.org/W2171081680","https://openalex.org/W2171108134","https://openalex.org/W2327315803","https://openalex.org/W3098497574","https://openalex.org/W3154566661","https://openalex.org/W3157439875","https://openalex.org/W4210777595","https://openalex.org/W4230392683","https://openalex.org/W6604748481","https://openalex.org/W6657558948"],"related_works":["https://openalex.org/W2391746102","https://openalex.org/W2126267872","https://openalex.org/W1553495564","https://openalex.org/W1722900882","https://openalex.org/W1578136679","https://openalex.org/W1978007328","https://openalex.org/W2378339845","https://openalex.org/W4221026033","https://openalex.org/W115293203","https://openalex.org/W2119683611"],"abstract_inverted_index":{"MOTIVATION:":[0],"Given":[1],"a":[2,14,55,63,80,111,121],"pair":[3,56],"of":[4,9,19,40,48,52,57,98,150,181],"metabolic":[5,58,132],"pathways,":[6],"an":[7],"alignment":[8,65,76,129],"the":[10,20,46,69,74,124,170,174,182],"pathways":[11],"corresponds":[12],"to":[13,68],"mapping":[15],"between":[16],"similar":[17],"substructures":[18],"pair.":[21],"Successful":[22],"alignments":[23,51],"may":[24,36],"provide":[25,62],"useful":[26,167],"applications":[27],"in":[28,54,79],"phylogenetic":[29],"tree":[30],"reconstruction,":[31],"drug":[32],"design":[33],"and":[34,142,173],"overall":[35],"enhance":[37],"our":[38,95,151],"understanding":[39],"cellular":[41],"metabolism.":[42],"RESULTS:":[43],"We":[44,60,71,93],"consider":[45],"problem":[47,77],"providing":[49],"one-to-many":[50],"reactions":[53],"pathways.":[59],"first":[61],"constrained":[64,75],"framework":[66],"applicable":[67],"problem.":[70],"show":[72],"that":[73,117],"even":[78],"primitive":[81],"setting":[82],"is":[83],"computationally":[84],"intractable,":[85],"which":[86],"justifies":[87],"efforts":[88],"for":[89,104],"designing":[90],"efficient":[91],"heuristics.":[92],"present":[94],"Constrained":[96],"Alignment":[97],"Metabolic":[99],"Pathways":[100],"(CAMPways)":[101],"algorithm":[102,126,152],"designed":[103],"this":[105],"purpose.":[106],"Through":[107],"extensive":[108],"experiments":[109],"involving":[110],"large":[112],"pathway":[113],"database,":[114],"we":[115],"demonstrate":[116],"when":[118],"compared":[119],"with":[120],"state-of-the-art":[122],"alternative,":[123],"CAMPways":[125],"provides":[127],"better":[128],"results":[130,175],"on":[131,139],"networks":[133],"as":[134,136,179],"far":[135],"measures":[137],"based":[138],"same-pathway":[140],"inclusion":[141],"biochemical":[143],"significance":[144],"are":[145,176,191],"concerned.":[146],"The":[147],"execution":[148],"speed":[149],"constitutes":[153],"yet":[154],"another":[155],"important":[156],"improvement":[157],"over":[158],"alternative":[159],"algorithms.":[160],"AVAILABILITY:":[161],"Open":[162],"source":[163],"codes,":[164],"executable":[165],"binary,":[166],"scripts,":[168],"all":[169],"experimental":[171],"data":[172,190],"freely":[177],"available":[178,192],"part":[180],"Supplementary":[183,189],"Material":[184],"at":[185,193],"http://code.google.com/p/campways/.":[186],"SUPPLEMENTARY":[187],"INFORMATION:":[188],"Bioinformatics":[194],"online.":[195]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}