{"id":"https://openalex.org/W4400242689","doi":"https://doi.org/10.1186/s12859-024-05823-5","title":"Unsupervised modeling of mutational landscapes of adeno-associated viruses viability","display_name":"Unsupervised modeling of mutational landscapes of adeno-associated viruses viability","publication_year":2024,"publication_date":"2024-07-02","ids":{"openalex":"https://openalex.org/W4400242689","doi":"https://doi.org/10.1186/s12859-024-05823-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/38956474"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05823-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05823-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05823-5","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/counter/pdf/10.1186/s12859-024-05823-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093130928","display_name":"Matteo De Leonardis","orcid":"https://orcid.org/0000-0003-4082-4170"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Matteo De Leonardis","raw_affiliation_strings":["DISAT, Politecnico di Torino, Corso Duca degli Abruzzi, 10129, Torino, Italy. matteo.deleonardis@polito.it","DISAT - Department of Applied Science and Technology [Politecnico di Torino] (Politecnico di Torino - Corso Duca degli Abruzzi, 24 - 10129 Torino, ITALY - Italy)"],"affiliations":[{"raw_affiliation_string":"DISAT, Politecnico di Torino, Corso Duca degli Abruzzi, 10129, Torino, Italy. matteo.deleonardis@polito.it","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"DISAT - Department of Applied Science and Technology [Politecnico di Torino] (Politecnico di Torino - Corso Duca degli Abruzzi, 24 - 10129 Torino, ITALY - Italy)","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002616738","display_name":"Jorge Fern\u00e1ndez-de-Cossio-D\u00edaz","orcid":"https://orcid.org/0000-0002-4476-805X"},"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/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210091437","display_name":"Sorbonne Paris Cit\u00e9","ror":"https://ror.org/001z21q04","country_code":"FR","type":"other","lineage":["https://openalex.org/I4210091437"]},{"id":"https://openalex.org/I4210129651","display_name":"Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure","ror":"https://ror.org/03a26mh11","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I277688954","https://openalex.org/I29607241","https://openalex.org/I39804081","https://openalex.org/I4210129651","https://openalex.org/I4210148025","https://openalex.org/I4210148430"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jorge Fernandez-de-Cossio-Diaz","raw_affiliation_strings":["Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure, CNRS, PSL University, Sorbonne Universit\u00e9, Universite, Paris-Cit\u00e9, 75005, Paris, France","Physique Statistique et Inf\u00e9rence pour la Biologie (24 rue Lhomond 75005 Paris - France)","LPENS - Laboratoire de physique de l'ENS - ENS Paris (24, rue Lhomond\r\n75005 Paris - France)"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure, CNRS, PSL University, Sorbonne Universit\u00e9, Universite, Paris-Cit\u00e9, 75005, Paris, France","institution_ids":["https://openalex.org/I204730241","https://openalex.org/I1294671590","https://openalex.org/I4210091437","https://openalex.org/I39804081","https://openalex.org/I2746051580"]},{"raw_affiliation_string":"Physique Statistique et Inf\u00e9rence pour la Biologie (24 rue Lhomond 75005 Paris - France)","institution_ids":[]},{"raw_affiliation_string":"LPENS - Laboratoire de physique de l'ENS - ENS Paris (24, rue Lhomond\r\n75005 Paris - France)","institution_ids":["https://openalex.org/I4210129651","https://openalex.org/I29607241"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086941438","display_name":"Guido Uguzzoni","orcid":"https://orcid.org/0000-0003-4192-2864"},"institutions":[{"id":"https://openalex.org/I4210123319","display_name":"Italian institute for Genomic Medicine","ror":"https://ror.org/036054d36","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210123319"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Guido Uguzzoni","raw_affiliation_strings":["Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, 10060, Candiolo, Italy","IIGM - Italian Institute for Genomic Medicine (c/o IRCCS \u2013 SP142 km 3,95 \u2013 10060 \u2013 Candiolo (TO) - Italy)"],"affiliations":[{"raw_affiliation_string":"Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, 10060, Candiolo, Italy","institution_ids":["https://openalex.org/I4210123319"]},{"raw_affiliation_string":"IIGM - Italian Institute for Genomic Medicine (c/o IRCCS \u2013 SP142 km 3,95 \u2013 10060 \u2013 Candiolo (TO) - Italy)","institution_ids":["https://openalex.org/I4210123319"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011435835","display_name":"Andrea Pagnani","orcid":"https://orcid.org/0000-0002-6509-0807"},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]},{"id":"https://openalex.org/I4210123319","display_name":"Italian institute for Genomic Medicine","ror":"https://ror.org/036054d36","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210123319"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Pagnani","raw_affiliation_strings":["DISAT, Politecnico di Torino, Corso Duca degli Abruzzi, 10129, Torino, Italy","Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, 10060, Candiolo, Italy","DISAT - Department of Applied Science and Technology [Politecnico di Torino] (Politecnico di Torino - Corso Duca degli Abruzzi, 24 - 10129 Torino, ITALY - Italy)","IIGM - Italian Institute for Genomic Medicine (c/o IRCCS \u2013 SP142 km 3,95 \u2013 10060 \u2013 Candiolo (TO) - Italy)"],"affiliations":[{"raw_affiliation_string":"DISAT, Politecnico di Torino, Corso Duca degli Abruzzi, 10129, Torino, Italy","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, 10060, Candiolo, Italy","institution_ids":["https://openalex.org/I4210123319"]},{"raw_affiliation_string":"DISAT - Department of Applied Science and Technology [Politecnico di Torino] (Politecnico di Torino - Corso Duca degli Abruzzi, 24 - 10129 Torino, ITALY - Italy)","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"IIGM - Italian Institute for Genomic Medicine (c/o IRCCS \u2013 SP142 km 3,95 \u2013 10060 \u2013 Candiolo (TO) - Italy)","institution_ids":["https://openalex.org/I4210123319"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5093130928"],"corresponding_institution_ids":["https://openalex.org/I177477856"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.2024,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.8784502,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"229","last_page":"229"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10613","display_name":"Virus-based gene therapy research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10613","display_name":"Virus-based gene therapy research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9991000294685364,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9965999722480774,"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/computational-biology","display_name":"Computational biology","score":0.6835306882858276},{"id":"https://openalex.org/keywords/fitness-landscape","display_name":"Fitness landscape","score":0.5627989172935486},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.533638596534729},{"id":"https://openalex.org/keywords/capsid","display_name":"Capsid","score":0.5133010745048523},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.49117013812065125},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.4733429253101349},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4589148759841919},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3932619094848633},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3885366916656494},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3797936737537384},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2875571548938751},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.25224894285202026}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6835306882858276},{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.5627989172935486},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.533638596534729},{"id":"https://openalex.org/C202878990","wikidata":"https://www.wikidata.org/wiki/Q830465","display_name":"Capsid","level":3,"score":0.5133010745048523},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.49117013812065125},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.4733429253101349},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4589148759841919},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3932619094848633},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3885366916656494},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3797936737537384},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2875571548938751},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.25224894285202026},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000229","descriptor_name":"Dependovirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000229","descriptor_name":"Dependovirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000229","descriptor_name":"Dependovirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000229","descriptor_name":"Dependovirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000229","descriptor_name":"Dependovirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019219","descriptor_name":"Parvovirinae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019219","descriptor_name":"Parvovirinae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019219","descriptor_name":"Parvovirinae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019219","descriptor_name":"Parvovirinae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019219","descriptor_name":"Parvovirinae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-024-05823-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05823-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05823-5","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:38956474","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38956474","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:HAL:hal-04733979v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04733979","pdf_url":"https://hal.science/hal-04733979/document","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2024, 25 (1), pp.229. &#x27E8;10.1186/s12859-024-05823-5&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:11221173","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11221173","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11221173/pdf/12859_2024_Article_5823.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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:553499d5eb064011adeae295355f32b3","is_oa":true,"landing_page_url":"https://doaj.org/article/553499d5eb064011adeae295355f32b3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-19 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05823-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05823-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05823-5","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/G8886304095","display_name":null,"funder_award_id":"734439","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400242689.pdf","grobid_xml":"https://content.openalex.org/works/W4400242689.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1989901670","https://openalex.org/W2009681413","https://openalex.org/W2060588922","https://openalex.org/W2085144875","https://openalex.org/W2160986529","https://openalex.org/W2227467442","https://openalex.org/W2617246817","https://openalex.org/W2744336424","https://openalex.org/W2755853637","https://openalex.org/W2790509526","https://openalex.org/W2889326414","https://openalex.org/W2917580301","https://openalex.org/W2944831967","https://openalex.org/W2991022372","https://openalex.org/W3017224485","https://openalex.org/W3047799377","https://openalex.org/W3127426316","https://openalex.org/W3139465356","https://openalex.org/W4281401786","https://openalex.org/W4387936896"],"related_works":["https://openalex.org/W4401246297","https://openalex.org/W2137572138","https://openalex.org/W4316495397","https://openalex.org/W2968050865","https://openalex.org/W2977306144","https://openalex.org/W2076921277","https://openalex.org/W2033677185","https://openalex.org/W2079290149","https://openalex.org/W2464882480","https://openalex.org/W2900897541"],"abstract_inverted_index":{"Adeno-associated":[0],"viruses":[1,6],"2":[2],"(AAV2)":[3],"are":[4],"minute":[5],"renowned":[7],"for":[8,128,227],"their":[9,34,45,57,67,84,103,129],"capacity":[10],"to":[11,33,59,69,101,120,137,160,174,199,240],"infect":[12],"human":[13],"cells":[14],"and":[15,40,232,245],"akin":[16],"organisms.":[17],"They":[18],"have":[19,88],"recently":[20],"emerged":[21],"as":[22,51,236],"prominent":[23],"candidates":[24],"in":[25,38,141,167],"the":[26,41,76,79,98,123,145,162,179,204,209,215,228],"field":[27],"of":[28,49,74,78,107,125,164,178,203,214,230],"gene":[29,52],"therapy,":[30],"primarily":[31],"attributed":[32],"inherent":[35],"non-pathogenic":[36],"nature":[37],"humans":[39],"safety":[42],"associated":[43],"with":[44,194],"manipulation.":[46],"The":[47,105],"efficacy":[48],"AAV2":[50],"therapy":[53],"vectors":[54],"hinges":[55],"on":[56,66,219],"ability":[58],"infiltrate":[60],"host":[61],"cells,":[62],"a":[63,71,156,175,237],"phenomenon":[64],"reliant":[65],"competence":[68],"construct":[70],"capsid":[72,184],"capable":[73],"breaching":[75],"nucleus":[77],"target":[80],"cell.":[81],"To":[82,186],"enhance":[83],"infection":[85],"potential,":[86],"researchers":[87],"extensively":[89],"scrutinized":[90],"various":[91],"combinatorial":[92],"libraries":[93,127],"by":[94,208],"introducing":[95],"mutations":[96],"into":[97,243],"capsid,":[99],"aiming":[100],"boost":[102],"effectiveness.":[104],"emergence":[106],"high-throughput":[108],"experimental":[109],"techniques,":[110],"like":[111],"deep":[112],"mutational":[113,146,205],"scanning":[114],"(DMS),":[115],"has":[116],"made":[117],"it":[118,235],"feasible":[119],"experimentally":[121],"assess":[122],"fitness":[124],"these":[126],"intended":[130],"purpose.":[131],"Notably,":[132],"machine":[133],"learning":[134],"is":[135,172],"starting":[136],"demonstrate":[138],"its":[139,188],"potential":[140],"addressing":[142],"predictions":[143],"within":[144,182],"landscape":[147,206],"from":[148],"sequence":[149],"data.":[150],"In":[151],"this":[152],"context,":[153],"we":[154,190],"introduce":[155],"biophysically-inspired":[157],"model":[158,171,192,217],"designed":[159],"predict":[161],"viability":[163],"genetic":[165],"variants":[166,231],"DMS":[168],"experiments.":[169],"This":[170],"tailored":[173,198],"specific":[176],"segment":[177],"CAP":[180],"region":[181],"AAV2's":[183],"protein.":[185],"evaluate":[187],"effectiveness,":[189],"conduct":[191],"training":[193],"diverse":[195],"datasets,":[196],"each":[197],"explore":[200],"different":[201],"aspects":[202],"influenced":[207],"selection":[210],"process.":[211],"Our":[212],"assessment":[213],"biophysical":[216],"centers":[218],"two":[220],"primary":[221],"objectives:":[222],"(i)":[223],"providing":[224],"quantitative":[225],"forecasts":[226],"log-selectivity":[229],"(ii)":[233],"deploying":[234],"binary":[238],"classifier":[239],"categorize":[241],"sequences":[242],"viable":[244],"non-viable":[246],"classes.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
