{"id":"https://openalex.org/W3111455950","doi":"https://doi.org/10.1016/j.chom.2020.11.002","title":"Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes","display_name":"Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes","publication_year":2020,"publication_date":"2020-12-07","ids":{"openalex":"https://openalex.org/W3111455950","doi":"https://doi.org/10.1016/j.chom.2020.11.002","mag":"3111455950","pmid":"https://pubmed.ncbi.nlm.nih.gov/33290720","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7856248"},"language":"en","primary_location":{"id":"doi:10.1016/j.chom.2020.11.002","doi":"https://doi.org/10.1016/j.chom.2020.11.002","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.chom.2020.11.002","pdf_url":"http://www.cell.com/article/S1931312820306193/pdf","source":{"id":"https://openalex.org/S207313999","display_name":"Cell Host & Microbe","issn_l":"1931-3128","issn":["1931-3128","1934-6069"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315673","host_organization_name":"Cell Press","host_organization_lineage":["https://openalex.org/P4310315673","https://openalex.org/P4310320990"],"host_organization_lineage_names":["Cell Press","Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Host &amp; Microbe","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"http://www.cell.com/article/S1931312820306193/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066121433","display_name":"Matthew G. Durrant","orcid":"https://orcid.org/0000-0001-8433-1760","observed_orcids":["https://orcid.org/0000-0001-8433-1760"]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew G. Durrant","raw_affiliation_strings":["Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA","Department of Genetics, Stanford University, Stanford, CA 94305, USA","Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080667439","display_name":"Ami Siddharth Bhatt","orcid":"https://orcid.org/0000-0001-8099-2975","observed_orcids":["https://orcid.org/0000-0001-8099-2975"]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ami S. Bhatt","raw_affiliation_strings":["Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA. Electronic address: asbhatt@stanford.edu","Department of Genetics, Stanford University, Stanford, CA 94305, USA","Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA. Electronic address: asbhatt@stanford.edu","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5080667439"],"corresponding_institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"],"apc_list":{"value":5200,"currency":"USD","value_usd":5200},"apc_paid":null,"fwci":1.3618,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.80297126,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"29","issue":"1","first_page":"121","last_page":"131.e4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9868000149726868,"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":0.9868000149726868,"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":0.005200000014156103,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.00279999990016222,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/small-open-reading-frames","display_name":"small open reading frames","score":0.9990000128746033},{"id":"https://openalex.org/keywords/microproteins","display_name":"microproteins","score":0.9750000238418579},{"id":"https://openalex.org/keywords/profile-hidden-markov-models","display_name":"profile hidden Markov models","score":0.8899999856948853},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.9089999794960022},{"id":"https://openalex.org/keywords/shine-dalgarno-sequence","display_name":"Shine-Dalgarno sequence","score":0.9440000057220459},{"id":"https://openalex.org/keywords/codon-usage","display_name":"codon usage","score":0.7680000066757202},{"id":"https://openalex.org/keywords/metagenome-annotation","display_name":"metagenome annotation","score":0.6869999766349792},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.8629999756813049}],"concepts":[{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.8221924901008606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7500817775726318},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6572927236557007},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6385399103164673},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.5778641104698181},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5599156618118286},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.45886796712875366},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.4428957998752594},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.43281498551368713},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4269295334815979},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3342031240463257},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32747483253479004},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3222670555114746},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19558849930763245},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.08628737926483154}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","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":"D008390","descriptor_name":"Markov Chains","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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1016/j.chom.2020.11.002","doi":"https://doi.org/10.1016/j.chom.2020.11.002","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.chom.2020.11.002","pdf_url":"http://www.cell.com/article/S1931312820306193/pdf","source":{"id":"https://openalex.org/S207313999","display_name":"Cell Host & Microbe","issn_l":"1931-3128","issn":["1931-3128","1934-6069"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315673","host_organization_name":"Cell Press","host_organization_lineage":["https://openalex.org/P4310315673","https://openalex.org/P4310320990"],"host_organization_lineage_names":["Cell Press","Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Host &amp; Microbe","raw_type":"journal-article"},{"id":"doi:10.1101/2020.07.27.224071","doi":"https://doi.org/10.1101/2020.07.27.224071","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2020.07.27.224071","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/07/28/2020.07.27.224071.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:33290720","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33290720","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,"listed_in":[],"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":"Cell host & microbe","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7856248","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7856248","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,"listed_in":[],"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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Cell Host Microbe","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/j.chom.2020.11.002","doi":"https://doi.org/10.1016/j.chom.2020.11.002","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.chom.2020.11.002","pdf_url":"http://www.cell.com/article/S1931312820306193/pdf","source":{"id":"https://openalex.org/S207313999","display_name":"Cell Host & Microbe","issn_l":"1931-3128","issn":["1931-3128","1934-6069"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315673","host_organization_name":"Cell Press","host_organization_lineage":["https://openalex.org/P4310315673","https://openalex.org/P4310320990"],"host_organization_lineage_names":["Cell Press","Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Host &amp; Microbe","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1118961925","display_name":"Emerging novel mechanisms of antibiotic resistance in the prevalent foodborne pathogen, Salmonella","funder_award_id":"R01AI148623","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4969444111","display_name":"Culture-free pathogen tracking in hospitalized patients","funder_award_id":"R01AI143757","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G9000859589","display_name":"Stanford Cancer Institute","funder_award_id":"P30CA124435","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3111455950.pdf","grobid_xml":"https://content.openalex.org/works/W3111455950.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1602283030","https://openalex.org/W1999137349","https://openalex.org/W2012681204","https://openalex.org/W2045204781","https://openalex.org/W2050541807","https://openalex.org/W2058832897","https://openalex.org/W2079517684","https://openalex.org/W2081090039","https://openalex.org/W2096093282","https://openalex.org/W2097606916","https://openalex.org/W2102619694","https://openalex.org/W2109986833","https://openalex.org/W2118861614","https://openalex.org/W2121350645","https://openalex.org/W2132833976","https://openalex.org/W2132926880","https://openalex.org/W2140874466","https://openalex.org/W2143485490","https://openalex.org/W2151831732","https://openalex.org/W2157009395","https://openalex.org/W2170551349","https://openalex.org/W2170747616","https://openalex.org/W2605409611","https://openalex.org/W2612690371","https://openalex.org/W2618851150","https://openalex.org/W2766288908","https://openalex.org/W2810973266","https://openalex.org/W2897496220","https://openalex.org/W2898402099","https://openalex.org/W2901218091","https://openalex.org/W2906991531","https://openalex.org/W2917341168","https://openalex.org/W2949068808","https://openalex.org/W2949203875","https://openalex.org/W2949435868","https://openalex.org/W2950150251","https://openalex.org/W2959763773","https://openalex.org/W2963815651","https://openalex.org/W2964121744","https://openalex.org/W2968334948","https://openalex.org/W2987349979","https://openalex.org/W2991012415","https://openalex.org/W3011414077","https://openalex.org/W3021822345","https://openalex.org/W3037676786","https://openalex.org/W4241036346"],"related_works":["https://openalex.org/W4361267598","https://openalex.org/W3093176393","https://openalex.org/W3021822345","https://openalex.org/W3170179436","https://openalex.org/W2992003657","https://openalex.org/W4401015600","https://openalex.org/W3199765866","https://openalex.org/W3019862115","https://openalex.org/W4402098128","https://openalex.org/W2917341168"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2020-12-21T00:00:00"}
