{"id":"https://openalex.org/W2103779449","doi":"https://doi.org/10.1186/1471-2105-11-s3-s10","title":"Bacillus anthracis genome organization in light of whole transcriptome sequencing","display_name":"Bacillus anthracis genome organization in light of whole transcriptome sequencing","publication_year":2010,"publication_date":"2010-04-01","ids":{"openalex":"https://openalex.org/W2103779449","doi":"https://doi.org/10.1186/1471-2105-11-s3-s10","mag":"2103779449","pmid":"https://pubmed.ncbi.nlm.nih.gov/20438648","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2863060"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s3-s10","doi":"https://doi.org/10.1186/1471-2105-11-s3-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s3-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011861863","display_name":"Jeff Vance Martin","orcid":"https://orcid.org/0000-0001-5575-2873","observed_orcids":["https://orcid.org/0000-0001-5575-2873"]},"institutions":[{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey Martin","raw_affiliation_strings":["DOE Joint Genome Institute, Walnut Creek, CA 94598, USA","DOE Joint Genome Institute, Walnut Creek, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DOE Joint Genome Institute, Walnut Creek, CA 94598, USA","institution_ids":["https://openalex.org/I196679689"]},{"raw_affiliation_string":"DOE Joint Genome Institute, Walnut Creek, USA","institution_ids":["https://openalex.org/I196679689"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073353299","display_name":"Wenhan Zhu","orcid":"https://orcid.org/0000-0003-3771-0842","observed_orcids":["https://orcid.org/0000-0003-3771-0842"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenhan Zhu","raw_affiliation_strings":["School of Biology, Georgia Tech, Atlanta, GA, 30332, USA","School of Biology, Georgia Tech, Atlanta, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Tech, Atlanta, GA, 30332, USA","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"School of Biology, Georgia Tech, Atlanta, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032973104","display_name":"Karla D. Passalacqua","orcid":"https://orcid.org/0000-0002-2672-3261","observed_orcids":["https://orcid.org/0000-0002-2672-3261"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karla D Passalacqua","raw_affiliation_strings":["School of Biology, Georgia Tech, Atlanta, GA, 30332, USA","School of Biology, Georgia Tech, Atlanta, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology, Georgia Tech, Atlanta, GA, 30332, USA","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"School of Biology, Georgia Tech, Atlanta, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030675176","display_name":"Nicholas H. Bergman","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Bergman","raw_affiliation_strings":["National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA","School of Biology, Georgia Tech, Atlanta, GA, 30332, USA","School of Biology, Georgia Tech, Atlanta, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA","institution_ids":[]},{"raw_affiliation_string":"School of Biology, Georgia Tech, Atlanta, GA, 30332, USA","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"School of Biology, Georgia Tech, Atlanta, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057317686","display_name":"Mark Yu. Borodovsky","orcid":"https://orcid.org/0000-0002-1401-4046","observed_orcids":["https://orcid.org/0000-0002-1401-4046"]},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]},{"id":"https://openalex.org/I2802612298","display_name":"The Wallace H. Coulter Department of Biomedical Engineering","ror":"https://ror.org/02j15s898","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444","https://openalex.org/I150468666","https://openalex.org/I2802612298"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Borodovsky","raw_affiliation_strings":["Center for Bioinformatics and Computational Genomics, Georgia Tech, Atlanta, GA, 30332, USA","Wallace H. Coulter Department of Biomedical Engineering and School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, 30332, USA","Wallace H. Coulter Department of Biomedical Engineering and School of Computational Science and Engineering, Georgia Tech, Atlanta, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Genomics, Georgia Tech, Atlanta, GA, 30332, USA","institution_ids":["https://openalex.org/I130701444"]},{"raw_affiliation_string":"Wallace H. Coulter Department of Biomedical Engineering and School of Computational Science and Engineering, Georgia Tech, Atlanta, GA, 30332, USA","institution_ids":["https://openalex.org/I130701444","https://openalex.org/I2802612298"]},{"raw_affiliation_string":"Wallace H. Coulter Department of Biomedical Engineering and School of Computational Science and Engineering, Georgia Tech, Atlanta, USA","institution_ids":["https://openalex.org/I130701444","https://openalex.org/I2802612298"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057317686"],"corresponding_institution_ids":["https://openalex.org/I130701444","https://openalex.org/I2802612298"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":3.9053,"has_fulltext":true,"cited_by_count":61,"citation_normalized_percentile":{"value":0.94709455,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"11","issue":"S3","first_page":"S10","last_page":"S10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9643999934196472,"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":0.9643999934196472,"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":0.014399999752640724,"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"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.009700000286102295,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bacillus-anthracis","display_name":"Bacillus anthracis","score":1.0},{"id":"https://openalex.org/keywords/gene-expression","display_name":"gene expression","score":0.6600000262260437},{"id":"https://openalex.org/keywords/promoter-strength","display_name":"promoter strength","score":0.6980000138282776},{"id":"https://openalex.org/keywords/codon-adaptation-index","display_name":"codon adaptation index","score":0.9959999918937683},{"id":"https://openalex.org/keywords/translation-speed","display_name":"translation speed","score":0.7429999709129333},{"id":"https://openalex.org/keywords/genome-annotation","display_name":"genome annotation","score":0.7670000195503235},{"id":"https://openalex.org/keywords/pseudogenes","display_name":"pseudogenes","score":0.8370000123977661},{"id":"https://openalex.org/keywords/transcriptome-mapping","display_name":"transcriptome mapping","score":0.5770000219345093},{"id":"https://openalex.org/keywords/genome-organization","display_name":"genome organization","score":0.46799999475479126}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.715732216835022},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.695321261882782},{"id":"https://openalex.org/C34957205","wikidata":"https://www.wikidata.org/wiki/Q277338","display_name":"Pseudogene","level":4,"score":0.6480370759963989},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6235100626945496},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6204107403755188},{"id":"https://openalex.org/C178046730","wikidata":"https://www.wikidata.org/wiki/Q331824","display_name":"Terminator (solar)","level":3,"score":0.6004688739776611},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5756793022155762},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.5402528643608093},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5100293755531311},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.453464150428772},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4277692437171936},{"id":"https://openalex.org/C2780239966","wikidata":"https://www.wikidata.org/wiki/Q614156","display_name":"Bacillus anthracis","level":3,"score":0.41460371017456055},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.41449445486068726},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3391960859298706},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C116403925","wikidata":"https://www.wikidata.org/wiki/Q162219","display_name":"Ionosphere","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001408","descriptor_name":"Bacillus anthracis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D012329","descriptor_name":"RNA, Bacterial","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D013728","descriptor_name":"Terminator Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015964","descriptor_name":"Gene Expression Regulation, 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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1186/1471-2105-11-s3-s10","doi":"https://doi.org/10.1186/1471-2105-11-s3-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s3-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2863060","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2863060","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmid:20438648","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20438648","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:info:ark/67531/metadc1014080","doi":null,"is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc1014080/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Name: BMC Bioinformatics; Journal Volume: 11; Journal Issue: Supplement 3","raw_type":"Article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt4vv355d4","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/4vv355d4","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":"","raw_type":"article"},{"id":"pmh:oai:osti.gov:985903","doi":null,"is_oa":false,"landing_page_url":"https://www.osti.gov/biblio/985903","pdf_url":null,"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:smartech.gatech.edu:1853/47407","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1853/47407","pdf_url":null,"source":{"id":"https://openalex.org/S4377196313","display_name":"SMARTech Repository (Georgia Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I130701444","host_organization_name":"Georgia Institute of Technology","host_organization_lineage":["https://openalex.org/I130701444"],"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":"Text"},{"id":"pmh:qt4vv355d4","doi":null,"is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/4vv355d4","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":"Martin, Jeffrey. (2010). Bacillus anthracis genome organization in light of whole transcriptome sequencing. Lawrence Berkeley National Laboratory. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/4vv355d4","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s3-s10","doi":"https://doi.org/10.1186/1471-2105-11-s3-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s3-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S3-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2880384052","display_name":null,"funder_award_id":"Contract DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G3031498855","display_name":null,"funder_award_id":"HG 00783","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G382641700","display_name":null,"funder_award_id":"DE-AC02\u201305CH11231","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G419881185","display_name":null,"funder_award_id":"DEAC02\u201305CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G42916606","display_name":null,"funder_award_id":"DE AC02 05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G465867758","display_name":null,"funder_award_id":"Contract DE-AC02-05CH11231.","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5047612491","display_name":"Gene Prediction by Markov Models and Complementary Methods","funder_award_id":"R01HG000783","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G6652958823","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7205239661","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G834277795","display_name":null,"funder_award_id":"DE\u2013AC02\u201305CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320333761","display_name":"Wallace H. Coulter Department of Biomedical Engineering","ror":"https://ror.org/02j15s898"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103779449.pdf","grobid_xml":"https://content.openalex.org/works/W2103779449.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1527267184","https://openalex.org/W1967656821","https://openalex.org/W2004146038","https://openalex.org/W2018590530","https://openalex.org/W2030205072","https://openalex.org/W2051406384","https://openalex.org/W2068694787","https://openalex.org/W2081746271","https://openalex.org/W2106090237","https://openalex.org/W2107804881","https://openalex.org/W2109295007","https://openalex.org/W2115228331","https://openalex.org/W2115749923","https://openalex.org/W2119490692","https://openalex.org/W2143221412","https://openalex.org/W2143235667","https://openalex.org/W2144795887","https://openalex.org/W2144870003","https://openalex.org/W2145477956","https://openalex.org/W2149429041","https://openalex.org/W2151695055","https://openalex.org/W2153515666","https://openalex.org/W2162111678","https://openalex.org/W2162277333","https://openalex.org/W4250052351"],"related_works":["https://openalex.org/W2151695055","https://openalex.org/W2153515666","https://openalex.org/W117536713","https://openalex.org/W2163069781","https://openalex.org/W2766330166","https://openalex.org/W329997404","https://openalex.org/W7095258235","https://openalex.org/W2042645150","https://openalex.org/W7099425792","https://openalex.org/W7095993919"],"abstract_inverted_index":{"Emerging":[0],"knowledge":[1],"of":[2,10,18,35,61,70,90,101,122,124,127,144],"whole":[3,57],"prokaryotic":[4],"transcriptomes":[5],"could":[6],"validate":[7],"a":[8,62,87,147,171],"number":[9],"theoretical":[11],"concepts":[12],"introduced":[13],"in":[14,130,151],"the":[15,22,56,105,131,139,152],"early":[16],"days":[17],"genomics.":[19],"What":[20],"are":[21],"rules":[23],"connecting":[24],"gene":[25,52,71,91,118,160],"expression":[26,72],"levels":[27],"with":[28,74,86,104,173],"sequence":[29,172],"determinants":[30],"such":[31],"as":[32,83,85],"quantitative":[33],"scores":[34],"promoters":[36,179],"and":[37,47,77],"terminators?":[38],"Are":[39],"translation":[40,95],"efficiency":[41],"measures,":[42],"e.g.":[43],"codon":[44,80],"adaptation":[45,81],"index":[46],"RBS":[48,78],"score":[49],"related":[50],"to":[51,67],"expression?":[53],"We":[54,97],"used":[55],"transcriptome":[58,140],"shotgun":[59],"sequencing":[60],"bacterial":[63],"pathogen":[64],"Bacillus":[65],"anthracis":[66,133],"assess":[68],"correlation":[69],"level":[73],"promoter,":[75],"terminator":[76],"scores,":[79],"index,":[82],"well":[84],"new":[88],"measure":[89],"translational":[92],"efficiency,":[93],"average":[94],"speed.":[96],"compared":[98],"computational":[99],"predictions":[100],"operon":[102],"topologies":[103],"transcript":[106],"borders":[107],"inferred":[108],"from":[109],"RNA-Seq":[110],"reads.":[111],"Transcriptome":[112],"mapping":[113],"may":[114],"also":[115,178],"improve":[116],"existing":[117],"annotation.":[119],"Upon":[120],"assessment":[121],"accuracy":[123],"current":[125],"annotation":[126,153],"protein-coding":[128],"genes":[129,149],"B.":[132],"genome":[134],"we":[135,163],"have":[136],"shown":[137],"that":[138,165,180],"data":[141],"indicate":[142],"existence":[143],"more":[145],"than":[146],"hundred":[148],"missing":[150],"though":[154],"predicted":[155],"by":[156],"an":[157],"ab":[158],"initio":[159],"finder.":[161],"Interestingly,":[162],"observed":[164],"many":[166],"pseudogenes":[167],"possess":[168],"not":[169],"only":[170],"detectable":[174],"coding":[175],"potential":[176],"but":[177],"maintain":[181],"transcriptional":[182],"activity.":[183]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":6}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
