{"id":"https://openalex.org/W2124527296","doi":"https://doi.org/10.1093/bioinformatics/bth317","title":"Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication","display_name":"Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication","publication_year":2004,"publication_date":"2004-05-14","ids":{"openalex":"https://openalex.org/W2124527296","doi":"https://doi.org/10.1093/bioinformatics/bth317","mag":"2124527296","pmid":"https://pubmed.ncbi.nlm.nih.gov/15145803"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth317","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2719/48906254/bioinformatics_20_16_2719.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2719/48906254/bioinformatics_20_16_2719.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063289045","display_name":"Nicolas Omont","orcid":"https://orcid.org/0000-0003-3348-9853"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nicolas Omont","raw_affiliation_strings":["ATGC, CNRS UMR 8071/genopole\u00ae, 523 Terrasses de l'Agora, 91000 Evry, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ATGC, CNRS UMR 8071/genopole\u00ae, 523 Terrasses de l'Agora, 91000 Evry, France","institution_ids":["https://openalex.org/I4210128926","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052082741","display_name":"Fran\u00e7ois K\u00e9p\u00e8s","orcid":"https://orcid.org/0000-0001-5766-4957"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210128926","display_name":"Genopole (France)","ror":"https://ror.org/0380k9k47","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210128926"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fran\u00e7ois K\u00e9p\u00e8s","raw_affiliation_strings":["ATGC, CNRS UMR 8071/genopole\u00ae, 523 Terrasses de l'Agora, 91000 Evry, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ATGC, CNRS UMR 8071/genopole\u00ae, 523 Terrasses de l'Agora, 91000 Evry, France","institution_ids":["https://openalex.org/I4210128926","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5063289045"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210128926"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8998,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.76204329,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"20","issue":"16","first_page":"2719","last_page":"2725"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9995999932289124,"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":0.9980000257492065,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9976999759674072,"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/transcription","display_name":"Transcription (linguistics)","score":0.7136009931564331},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5762814283370972},{"id":"https://openalex.org/keywords/dna-replication","display_name":"DNA replication","score":0.5646476149559021},{"id":"https://openalex.org/keywords/lagging","display_name":"Lagging","score":0.5103306174278259},{"id":"https://openalex.org/keywords/replication","display_name":"Replication (statistics)","score":0.4725223183631897},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4571078419685364},{"id":"https://openalex.org/keywords/origin-of-replication","display_name":"Origin of replication","score":0.44869449734687805},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.38489046692848206},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3520510196685791},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1645270586013794},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12579193711280823},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.055015236139297485}],"concepts":[{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.7136009931564331},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5762814283370972},{"id":"https://openalex.org/C73573662","wikidata":"https://www.wikidata.org/wiki/Q130996","display_name":"DNA replication","level":3,"score":0.5646476149559021},{"id":"https://openalex.org/C2776962539","wikidata":"https://www.wikidata.org/wiki/Q6472078","display_name":"Lagging","level":2,"score":0.5103306174278259},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.4725223183631897},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4571078419685364},{"id":"https://openalex.org/C58337764","wikidata":"https://www.wikidata.org/wiki/Q976651","display_name":"Origin of replication","level":4,"score":0.44869449734687805},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.38489046692848206},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3520510196685791},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1645270586013794},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12579193711280823},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.055015236139297485},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012093","descriptor_name":"Replicon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012093","descriptor_name":"Replicon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012093","descriptor_name":"Replicon","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth317","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2719/48906254/bioinformatics_20_16_2719.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15145803","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15145803","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.965.3553","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.965.3553","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2004/05/14/bioinformatics.bth317.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth317","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth317","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2719/48906254/bioinformatics_20_16_2719.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W129666705","https://openalex.org/W749297700","https://openalex.org/W1009707322","https://openalex.org/W1493097357","https://openalex.org/W1528293448","https://openalex.org/W1602283030","https://openalex.org/W1972204126","https://openalex.org/W1974527579","https://openalex.org/W1993973779","https://openalex.org/W2008490130","https://openalex.org/W2016988643","https://openalex.org/W2020271217","https://openalex.org/W2025853251","https://openalex.org/W2026600225","https://openalex.org/W2053501576","https://openalex.org/W2058213686","https://openalex.org/W2084581607","https://openalex.org/W2086084754","https://openalex.org/W2089287013","https://openalex.org/W2091011084","https://openalex.org/W2091355621","https://openalex.org/W2096652923","https://openalex.org/W2159298742"],"related_works":["https://openalex.org/W2329795915","https://openalex.org/W1970722699","https://openalex.org/W1981922425","https://openalex.org/W2102366565","https://openalex.org/W2082627754","https://openalex.org/W2123987161","https://openalex.org/W2043025987","https://openalex.org/W84663166","https://openalex.org/W2059208699","https://openalex.org/W2084837006"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,154],"costs":[2],"of":[3,33,46,50,55,82,101,143,162],"head-on":[4,163],"versus":[5,164],"codirectional":[6,165],"collisions":[7,51],"between":[8,84],"the":[9,13,19,31,36,43,48,53,71,78,85,96,99,108],"replication":[10],"complex":[11,17],"and":[12,134,145,151],"much":[14,24],"slower":[15],"transcription":[16,56,65,131],"on":[18,35,42,52,70,95],"circular":[20],"bacterial":[21],"chromosomes":[22],"are":[23,58,67,156],"debated.":[25],"Although":[26],"it":[27],"is":[28,39,107,118,138],"established":[29],"that":[30,64,98,119],"number":[32,81],"genes":[34],"leading":[37,72],"strand":[38,45],"higher":[40],"than":[41],"lagging":[44],"replication,":[47],"consequences":[49],"length":[54,133],"units":[57,66,83,147],"unknown.":[59],"RESULTS:":[60],"Here,":[61],"we":[62],"show":[63],"generally":[68],"longer":[69],"strand,":[73],"in":[74,80,148],"rough":[75],"proportion":[76,100],"to":[77,112],"bias":[79,129],"two":[86],"strands.":[87],"We":[88],"propose":[89],"a":[90,120,126],"statistical":[91],"physics":[92],"model,":[93],"based":[94],"assumption":[97],"interrupted":[102],"transcripts":[103],"for":[104,130],"each":[105],"unit":[106,132],"major":[109],"factor":[110],"contributing":[111],"these":[113],"biases.":[114],"Its":[115],"main":[116],"prediction":[117],"large":[121],"replication/transcription":[122],"speed":[123],"ratio":[124],"implies":[125],"low":[127],"leading/lagging":[128],"number.":[135],"This":[136],"model":[137],"validated":[139],"by":[140],"an":[141,159],"analysis":[142],"proven":[144],"predicted":[146],"Escherichia":[149],"coli":[150],"Bacillus":[152],"subtilis.":[153],"results":[155],"consistent":[157],"with":[158],"equal":[160],"cost":[161],"collisions.":[166]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}