{"id":"https://openalex.org/W2072561431","doi":"https://doi.org/10.1371/journal.pcbi.1002230","title":"A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes","display_name":"A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes","publication_year":2011,"publication_date":"2011-10-20","ids":{"openalex":"https://openalex.org/W2072561431","doi":"https://doi.org/10.1371/journal.pcbi.1002230","mag":"2072561431","pmid":"https://pubmed.ncbi.nlm.nih.gov/22028637","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3197636"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002230","doi":"https://doi.org/10.1371/journal.pcbi.1002230","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002230","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002230&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002230&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006109392","display_name":"Alexis P Yelton","orcid":null,"observed_orcids":[]},"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":"Alexis P. Yelton","raw_affiliation_strings":["Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037479481","display_name":"Brian C. Thomas","orcid":"https://orcid.org/0000-0002-4806-333X","observed_orcids":["https://orcid.org/0000-0002-4806-333X"]},"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":"Brian C. Thomas","raw_affiliation_strings":["Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020753648","display_name":"Sheri L. Simmons","orcid":"https://orcid.org/0000-0001-7046-8862","observed_orcids":["https://orcid.org/0000-0001-7046-8862"]},"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":"Sheri L. Simmons","raw_affiliation_strings":["Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076512847","display_name":"Paul Wilmes","orcid":"https://orcid.org/0000-0002-6478-2924","observed_orcids":["https://orcid.org/0000-0002-6478-2924"]},"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":"Paul Wilmes","raw_affiliation_strings":["Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083445132","display_name":"Adam T Zemla","orcid":"https://orcid.org/0000-0003-0504-8647","observed_orcids":["https://orcid.org/0000-0003-0504-8647"]},"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":"Adam Zemla","raw_affiliation_strings":["Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045273277","display_name":"Michael P. Thelen","orcid":"https://orcid.org/0000-0002-2479-5480","observed_orcids":["https://orcid.org/0000-0002-2479-5480"]},"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":"Michael P. Thelen","raw_affiliation_strings":["Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002764099","display_name":"Nicholas B. Justice","orcid":null,"observed_orcids":[]},"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":"Nicholas Justice","raw_affiliation_strings":["Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045720453","display_name":"Jillian F. Banfield","orcid":"https://orcid.org/0000-0001-8203-8771","observed_orcids":["https://orcid.org/0000-0001-8203-8771","https://orcid.org/0000-0003-0406-9542"]},"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":"Jillian F. Banfield","raw_affiliation_strings":["Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America","Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045720453"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3043,"currency":"USD","value_usd":3043},"apc_paid":{"value":3043,"currency":"USD","value_usd":3043},"fwci":1.3687,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.78540593,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":87,"max":99},"biblio":{"volume":"7","issue":"10","first_page":"e1002230","last_page":"e1002230"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0007999999797903001,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.0003000000142492354,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/synteny","display_name":"synteny","score":0.8970000147819519},{"id":"https://openalex.org/keywords/gene-function-prediction","display_name":"gene function prediction","score":0.6679999828338623},{"id":"https://openalex.org/keywords/hypothetical-protein","display_name":"hypothetical protein","score":0.6340000033378601},{"id":"https://openalex.org/keywords/bacterial-genomes","display_name":"bacterial genomes","score":0.671999990940094},{"id":"https://openalex.org/keywords/archaeal-genomes","display_name":"archaeal genomes","score":0.9919999837875366},{"id":"https://openalex.org/keywords/genomic-rearrangements","display_name":"genome rearrangement","score":0.7889999747276306},{"id":"https://openalex.org/keywords/sequence-divergence","display_name":"sequence divergence","score":0.9710000157356262},{"id":"https://openalex.org/keywords/functional-conservation","display_name":"functional conservation","score":0.6309999823570251},{"id":"https://openalex.org/keywords/uncultivated-archaea","display_name":"uncultivated archaea","score":0.7789999842643738},{"id":"https://openalex.org/keywords/genome-annotation","display_name":"genome annotation","score":0.36399999260902405}],"concepts":[{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.9885568022727966},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7869350910186768},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7055231332778931},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5443124771118164},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5376123189926147},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5224460959434509},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4711274802684784},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.457007497549057},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.45423927903175354},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.41030001640319824},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39685454964637756},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3613203167915344},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.30123716592788696},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.15753602981567383}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019766","descriptor_name":"Genes, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019843","descriptor_name":"Archaeal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019843","descriptor_name":"Archaeal Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":12,"locations":[{"id":"doi:10.1371/journal.pcbi.1002230","doi":"https://doi.org/10.1371/journal.pcbi.1002230","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002230","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002230&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2201963","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3197636","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmid:22028637","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22028637","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":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3197636","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3197636/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:orbilu.uni.lu:10993/7788","doi":null,"is_oa":true,"landing_page_url":"https://orbilu.uni.lu/handle/10993/7788","pdf_url":"https://orbilu.uni.lu/bitstream/10993/7788/1/Yelton%282011%29PLoSCompBiol.pdf","source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 7 (10), e1002230 (2011)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:osti.gov:1627217","doi":null,"is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1627217","pdf_url":"https://www.osti.gov/servlets/purl/1627217","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,"listed_in":[],"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:CiteSeerX.psu:10.1.1.289.9705","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.289.9705","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/20/6a/PLoS_Comput_Biol_2011_Oct_20_7(10)_e1002230.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:944a944f8efb47d1bb6509bd53a851da","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/944a944f8efb47d1bb6509bd53a851da","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 7, Iss 10, p e1002230 (2011)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt1h34v7h2","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/1h34v7h2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 7, iss 10","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/132190","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_Semi_Quantitative_Synteny_Based_Method_to_Improve_Functional_Predictions_for_Hypothetical_and_Poorly_Annotated_Bacterial_and_Archaeal_Genes/132190","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/305334","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/11343/305334","pdf_url":null,"source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":"Journal Article"},{"id":"pmh:qt1h34v7h2","doi":null,"is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/1h34v7h2","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Yelton, AP; Thomas, BC; Simmons, SL; Wilmes, P; Zemla, A; Thelen, MP; \u00c2\u00a0et al.(2011). A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Computational Biology, 7(10). doi: 10.1371/journal.pcbi.1002230. UC Office of the President: Research Grants Program Office (RGPO). Retrieved from: http://www.escholarship.org/uc/item/1h34v7h2","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002230","doi":"https://doi.org/10.1371/journal.pcbi.1002230","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002230","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002230&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1804768066","display_name":"PROTEOGENOMIC APPROACHES FOR THE MOLECULAR CHARACTERIZATION OF NATURAL MICROBIAL COMMUNITIES","funder_award_id":"FG02-05ER64134","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2016868406","display_name":"PROTEOGENOMIC APPROACHES FOR THE MOLECULAR CHARACTERIZATION OF NATURAL MICROBIAL COMMUNITIES","funder_award_id":"FG02-05ER64134","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G222768804","display_name":null,"funder_award_id":"DE\u2010FG02\u2010","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2809806008","display_name":"TAS::89 0222::TAS  DEVELOPMENT OF A KNOWLEDGEBASE TO INTEGRATE, ANALYZE, DISTRIBUTE, AND VISUALIZE MICROBIAL COMMUNITY SYSTEMS BIOLOGY DATA","funder_award_id":"DESC0004918","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7069325280","display_name":"TAS::89 0222::TAS; NEW; TITLE: DEVELOPMENT AND INTEGRATION OF GENOME-ENABLED TECHNIQUES TO TRACK AND PREDICT THE CYCLING OF CARBON IN MODEL MICROBIAL","funder_award_id":"DESC0004665","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320331934","display_name":"NASA Astrobiology Institute","ror":"https://ror.org/01qxmdg18"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2072561431.pdf","grobid_xml":"https://content.openalex.org/works/W2072561431.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1972314084","https://openalex.org/W1995117714","https://openalex.org/W1996993655","https://openalex.org/W2002727587","https://openalex.org/W2006205474","https://openalex.org/W2009154103","https://openalex.org/W2010906017","https://openalex.org/W2013410948","https://openalex.org/W2017003789","https://openalex.org/W2017608263","https://openalex.org/W2034543587","https://openalex.org/W2036847531","https://openalex.org/W2050425822","https://openalex.org/W2053019594","https://openalex.org/W2074009961","https://openalex.org/W2098023550","https://openalex.org/W2106391842","https://openalex.org/W2107424557","https://openalex.org/W2107717979","https://openalex.org/W2119027485","https://openalex.org/W2119766894","https://openalex.org/W2121862891","https://openalex.org/W2123965484","https://openalex.org/W2124637227","https://openalex.org/W2125347557","https://openalex.org/W2128777911","https://openalex.org/W2137896807","https://openalex.org/W2143485490","https://openalex.org/W2145506897","https://openalex.org/W2151018240","https://openalex.org/W2157975034","https://openalex.org/W2169507523"],"related_works":["https://openalex.org/W2045489348","https://openalex.org/W2161012147","https://openalex.org/W4400120209","https://openalex.org/W2032066426","https://openalex.org/W2171512516","https://openalex.org/W2108274573","https://openalex.org/W2139380074","https://openalex.org/W2228579125","https://openalex.org/W7096633073","https://openalex.org/W2137926113"],"abstract_inverted_index":{"During":[0],"microbial":[1],"evolution,":[2],"genome":[3,135],"rearrangement":[4],"increases":[5],"with":[6],"increasing":[7],"sequence":[8,16,58],"divergence.":[9],"If":[10],"the":[11,43,69,93,101,106,126,142,165,179,195],"relationship":[12],"between":[13,55,95,134],"synteny":[14,31,56,96,187],"and":[15,35,50,57,65,72,91,97,145,193],"divergence":[17,59],"can":[18,32],"be":[19,33],"modeled,":[20],"gene":[21,116,161,182],"clusters":[22],"in":[23,60,100,105,149],"genomes":[24,67,76,103,156],"of":[25,77,128,131,178,181],"distantly":[26],"related":[27],"organisms":[28],"exhibiting":[29],"anomalous":[30],"identified":[34],"used":[36],"to":[37,48,124,141,157,168,172],"infer":[38],"functional":[39,98,117,129,183],"conservation.":[40],"We":[41],"applied":[42,140],"phylogenetic":[44],"pairwise":[45],"comparison":[46],"method":[47,119,138,167],"establish":[49],"model":[51],"a":[52,115,189],"strong":[53],"correlation":[54],"all":[61],"634":[62],"available":[63,104],"Archaeal":[64,155],"Bacterial":[66],"from":[68,80],"NCBI":[70],"database":[71],"four":[73],"newly":[74,150],"assembled":[75,151],"uncultivated":[78],"Archaea":[79],"an":[81],"acid":[82,152],"mine":[83,153],"drainage":[84,154],"(AMD)":[85],"community.":[86],"In":[87],"parallel,":[88],"we":[89,113],"established":[90],"modeled":[92],"trend":[94],"relatedness":[99],"118":[102],"STRING":[107],"database.":[108],"By":[109],"combining":[110],"these":[111],"models,":[112],"developed":[114],"annotation":[118],"that":[120],"weights":[121],"evolutionary":[122,191],"distance":[123],"estimate":[125],"probability":[127,180],"associations":[130],"syntenous":[132],"proteins":[133,144],"pairs.":[136],"The":[137],"was":[139],"hypothetical":[143],"poorly":[146,173],"annotated":[147,174],"genes":[148,175],"add":[158],"or":[159],"improve":[160],"annotations.":[162],"This":[163],"is":[164],"first":[166],"assign":[169],"possible":[170],"functions":[171],"through":[176],"quantification":[177],"relationships":[184],"based":[185],"on":[186],"at":[188],"significant":[190],"distance,":[192],"has":[194],"potential":[196],"for":[197],"broad":[198],"application.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2016-06-24T00:00:00"}