{"id":"https://openalex.org/W4392885478","doi":"https://doi.org/10.1186/s13015-024-00258-2","title":"Infrared: a declarative tree decomposition-powered framework for bioinformatics","display_name":"Infrared: a declarative tree decomposition-powered framework for bioinformatics","publication_year":2024,"publication_date":"2024-03-16","ids":{"openalex":"https://openalex.org/W4392885478","doi":"https://doi.org/10.1186/s13015-024-00258-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/38493130"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-024-00258-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00258-2","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00258-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00258-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025033338","display_name":"Hua-Ting Yao","orcid":"https://orcid.org/0000-0002-1720-5737"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"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"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["AT","CA","FR"],"is_corresponding":false,"raw_author_name":"Hua-Ting Yao","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Vienna, Vienna, Austria. htyao@tbi.univie.ac.at","LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France. htyao@tbi.univie.ac.at","School of Computer Science, McGill University, Montreal, Canada. htyao@tbi.univie.ac.at","University of Vienna [Vienna] (Universit\u00e4tsring 1,  1010 Wien - Austria)","AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, Vienna, Austria. htyao@tbi.univie.ac.at","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France. htyao@tbi.univie.ac.at","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"School of Computer Science, McGill University, Montreal, Canada. htyao@tbi.univie.ac.at","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"University of Vienna [Vienna] (Universit\u00e4tsring 1,  1010 Wien - Austria)","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014123931","display_name":"Bertrand Marchand","orcid":"https://orcid.org/0000-0001-8060-6640"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210152518","display_name":"Laboratoire d'Informatique Gaspard-Monge","ror":"https://ror.org/04t50yk91","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I142631665","https://openalex.org/I4210145102","https://openalex.org/I4210152518","https://openalex.org/I4210154111","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210154111","display_name":"Universit\u00e9 Gustave Eiffel","ror":"https://ror.org/03x42jk29","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210154111"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Bertrand Marchand","raw_affiliation_strings":["LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France","LIGM - Laboratoire d'Informatique Gaspard-Monge (Universit\u00e9 Gustave Eiffel, Cit\u00e9 Descartes, B\u00e2timent Copernic, 5 bd Descartes, 77454 Marne-la-Vall\u00e9e Cedex 2 - France)","LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (Route de Saclay 91128 PALAISEAU CEDEX - France)","AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"LIGM - Laboratoire d'Informatique Gaspard-Monge (Universit\u00e9 Gustave Eiffel, Cit\u00e9 Descartes, B\u00e2timent Copernic, 5 bd Descartes, 77454 Marne-la-Vall\u00e9e Cedex 2 - France)","institution_ids":["https://openalex.org/I4210152518","https://openalex.org/I4210154111"]},{"raw_affiliation_string":"LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (Route de Saclay 91128 PALAISEAU CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]},{"raw_affiliation_string":"AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083644159","display_name":"Sarah J. Berkemer","orcid":"https://orcid.org/0000-0003-2028-7670"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210111488","display_name":"Life Science Institute","ror":"https://ror.org/01yeyd808","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210111488"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR","JP"],"is_corresponding":false,"raw_author_name":"Sarah J. Berkemer","raw_affiliation_strings":["Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan","LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France","AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (Route de Saclay 91128 PALAISEAU CEDEX - France)","X - \u00c9cole polytechnique (\u00c9cole polytechnique, 91128 Palaiseau Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I4210111488","https://openalex.org/I114531698"]},{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]},{"raw_affiliation_string":"LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (Route de Saclay 91128 PALAISEAU CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]},{"raw_affiliation_string":"X - \u00c9cole polytechnique (\u00c9cole polytechnique, 91128 Palaiseau Cedex - France)","institution_ids":["https://openalex.org/I142476485"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076325273","display_name":"Yann Ponty","orcid":"https://orcid.org/0000-0002-7615-3930"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yann Ponty","raw_affiliation_strings":["LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France","AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103135268","display_name":"Sebastian Will","orcid":"https://orcid.org/0000-0002-2376-9205"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sebastian Will","raw_affiliation_strings":["LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France. sebastian.will@polytechnique.edu","AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France. sebastian.will@polytechnique.edu","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"AMIBIO - Algorithms and Models for Integrative BIOlogy (Laboratoire d'Informatique de l'\u00c9cole polytechnique\r\nRoute de Saclay\r\n91128 Palaiseau CEDEX - France)","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I142476485"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":1.0206,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.74272271,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"19","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6661999821662903,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6661999821662903,"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":0.08269999921321869,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.03669999912381172,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.8158109784126282},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5126611590385437},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.45348992943763733},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4393947124481201},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.362240731716156},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3323085308074951},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11563950777053833}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8158109784126282},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5126611590385437},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.45348992943763733},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4393947124481201},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.362240731716156},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3323085308074951},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11563950777053833},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-024-00258-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00258-2","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00258-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:38493130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38493130","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:HAL:hal-04211173v2","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-04211173","pdf_url":"https://inria.hal.science/hal-04211173v2/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Algorithms for Molecular Biology, 2024, 19 (1), pp.13. &#x27E8;10.1186/s13015-024-00258-2&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:10943887","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10943887","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10943887/pdf/13015_2024_Article_258.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:a2492a3f7a8045d591547dfa7e014558","is_oa":true,"landing_page_url":"https://doaj.org/article/a2492a3f7a8045d591547dfa7e014558","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-29 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13015-024-00258-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00258-2","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00258-2","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2829479763","display_name":null,"funder_award_id":"10102967","funder_id":"https://openalex.org/F4320338438","funder_display_name":"HORIZON EUROPE Marie Sklodowska-Curie Actions"},{"id":"https://openalex.org/G3159781602","display_name":null,"funder_award_id":"ANR-21-CE45-0034-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8987941965","display_name":null,"funder_award_id":"I 4520","funder_id":"https://openalex.org/F4320321181","funder_display_name":"Austrian Science Fund"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320321181","display_name":"Austrian Science Fund","ror":"https://ror.org/013tf3c58"},{"id":"https://openalex.org/F4320321691","display_name":"Universit\u00e4t Wien","ror":"https://ror.org/03prydq77"},{"id":"https://openalex.org/F4320338438","display_name":"HORIZON EUROPE Marie Sklodowska-Curie Actions","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392885478.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W131311523","https://openalex.org/W1507341838","https://openalex.org/W1518705996","https://openalex.org/W1572255008","https://openalex.org/W1577939718","https://openalex.org/W1585295485","https://openalex.org/W1834982196","https://openalex.org/W1934768785","https://openalex.org/W1970055835","https://openalex.org/W1972390207","https://openalex.org/W1977815530","https://openalex.org/W1984675364","https://openalex.org/W1987010534","https://openalex.org/W2009818318","https://openalex.org/W2021180976","https://openalex.org/W2024291212","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2081293325","https://openalex.org/W2085550081","https://openalex.org/W2095258877","https://openalex.org/W2098558111","https://openalex.org/W2116793595","https://openalex.org/W2117869369","https://openalex.org/W2121691652","https://openalex.org/W2138309709","https://openalex.org/W2140505514","https://openalex.org/W2142676309","https://openalex.org/W2143407915","https://openalex.org/W2146696273","https://openalex.org/W2153140501","https://openalex.org/W2155858493","https://openalex.org/W2159117141","https://openalex.org/W2163892779","https://openalex.org/W2267187671","https://openalex.org/W2400986100","https://openalex.org/W2529918221","https://openalex.org/W2607526881","https://openalex.org/W2618108760","https://openalex.org/W2746724793","https://openalex.org/W2807635396","https://openalex.org/W2914414140","https://openalex.org/W2960475131","https://openalex.org/W2963352550","https://openalex.org/W3012765374","https://openalex.org/W3094704314","https://openalex.org/W4205129776","https://openalex.org/W4226045769","https://openalex.org/W4286539457","https://openalex.org/W4288937331","https://openalex.org/W4292230561","https://openalex.org/W4292471367","https://openalex.org/W4391271052","https://openalex.org/W4401058734","https://openalex.org/W6891663542"],"related_works":["https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2053286651","https://openalex.org/W2181743346","https://openalex.org/W2187401768","https://openalex.org/W2181413294","https://openalex.org/W2052122378","https://openalex.org/W2544423928","https://openalex.org/W2062023542","https://openalex.org/W4313731559"],"abstract_inverted_index":{"MOTIVATION:":[0],"Many":[1],"bioinformatics":[2,231,242],"problems":[3,66,195],"can":[4,68,322],"be":[5,69,323],"approached":[6],"as":[7,72,199],"optimization":[8,178],"or":[9,156,327],"controlled":[10,158],"sampling":[11,180],"tasks,":[12],"and":[13,16,35,39,129,179,212,232,238,247,265,303,318],"solved":[14,104,219],"exactly":[15],"efficiently":[17],"using":[18,105,325],"Dynamic":[19],"Programming":[20],"(DP).":[21],"However,":[22],"such":[23,52],"exact":[24,177],"methods":[25,250],"are":[26,102,122,196,208,216,294],"typically":[27,295],"tailored":[28,64],"towards":[29],"specific":[30],"settings,":[31],"complex":[32],"to":[33,37,41,50,146,152,174,297],"develop,":[34],"hard":[36],"implement":[38],"adapt":[40],"problem":[42],"variations.":[43],"METHODS:":[44],"We":[45,244],"introduce":[46],"the":[47,116,125,133,136,168,226,279,285,291,298],"Infrared":[48,169,229,306],"framework":[49],"overcome":[51],"hindrances":[53],"for":[54,251],"a":[55,76,85,97,112,184],"large":[56],"class":[57],"of":[58,78,89,99,115,127,135,190,201,228,241,249,259,267,278,288,300],"problems.":[59],"Its":[60],"underlying":[61],"paradigm":[62],"is":[63,94,307],"toward":[65],"that":[67],"declaratively":[70,197],"formalized":[71],"sparse":[73,140],"feature":[74,117,137,141],"networks,":[75,142],"generalization":[77],"constraint":[79],"networks.":[80],"Classic":[81],"Boolean":[82],"constraints":[83,211],"specify":[84],"search":[86],"space,":[87],"consisting":[88],"putative":[90],"solutions":[91],"whose":[92,206],"evaluation":[93],"performed":[95],"through":[96],"combination":[98],"features.":[100],"Problems":[101],"then":[103,217],"generic":[106,221],"cluster":[107],"tree":[108,113,185],"elimination":[109],"algorithms":[110,150,302],"over":[111,203],"decomposition":[114],"network.":[118,138],"Their":[119],"overall":[120],"complexities":[121,293],"linear":[123],"on":[124,183],"number":[126],"variables,":[128],"only":[130],"exponential":[131],"in":[132,230,262],"treewidth":[134],"For":[139],"associated":[143],"with":[144,160,281,311],"low":[145],"moderate":[147],"treewidths,":[148],"these":[149,166],"allow":[151],"find":[153],"optimal":[154],"solutions,":[155],"generate":[157],"samples,":[159],"practical":[161,286],"empirical":[162],"efficiency.":[163],"RESULTS:":[164],"Implementing":[165],"methods,":[167],"software":[170],"allows":[171],"Python":[172],"programmers":[173],"rapidly":[175],"develop":[176],"applications":[181,277],"based":[182],"decomposition-based":[186],"efficient":[187],"processing.":[188],"Instead":[189],"directly":[191],"coding":[192,268],"specialized":[193,301],"algorithms,":[194],"modeled":[198],"sets":[200],"variables":[202],"finite":[204],"domains,":[205],"dependencies":[207],"captured":[209],"by":[210,220],"functions.":[213],"Such":[214],"models":[215],"automatically":[218],"DP":[222],"algorithms.":[223],"To":[224],"illustrate":[225],"applicability":[227],"guide":[233],"new":[234],"users,":[235],"we":[236,271],"model":[237],"discuss":[239],"variants":[240],"applications.":[243],"provide":[245],"reimplementations":[246],"extensions":[248],"RNA":[252,254],"design,":[253],"sequence-structure":[255],"alignment,":[256],"parsimony-driven":[257],"inference":[258],"ancestral":[260],"traits":[261],"phylogenetic":[263],"trees/networks,":[264],"design":[266],"sequences.":[269],"Moreover,":[270],"demonstrate":[272],"multidimensional":[273],"Boltzmann":[274],"sampling.":[275],"These":[276],"framework-together":[280],"our":[282],"novel":[283],"results-underline":[284],"relevance":[287],"Infrared.":[289],"Remarkably,":[290],"achieved":[292],"equivalent":[296],"ones":[299],"implementations.":[304],"AVAILABILITY:":[305],"available":[308],"at":[309],"https://amibio.gitlabpages.inria.fr/Infrared":[310],"extensive":[312],"documentation,":[313],"including":[314],"various":[315],"usage":[316],"examples":[317],"API":[319],"reference;":[320],"it":[321],"installed":[324],"Conda":[326],"from":[328],"source.":[329]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
