{"id":"https://openalex.org/W4408588361","doi":"https://doi.org/10.1007/978-3-031-90252-9_7","title":"A Phylogenetic Approach to\u00a0Genomic Language Modeling","display_name":"A Phylogenetic Approach to\u00a0Genomic Language Modeling","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4408588361","doi":"https://doi.org/10.1007/978-3-031-90252-9_7","pmid":"https://pubmed.ncbi.nlm.nih.gov/40093357"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-031-90252-9_7","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-031-90252-9_7","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028226293","display_name":"Carlos Albors","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carlos Albors","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061059626","display_name":"Jianan Canal Li","orcid":"https://orcid.org/0009-0001-7772-5742"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianan Canal Li","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037139627","display_name":"Gonzalo Benegas","orcid":"https://orcid.org/0000-0002-6639-4394"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gonzalo Benegas","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001464530","display_name":"Chengzhong Ye","orcid":"https://orcid.org/0000-0002-5710-1078"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengzhong Ye","raw_affiliation_strings":["Department of Statistics, University of California, Berkeley, CA, 94720, USA","Department of Statistics, University of California, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050837693","display_name":"Yun S. Song","orcid":"https://orcid.org/0000-0002-0734-9868"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yun S. Song","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","Department of Statistics, University of California, Berkeley, CA, 94720, USA","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA","Department of Statistics, University of California, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5028226293"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":26.6776,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.9958031,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"99","last_page":"117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.996999979019165,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9902999997138977,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7648595571517944},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5212962627410889},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5182670950889587},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49385887384414673},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.492591917514801},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.46466171741485596},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4113646447658539},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4035526514053345},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37195366621017456},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35289010405540466},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3461306691169739},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1922408938407898},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12364548444747925}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7648595571517944},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5212962627410889},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5182670950889587},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49385887384414673},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.492591917514801},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.46466171741485596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4113646447658539},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4035526514053345},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37195366621017456},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35289010405540466},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3461306691169739},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1922408938407898},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12364548444747925}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-031-90252-9_7","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-031-90252-9_7","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmid:40093357","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40093357","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":"ArXiv","raw_type":null},{"id":"pmh:oai:europepmc.org:10724515","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11908359","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.7200000286102295,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W2102424972","https://openalex.org/W2145191876","https://openalex.org/W2157001909","https://openalex.org/W2165698076","https://openalex.org/W2167852161","https://openalex.org/W2510298658","https://openalex.org/W2584834072","https://openalex.org/W2770026599","https://openalex.org/W2962784628","https://openalex.org/W3012842442","https://openalex.org/W3105951520","https://openalex.org/W3127238141","https://openalex.org/W3179485843","https://openalex.org/W3211728297","https://openalex.org/W4210672654","https://openalex.org/W4230357098","https://openalex.org/W4367173606","https://openalex.org/W4367676667","https://openalex.org/W4380488316","https://openalex.org/W4382603228","https://openalex.org/W4382893389","https://openalex.org/W4385637034","https://openalex.org/W4385737488","https://openalex.org/W4386408026","https://openalex.org/W4386861232","https://openalex.org/W4388962805","https://openalex.org/W4389132733","https://openalex.org/W4389367121","https://openalex.org/W4390616142","https://openalex.org/W4392302569","https://openalex.org/W4392575276","https://openalex.org/W4401103147","https://openalex.org/W4404821554","https://openalex.org/W4405628218","https://openalex.org/W4405995672","https://openalex.org/W4407553679","https://openalex.org/W6702248584"],"related_works":["https://openalex.org/W4312203868","https://openalex.org/W2069013776","https://openalex.org/W2038264393","https://openalex.org/W2059637021","https://openalex.org/W2378282666","https://openalex.org/W4210644918","https://openalex.org/W2243442814","https://openalex.org/W2144958703","https://openalex.org/W2080410528","https://openalex.org/W2529820324"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
