{"id":"https://openalex.org/W2941437619","doi":"https://doi.org/10.1093/bioinformatics/btz265","title":"PHANOTATE: a novel approach to gene identification in phage genomes","display_name":"PHANOTATE: a novel approach to gene identification in phage genomes","publication_year":2019,"publication_date":"2019-04-16","ids":{"openalex":"https://openalex.org/W2941437619","doi":"https://doi.org/10.1093/bioinformatics/btz265","mag":"2941437619","pmid":"https://pubmed.ncbi.nlm.nih.gov/31329826"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz265","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4537/30706881/btz265.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4537/30706881/btz265.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011823938","display_name":"Katelyn McNair","orcid":"https://orcid.org/0000-0001-9036-3259"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Katelyn McNair","raw_affiliation_strings":["Computational Sciences Research Center, San Diego State University , San Diego, CA 92182, USA"],"affiliations":[{"raw_affiliation_string":"Computational Sciences Research Center, San Diego State University , San Diego, CA 92182, USA","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113814626","display_name":"Carol Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carol Zhou","raw_affiliation_strings":["Lawrence Livermore National Laboratory , Livermore, CA 94550, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory , Livermore, CA 94550, USA","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051908367","display_name":"Elizabeth A. Dinsdale","orcid":"https://orcid.org/0000-0002-2177-203X"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth A Dinsdale","raw_affiliation_strings":["Department of Biology, San Diego State University , San Diego, CA 92182, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, San Diego State University , San Diego, CA 92182, USA","institution_ids":["https://openalex.org/I26538001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110750689","display_name":"Brian Souza","orcid":"https://orcid.org/0009-0002-8341-5561"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian Souza","raw_affiliation_strings":["Lawrence Livermore National Laboratory , Livermore, CA 94550, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Livermore National Laboratory , Livermore, CA 94550, USA","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036802114","display_name":"Robert A. Edwards","orcid":"https://orcid.org/0000-0001-8383-8949"},"institutions":[{"id":"https://openalex.org/I26538001","display_name":"San Diego State University","ror":"https://ror.org/0264fdx42","country_code":"US","type":"education","lineage":["https://openalex.org/I26538001"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert A Edwards","raw_affiliation_strings":["Computational Sciences Research Center, San Diego State University , San Diego, CA 92182, USA","Department of Biology, San Diego State University , San Diego, CA 92182, USA","Viral Information Institute, San Diego State University , San Diego, CA 92182, USA"],"affiliations":[{"raw_affiliation_string":"Computational Sciences Research Center, San Diego State University , San Diego, CA 92182, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Department of Biology, San Diego State University , San Diego, CA 92182, USA","institution_ids":["https://openalex.org/I26538001"]},{"raw_affiliation_string":"Viral Information Institute, San Diego State University , San Diego, CA 92182, USA","institution_ids":["https://openalex.org/I26538001"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011823938","https://openalex.org/A5036802114"],"corresponding_institution_ids":["https://openalex.org/I26538001"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":9.2763,"has_fulltext":true,"cited_by_count":313,"citation_normalized_percentile":{"value":0.98697042,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"22","first_page":"4537","last_page":"4542"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10494","display_name":"Plant Virus Research Studies","score":0.9639999866485596,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8517565131187439},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.7809269428253174},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.7729696035385132},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6007756590843201},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5531651377677917},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5476993918418884},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.4694475829601288}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8517565131187439},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.7809269428253174},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.7729696035385132},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6007756590843201},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5531651377677917},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5476993918418884},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.4694475829601288}],"mesh":[{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz265","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4537/30706881/btz265.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31329826","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31329826","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:osti.gov:1625296","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1625296","pdf_url":"https://www.osti.gov/servlets/purl/1625296","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:europepmc.org:5823474","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6853651","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz265","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/22/4537/30706881/btz265.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G1044286447","display_name":"Broadening Opportunities for Interdisciplinary Computational Science and Engineering Research Training (ICSERT)","funder_award_id":"1259951","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3953509371","display_name":null,"funder_award_id":"10027","funder_id":"https://openalex.org/F4320332186","funder_display_name":"Defense Threat Reduction Agency"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7274182330","display_name":null,"funder_award_id":"DUE-1259951","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7320824963","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320332186","display_name":"Defense Threat Reduction Agency","ror":"https://ror.org/04tz64554"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2941437619.pdf","grobid_xml":"https://content.openalex.org/works/W2941437619.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1975518579","https://openalex.org/W2013544175","https://openalex.org/W2018934868","https://openalex.org/W2026535661","https://openalex.org/W2053150867","https://openalex.org/W2054441951","https://openalex.org/W2055757491","https://openalex.org/W2096093282","https://openalex.org/W2096525273","https://openalex.org/W2099952329","https://openalex.org/W2130124027","https://openalex.org/W2130291362","https://openalex.org/W2130734064","https://openalex.org/W2141172196","https://openalex.org/W2143235667","https://openalex.org/W2143485490","https://openalex.org/W2154760096","https://openalex.org/W2162758337","https://openalex.org/W2169899471","https://openalex.org/W2227557434","https://openalex.org/W2345791363","https://openalex.org/W2584861000","https://openalex.org/W2595562356","https://openalex.org/W2601963962","https://openalex.org/W2769504320","https://openalex.org/W2917702074","https://openalex.org/W3123255347","https://openalex.org/W4246954632","https://openalex.org/W4251386234","https://openalex.org/W4285719527","https://openalex.org/W4309520320","https://openalex.org/W6734786532"],"related_works":["https://openalex.org/W1993070549","https://openalex.org/W2987420353","https://openalex.org/W1491897707","https://openalex.org/W3094269189","https://openalex.org/W4321242349","https://openalex.org/W2112814626","https://openalex.org/W2130308509","https://openalex.org/W2114671460","https://openalex.org/W4380926374","https://openalex.org/W4205356040"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":25},{"year":2025,"cited_by_count":65},{"year":2024,"cited_by_count":65},{"year":2023,"cited_by_count":49},{"year":2022,"cited_by_count":33},{"year":2021,"cited_by_count":42},{"year":2020,"cited_by_count":28},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}
