{"id":"https://openalex.org/W3127732686","doi":"https://doi.org/10.1093/bib/bbab004","title":"Genome annotation of disease-causing microorganisms","display_name":"Genome annotation of disease-causing microorganisms","publication_year":2021,"publication_date":"2021-01-04","ids":{"openalex":"https://openalex.org/W3127732686","doi":"https://doi.org/10.1093/bib/bbab004","mag":"3127732686","pmid":"https://pubmed.ncbi.nlm.nih.gov/33537706"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab004","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab004","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7986607","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027267891","display_name":"Yibo Dong","orcid":"https://orcid.org/0000-0002-5264-1382"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yibo Dong","raw_affiliation_strings":["College of Public Health, University of South Florida, Tampa, FL, USA"],"raw_orcid":"https://orcid.org/0000-0002-5264-1382","affiliations":[{"raw_affiliation_string":"College of Public Health, University of South Florida, Tampa, FL, USA","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100429532","display_name":"Chang Li","orcid":"https://orcid.org/0000-0002-7823-3467"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chang Li","raw_affiliation_strings":["College of Public Health, University of South Florida, Tampa, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Public Health, University of South Florida, Tampa, FL, USA","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042341113","display_name":"Kami Kim","orcid":"https://orcid.org/0000-0003-3384-152X"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kami Kim","raw_affiliation_strings":["Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005484398","display_name":"Liwang Cui","orcid":"https://orcid.org/0000-0002-8338-1974"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liwang Cui","raw_affiliation_strings":["Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100409024","display_name":"Xiaoming Liu","orcid":"https://orcid.org/0000-0001-8285-5528"},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaoming Liu","raw_affiliation_strings":["College of Public Health, University of South Florida, Tampa, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Public Health, University of South Florida, Tampa, FL, USA","institution_ids":["https://openalex.org/I2613432"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027267891","https://openalex.org/A5100409024"],"corresponding_institution_ids":["https://openalex.org/I2613432"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.5468,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.82646219,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"22","issue":"2","first_page":"845","last_page":"854"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9991000294685364,"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/T11688","display_name":"Microbial infections and disease research","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.8431649208068848},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6621970534324646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5986701250076294},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.5864127278327942},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5269280672073364},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.5159597992897034},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5095229744911194},{"id":"https://openalex.org/keywords/microorganism","display_name":"Microorganism","score":0.46266746520996094},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4258244037628174},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3477296233177185},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3312775492668152},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.17573219537734985}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8431649208068848},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6621970534324646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5986701250076294},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.5864127278327942},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5269280672073364},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.5159597992897034},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5095229744911194},{"id":"https://openalex.org/C175605896","wikidata":"https://www.wikidata.org/wiki/Q39833","display_name":"Microorganism","level":3,"score":0.46266746520996094},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4258244037628174},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3477296233177185},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3312775492668152},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.17573219537734985}],"mesh":[{"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":"D014774","descriptor_name":"Virulence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014774","descriptor_name":"Virulence","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016680","descriptor_name":"Genome, Bacterial","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":"D016680","descriptor_name":"Genome, Bacterial","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":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbab004","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab004","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33537706","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33537706","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7986607","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7986607","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7986607","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7986607","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4528758607","display_name":null,"funder_award_id":"3U19AI089672","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":80,"referenced_works":["https://openalex.org/W957639803","https://openalex.org/W1484347389","https://openalex.org/W1484811165","https://openalex.org/W1494453148","https://openalex.org/W1580768657","https://openalex.org/W1598875902","https://openalex.org/W1760213857","https://openalex.org/W1971403296","https://openalex.org/W1986288847","https://openalex.org/W1996053875","https://openalex.org/W2001913949","https://openalex.org/W2004510715","https://openalex.org/W2004548026","https://openalex.org/W2008856488","https://openalex.org/W2018782288","https://openalex.org/W2035942710","https://openalex.org/W2037714544","https://openalex.org/W2037885326","https://openalex.org/W2042938763","https://openalex.org/W2045204781","https://openalex.org/W2045843097","https://openalex.org/W2055043387","https://openalex.org/W2063756105","https://openalex.org/W2077514957","https://openalex.org/W2090392412","https://openalex.org/W2096093282","https://openalex.org/W2097749211","https://openalex.org/W2101291993","https://openalex.org/W2101343648","https://openalex.org/W2101786683","https://openalex.org/W2103017472","https://openalex.org/W2103685216","https://openalex.org/W2108108770","https://openalex.org/W2108787198","https://openalex.org/W2110155683","https://openalex.org/W2116072809","https://openalex.org/W2116829579","https://openalex.org/W2118970397","https://openalex.org/W2121840477","https://openalex.org/W2126883736","https://openalex.org/W2128242967","https://openalex.org/W2141165178","https://openalex.org/W2142428670","https://openalex.org/W2142678478","https://openalex.org/W2143485490","https://openalex.org/W2143801061","https://openalex.org/W2154139219","https://openalex.org/W2154775341","https://openalex.org/W2159170019","https://openalex.org/W2159482845","https://openalex.org/W2163124559","https://openalex.org/W2164154943","https://openalex.org/W2168292723","https://openalex.org/W2173732482","https://openalex.org/W2214186913","https://openalex.org/W2224056471","https://openalex.org/W2338978258","https://openalex.org/W2470052926","https://openalex.org/W2740662778","https://openalex.org/W2766330607","https://openalex.org/W2903912180","https://openalex.org/W2912380124","https://openalex.org/W2931319350","https://openalex.org/W2936373164","https://openalex.org/W2941035732","https://openalex.org/W2941629467","https://openalex.org/W2947780575","https://openalex.org/W2951098419","https://openalex.org/W2951216011","https://openalex.org/W2953836633","https://openalex.org/W2957309664","https://openalex.org/W2966590054","https://openalex.org/W2989608901","https://openalex.org/W3009469344","https://openalex.org/W3025319533","https://openalex.org/W3028206028","https://openalex.org/W4210702584","https://openalex.org/W4236358448","https://openalex.org/W4251336367","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2162782320","https://openalex.org/W2059565715","https://openalex.org/W3111061871","https://openalex.org/W2009940763","https://openalex.org/W2114034054","https://openalex.org/W4232413416","https://openalex.org/W1585937270","https://openalex.org/W2537312848","https://openalex.org/W45826765","https://openalex.org/W1760213857"],"abstract_inverted_index":{"Humans":[0],"have":[1,12,43],"coexisted":[2],"with":[3],"pathogenic":[4,18,41,71],"microorganisms":[5,42,72],"throughout":[6],"its":[7],"history":[8],"of":[9,17,23,30,36,40,48,70,88],"evolution.":[10],"We":[11],"never":[13],"halted":[14],"the":[15,21,27,64,67,74],"exploration":[16],"microorganisms.":[19],"With":[20],"improvement":[22],"genome-sequencing":[24],"technology":[25],"and":[26,73,83,98,104],"continuous":[28],"reduction":[29],"sequencing":[31],"costs,":[32],"an":[33],"increasing":[34],"number":[35],"complete":[37],"genome":[38,68,77],"sequences":[39],"become":[44,54],"available.":[45],"Genome":[46],"annotation":[47,69,78,90],"this":[49],"massive":[50],"sequence":[51],"information":[52],"has":[53],"a":[55],"daunting":[56],"task":[57],"in":[58],"biological":[59],"research.":[60],"This":[61],"paper":[62],"summarizes":[63],"approaches":[65],"to":[66],"available":[75],"popular":[76],"tools":[79,91],"for":[80],"prokaryotes,":[81,96],"eukaryotes":[82,97],"viruses.":[84],"Furthermore,":[85],"real-world":[86],"comparisons":[87],"different":[89],"using":[92],"12":[93],"genomes":[94],"from":[95],"viruses":[99],"were":[100,106],"conducted.":[101],"Current":[102],"challenges":[103],"problems":[105],"also":[107],"discussed.":[108]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":10}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
