{"id":"https://openalex.org/W4321436632","doi":"https://doi.org/10.1093/bioinformatics/btad095","title":"<tt>ecmtool</tt>: fast and memory-efficient enumeration of elementary conversion modes","display_name":"<tt>ecmtool</tt>: fast and memory-efficient enumeration of elementary conversion modes","publication_year":2023,"publication_date":"2023-02-21","ids":{"openalex":"https://openalex.org/W4321436632","doi":"https://doi.org/10.1093/bioinformatics/btad095","pmid":"https://pubmed.ncbi.nlm.nih.gov/36808187"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad095/49407400/btad095.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad095/49407400/btad095.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032000854","display_name":"Bianca Buchner","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138243","display_name":"Austrian Centre of Industrial Biotechnology (Austria)","ror":"https://ror.org/03dm7dd93","country_code":"AT","type":"company","lineage":["https://openalex.org/I4210138243"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Bianca Buchner","raw_affiliation_strings":["acib GmbH, Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"acib GmbH, Austrian Centre of Industrial Biotechnology , 1190 Vienna, Austria","institution_ids":["https://openalex.org/I4210138243"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073026524","display_name":"Tom J. Clement","orcid":"https://orcid.org/0000-0002-8811-324X"},"institutions":[{"id":"https://openalex.org/I865915315","display_name":"Vrije Universiteit Amsterdam","ror":"https://ror.org/008xxew50","country_code":"NL","type":"education","lineage":["https://openalex.org/I865915315"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Tom J Clement","raw_affiliation_strings":["Systems Biology Lab, Vrije Universiteit , 1081HV Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Systems Biology Lab, Vrije Universiteit , 1081HV Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I865915315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043007654","display_name":"Daan H. de Groot","orcid":"https://orcid.org/0000-0001-7070-8950"},"institutions":[{"id":"https://openalex.org/I1850255","display_name":"University of Basel","ror":"https://ror.org/02s6k3f65","country_code":"CH","type":"education","lineage":["https://openalex.org/I1850255"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Daan H de Groot","raw_affiliation_strings":["Biozentrum, Swiss Institute of Bioinformatics, University of Basel , 4056 Basel, Switzerland"],"affiliations":[{"raw_affiliation_string":"Biozentrum, Swiss Institute of Bioinformatics, University of Basel , 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I1850255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053663717","display_name":"J\u00fcrgen Zanghellini","orcid":"https://orcid.org/0000-0002-1964-2455"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"J\u00fcrgen Zanghellini","raw_affiliation_strings":["Department of Analytical Chemistry, University of Vienna , 1090 Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Analytical Chemistry, University of Vienna , 1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5043007654","https://openalex.org/A5053663717"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I129774422","https://openalex.org/I1850255"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7894,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.72182183,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"39","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9959999918937683,"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/enumeration","display_name":"Enumeration","score":0.8632089495658875},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7367503046989441},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6951064467430115},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6556997299194336},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5226399898529053},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4510006308555603},{"id":"https://openalex.org/keywords/vertex","display_name":"Vertex (graph theory)","score":0.42356210947036743},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.370580792427063},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.34275779128074646},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.15083834528923035},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14850583672523499},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.08335167169570923}],"concepts":[{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.8632089495658875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7367503046989441},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6951064467430115},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6556997299194336},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5226399898529053},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4510006308555603},{"id":"https://openalex.org/C80899671","wikidata":"https://www.wikidata.org/wiki/Q1304193","display_name":"Vertex (graph theory)","level":3,"score":0.42356210947036743},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.370580792427063},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34275779128074646},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.15083834528923035},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14850583672523499},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.08335167169570923},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","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":"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad095/49407400/btad095.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36808187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36808187","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:pubmedcentral.nih.gov:9982354","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9982354","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9982354/pdf/btad095.pdf","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:vu:oai:research.vu.nl:publications/c1a9c06f-38e4-418e-89e2-9dff6e764cb1","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/c1a9c06f-38e4-418e-89e2-9dff6e764cb1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"Bioinformatics (Oxford, England), 39(3):btad095, 1 - 2. Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad095","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad095/49407400/btad095.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4321436632.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W2046760236","https://openalex.org/W2057858265","https://openalex.org/W2110355460","https://openalex.org/W2120661262","https://openalex.org/W2170576111","https://openalex.org/W2910514964","https://openalex.org/W3115294611","https://openalex.org/W3211378051"],"related_works":["https://openalex.org/W108845024","https://openalex.org/W2578985712","https://openalex.org/W4300125793","https://openalex.org/W2406961474","https://openalex.org/W2143566611","https://openalex.org/W2013740965","https://openalex.org/W588267724","https://openalex.org/W2952598754","https://openalex.org/W2023656250","https://openalex.org/W2405661381"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2023-02-22T00:00:00"}