{"id":"https://openalex.org/W1630242350","doi":"https://doi.org/10.3233/isb-140462","title":"<i>In silico</i> analysis of division times of <i>Escherichia coli</i> populations as a function of the partitioning scheme of non-functional proteins","display_name":"<i>In silico</i> analysis of division times of <i>Escherichia coli</i> populations as a function of the partitioning scheme of non-functional proteins","publication_year":2015,"publication_date":"2015-07-03","ids":{"openalex":"https://openalex.org/W1630242350","doi":"https://doi.org/10.3233/isb-140462","mag":"1630242350","pmid":"https://pubmed.ncbi.nlm.nih.gov/25318468"},"language":"en","primary_location":{"id":"doi:10.3233/isb-140462","is_oa":false,"landing_page_url":"https://doi.org/10.3233/isb-140462","pdf_url":null,"source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077731218","display_name":"Abhishekh Gupta","orcid":"https://orcid.org/0000-0002-0212-3958"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Abhishekh Gupta","raw_affiliation_strings":["Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland","Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024131754","display_name":"Jason Lloyd\u2010Price","orcid":"https://orcid.org/0000-0002-0112-190X"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jason Lloyd-Price","raw_affiliation_strings":["Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland","Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040628945","display_name":"Andr\u00e9 S. Ribeiro","orcid":"https://orcid.org/0000-0002-7255-5211"},"institutions":[{"id":"https://openalex.org/I150589677","display_name":"Tampere University of Applied Sciences","ror":"https://ror.org/00bwtjf83","country_code":"FI","type":"education","lineage":["https://openalex.org/I150589677"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Andre S. Ribeiro","raw_affiliation_strings":["Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland","[Tampere Univ. of Tech.]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"[Tampere Univ. of Tech.]","institution_ids":["https://openalex.org/I150589677"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077731218"],"corresponding_institution_ids":["https://openalex.org/I4210133110"],"apc_list":null,"apc_paid":null,"fwci":0.9761,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.79159585,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"1-2","first_page":"9","last_page":"21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991999864578247,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991999864578247,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9983999729156494,"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":0.996999979019165,"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/in-silico","display_name":"In silico","score":0.7682767510414124},{"id":"https://openalex.org/keywords/cell-division","display_name":"Cell division","score":0.7640438079833984},{"id":"https://openalex.org/keywords/ftsz","display_name":"FtsZ","score":0.6350971460342407},{"id":"https://openalex.org/keywords/nucleoid","display_name":"Nucleoid","score":0.6293013095855713},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6010898947715759},{"id":"https://openalex.org/keywords/division","display_name":"Division (mathematics)","score":0.5014221668243408},{"id":"https://openalex.org/keywords/polar","display_name":"Polar","score":0.4923359155654907},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.4847123622894287},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4689601957798004},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.443491667509079},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.43836086988449097},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.4339519739151001},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40777668356895447},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.40431472659111023},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.370008647441864},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3596630096435547},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3348589539527893},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29969334602355957},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15252235531806946},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0844908058643341}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7682767510414124},{"id":"https://openalex.org/C85813293","wikidata":"https://www.wikidata.org/wiki/Q188909","display_name":"Cell division","level":3,"score":0.7640438079833984},{"id":"https://openalex.org/C2776237524","wikidata":"https://www.wikidata.org/wiki/Q24773445","display_name":"FtsZ","level":4,"score":0.6350971460342407},{"id":"https://openalex.org/C53642103","wikidata":"https://www.wikidata.org/wiki/Q459485","display_name":"Nucleoid","level":4,"score":0.6293013095855713},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6010898947715759},{"id":"https://openalex.org/C60798267","wikidata":"https://www.wikidata.org/wiki/Q1226939","display_name":"Division (mathematics)","level":2,"score":0.5014221668243408},{"id":"https://openalex.org/C29705727","wikidata":"https://www.wikidata.org/wiki/Q294562","display_name":"Polar","level":2,"score":0.4923359155654907},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.4847123622894287},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4689601957798004},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.443491667509079},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.43836086988449097},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.4339519739151001},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40777668356895447},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.40431472659111023},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.370008647441864},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3596630096435547},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3348589539527893},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29969334602355957},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15252235531806946},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0844908058643341},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"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/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.3233/isb-140462","is_oa":false,"landing_page_url":"https://doi.org/10.3233/isb-140462","pdf_url":null,"source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"In Silico Biology","raw_type":"journal-article"},{"id":"pmid:25318468","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25318468","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":"In silico biology","raw_type":null},{"id":"pmh:oai:europepmc.org:3887836","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4923715","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,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321726","display_name":"Suomen Kulttuurirahasto","ror":"https://ror.org/027xav248"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1482870101","https://openalex.org/W1498099361","https://openalex.org/W1575636604","https://openalex.org/W1638059342","https://openalex.org/W1897176773","https://openalex.org/W1979922817","https://openalex.org/W1980597219","https://openalex.org/W1982396530","https://openalex.org/W1982760825","https://openalex.org/W1984571004","https://openalex.org/W1985161570","https://openalex.org/W1989185632","https://openalex.org/W1996666978","https://openalex.org/W2004364835","https://openalex.org/W2009812778","https://openalex.org/W2009845005","https://openalex.org/W2010725868","https://openalex.org/W2011097028","https://openalex.org/W2013429682","https://openalex.org/W2013830587","https://openalex.org/W2016161490","https://openalex.org/W2021040301","https://openalex.org/W2021324774","https://openalex.org/W2021524400","https://openalex.org/W2023431124","https://openalex.org/W2026227075","https://openalex.org/W2026799761","https://openalex.org/W2026888821","https://openalex.org/W2029070164","https://openalex.org/W2034589999","https://openalex.org/W2035767053","https://openalex.org/W2041599076","https://openalex.org/W2042180447","https://openalex.org/W2049492969","https://openalex.org/W2053142943","https://openalex.org/W2054059225","https://openalex.org/W2055926450","https://openalex.org/W2064107535","https://openalex.org/W2077651691","https://openalex.org/W2079592589","https://openalex.org/W2082649271","https://openalex.org/W2087587427","https://openalex.org/W2090363184","https://openalex.org/W2097340351","https://openalex.org/W2098665638","https://openalex.org/W2100809095","https://openalex.org/W2101740624","https://openalex.org/W2101843722","https://openalex.org/W2105466636","https://openalex.org/W2116484220","https://openalex.org/W2117956780","https://openalex.org/W2118274513","https://openalex.org/W2120479418","https://openalex.org/W2137112190","https://openalex.org/W2140936142","https://openalex.org/W2147136931","https://openalex.org/W2151007518","https://openalex.org/W2153439292","https://openalex.org/W2155418451","https://openalex.org/W2156185271","https://openalex.org/W2156684470","https://openalex.org/W2159878156","https://openalex.org/W2165572439","https://openalex.org/W2170467788","https://openalex.org/W2170940406","https://openalex.org/W4233674089","https://openalex.org/W4236474107"],"related_works":["https://openalex.org/W2034954676","https://openalex.org/W3082882328","https://openalex.org/W2107565323","https://openalex.org/W2073229143","https://openalex.org/W2031200252","https://openalex.org/W103209986","https://openalex.org/W2148671780","https://openalex.org/W2031322150","https://openalex.org/W2070886055","https://openalex.org/W3025886617"],"abstract_inverted_index":{"Recent":[0],"evidence":[1],"suggests":[2],"that":[3,29,71,105,150,179],"cells":[4],"employ":[5],"functionally":[6],"asymmetric":[7,111],"partitioning":[8,42],"schemes":[9,19],"in":[10,20,43,49,94,126],"division":[11,89,106,121,131],"to":[12],"cope":[13],"with":[14,22],"aging.":[15],"We":[16,103],"explore":[17],"various":[18],"silico,":[21],"a":[23,167],"stochastic":[24],"model":[25,46],"of":[26,65,84,91,117,155,169,182,185,196],"Escherichia":[27],"coli":[28,198],"includes":[30],"gene":[31],"expression,":[32],"non-functional":[33,66,85,118,157,186],"proteins":[34,86,119,158],"generation,":[35],"aggregation":[36],"and":[37,40,69,75,141,190],"polar":[38,127,143,191],"retention,":[39,192],"molecule":[41],"division.":[44],"The":[45],"is":[47,145,166,174],"implemented":[48],"SGNS2,":[50],"which":[51],"allows":[52],"stochastic,":[53],"multi-delayed":[54],"reactions":[55],"within":[56],"hierarchical,":[57],"transient,":[58],"interlinked":[59],"compartments.":[60],"After":[61],"setting":[62],"parameter":[63],"values":[64],"proteins'":[67],"generation":[68],"effects":[70],"reproduce":[72],"realistic":[73],"intracellular":[74,183],"population":[76],"dynamics,":[77],"we":[78,148],"investigate":[79],"how":[80],"the":[81,115,124,135,138,151,160,180,194],"spatial":[82],"organization":[83,184],"affects":[87],"mean":[88,98],"times":[90,107],"cell":[92,99],"populations":[93],"lineages":[95],"and,":[96,172],"thus,":[97,173],"numbers":[100],"over":[101],"time.":[102],"find":[104],"decrease":[108],"for":[109],"increasingly":[110],"partitioning.":[112],"Also,":[113],"increasing":[114],"clustering":[116,189],"decreases":[120,130],"times.":[122],"Increasing":[123],"bias":[125,136],"segregation":[128],"further":[129],"times,":[132],"particularly":[133],"if":[134],"favors":[137],"older":[139,161],"pole":[140,162],"aggregates'":[142],"retention":[144,154],"robust.":[146],"Finally,":[147],"show":[149],"non-energy":[152],"consuming":[153],"inherited":[156],"at":[159],"via":[163],"nucleoid":[164],"occlusion":[165],"source":[168],"functional":[170],"asymmetries":[171],"advantageous.":[175],"Our":[176],"results":[177],"suggest":[178],"mechanisms":[181],"proteins,":[187],"including":[188],"affect":[193],"vitality":[195],"E.":[197],"populations.":[199]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-03T06:03:33.228499","created_date":"2025-10-10T00:00:00"}
