{"id":"https://openalex.org/W3103119995","doi":"https://doi.org/10.1186/s12859-020-03733-w","title":"Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks","display_name":"Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks","publication_year":2020,"publication_date":"2020-11-01","ids":{"openalex":"https://openalex.org/W3103119995","doi":"https://doi.org/10.1186/s12859-020-03733-w","mag":"3103119995","pmid":"https://pubmed.ncbi.nlm.nih.gov/33203352"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03733-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03733-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03733-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03733-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086194329","display_name":"Merc\u00e8 Llabr\u00e9s","orcid":"https://orcid.org/0000-0002-5358-6768"},"institutions":[{"id":"https://openalex.org/I4210126021","display_name":"Health Research Institute of the Balearic Islands","ror":"https://ror.org/037xbgq12","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210126021"]},{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Merc\u00e8 Llabr\u00e9s","raw_affiliation_strings":["Balearic Islands Health Research Institute, Palma de Mallorca, E-07010, Spain","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, E-07122, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Balearic Islands Health Research Institute, Palma de Mallorca, E-07010, Spain","institution_ids":["https://openalex.org/I4210126021"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, E-07122, Spain","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045448354","display_name":"Gabriel Riera","orcid":"https://orcid.org/0000-0003-1233-0931"},"institutions":[{"id":"https://openalex.org/I4210126021","display_name":"Health Research Institute of the Balearic Islands","ror":"https://ror.org/037xbgq12","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210126021"]},{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Gabriel Riera","raw_affiliation_strings":["Balearic Islands Health Research Institute, Palma de Mallorca, E-07010, Spain","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, E-07122, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Balearic Islands Health Research Institute, Palma de Mallorca, E-07010, Spain","institution_ids":["https://openalex.org/I4210126021"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, E-07122, Spain","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087466847","display_name":"Francesc Rossell\u00f3","orcid":"https://orcid.org/0000-0003-2897-5398"},"institutions":[{"id":"https://openalex.org/I4210126021","display_name":"Health Research Institute of the Balearic Islands","ror":"https://ror.org/037xbgq12","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210126021"]},{"id":"https://openalex.org/I50441567","display_name":"Universitat de les Illes Balears","ror":"https://ror.org/03e10x626","country_code":"ES","type":"education","lineage":["https://openalex.org/I50441567"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francesc Rossell\u00f3","raw_affiliation_strings":["Balearic Islands Health Research Institute, Palma de Mallorca, E-07010, Spain","Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, E-07122, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Balearic Islands Health Research Institute, Palma de Mallorca, E-07010, Spain","institution_ids":["https://openalex.org/I4210126021"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of the Balearic Islands, Palma de Mallorca, E-07122, Spain","institution_ids":["https://openalex.org/I50441567"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005629452","display_name":"Gabriel Valiente","orcid":"https://orcid.org/0000-0001-9194-2703"},"institutions":[{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gabriel Valiente","raw_affiliation_strings":["Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, E-08034, Spain. gabriel.valiente@upc.edu","Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, E-08034, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, E-08034, Spain. gabriel.valiente@upc.edu","institution_ids":["https://openalex.org/I9617848"]},{"raw_affiliation_string":"Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, E-08034, Spain","institution_ids":["https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005629452"],"corresponding_institution_ids":["https://openalex.org/I9617848"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.2237,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.50100773,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"21","issue":"S6","first_page":"434","last_page":"434"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8823999762535095,"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":0.8823999762535095,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.04050000011920929,"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":0.012500000186264515,"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/integer-programming","display_name":"Integer programming","score":0.7977020740509033},{"id":"https://openalex.org/keywords/linear-programming","display_name":"Linear programming","score":0.6485180854797363},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5932314395904541},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.5142533183097839},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4889470338821411},{"id":"https://openalex.org/keywords/linearization","display_name":"Linearization","score":0.4422445595264435},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41205528378486633},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2021699845790863},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16280946135520935},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.13254565000534058}],"concepts":[{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.7977020740509033},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.6485180854797363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5932314395904541},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.5142533183097839},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4889470338821411},{"id":"https://openalex.org/C11210021","wikidata":"https://www.wikidata.org/wiki/Q1520713","display_name":"Linearization","level":3,"score":0.4422445595264435},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41205528378486633},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2021699845790863},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16280946135520935},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.13254565000534058},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-020-03733-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03733-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03733-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33203352","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33203352","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:docusalut.com:20.500.13003/19432","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.13003/19432","pdf_url":"https://docusalut.com/bitstream/20.500.13003/19432/1/000594994500011.pdf","source":{"id":"https://openalex.org/S4306402504","display_name":"Docusalut (Conselleria de Salut i Consum del Govern de les Illes Balears)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210089844","host_organization_name":"Servei de Salut de les Illes Balears","host_organization_lineage":["https://openalex.org/I4210089844"],"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":"","raw_type":"research article"},{"id":"pmh:oai:doaj.org/article:0921383a40fd494ebf0614533afae762","is_oa":true,"landing_page_url":"https://doaj.org/article/0921383a40fd494ebf0614533afae762","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":"BMC Bioinformatics, Vol 21, Iss S6, Pp 1-14 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7671827","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7671827","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:upcommons.upc.edu:2117/334544","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/334544","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"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":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03733-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03733-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03733-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3062142014","display_name":null,"funder_award_id":"PGC2018-096956-B-C43","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6731467812","display_name":null,"funder_award_id":"PGC2018","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G7047877648","display_name":null,"funder_award_id":"PGC2018","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"}],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3103119995.pdf","grobid_xml":"https://content.openalex.org/works/W3103119995.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W2008389133","https://openalex.org/W2029983132","https://openalex.org/W2051986176","https://openalex.org/W2067127476","https://openalex.org/W2114025920","https://openalex.org/W2114938008","https://openalex.org/W2122037798","https://openalex.org/W2128408632","https://openalex.org/W2131298592","https://openalex.org/W2136845897","https://openalex.org/W2141185847","https://openalex.org/W2160648174","https://openalex.org/W2167222948","https://openalex.org/W2171108134","https://openalex.org/W2543855063","https://openalex.org/W2545536333","https://openalex.org/W2607363173","https://openalex.org/W2761430568","https://openalex.org/W2786741601","https://openalex.org/W2951589516","https://openalex.org/W2951679282","https://openalex.org/W3100057034","https://openalex.org/W4246410145"],"related_works":["https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2109912052","https://openalex.org/W1711527768","https://openalex.org/W4285278887","https://openalex.org/W2365237642","https://openalex.org/W2995925505","https://openalex.org/W3116484972","https://openalex.org/W2941986668","https://openalex.org/W4232431455"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,119],"alignment":[2,64],"of":[3,40,46,59,102,121,141],"protein-protein":[4,61,92,143],"interaction":[5,62,93,144],"networks":[6],"was":[7],"recently":[8],"formulated":[9],"as":[10,90],"an":[11],"integer":[12,25,33,55,75,123,132],"quadratic":[13],"programming":[14,27,57,77,125,134],"problem,":[15,65],"along":[16,80],"with":[17,81],"a":[18,37,53,99,105],"linearization":[19],"that":[20,85],"can":[21,67,95],"be":[22,68,96],"solved":[23,69],"by":[24],"linear":[26,34,56,76,124,133],"software":[28,78,135],"tools.":[29],"However,":[30],"the":[31,60,109,122],"resulting":[32,110],"program":[35],"has":[36],"huge":[38],"number":[39],"variables":[41],"and":[42,74,108,115,131],"constraints,":[43],"rendering":[44],"it":[45],"no":[47],"practical":[48],"use.":[49],"RESULTS:":[50],"We":[51],"present":[52],"compact":[54],"reformulation":[58,126],"network":[63],"which":[66],"using":[70,127],"state-of-the-art":[71],"mathematical":[72,129],"modeling":[73,130],"tools,":[79],"empirical":[82],"results":[83],"showing":[84],"small":[86],"biological":[87],"networks,":[88,94],"such":[89],"virus-host":[91,142],"aligned":[97],"in":[98],"reasonable":[100],"amount":[101],"time":[103],"on":[104],"personal":[106],"computer":[107],"alignments":[111,140],"are":[112],"structurally":[113],"coherent":[114],"biologically":[116,138],"meaningful.":[117],"CONCLUSIONS:":[118],"implementation":[120],"current":[128],"tools":[136],"provided":[137],"meaningful":[139],"networks.":[145]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-08-02T14:50:37.381335","created_date":"2025-10-10T00:00:00"}
