{"id":"https://openalex.org/W4293833705","doi":"https://doi.org/10.1142/s0219720022500214","title":"Behavioral dynamics of bacteriophage gene regulatory networks","display_name":"Behavioral dynamics of bacteriophage gene regulatory networks","publication_year":2022,"publication_date":"2022-08-31","ids":{"openalex":"https://openalex.org/W4293833705","doi":"https://doi.org/10.1142/s0219720022500214","pmid":"https://pubmed.ncbi.nlm.nih.gov/36102744"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720022500214","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720022500214","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1142/s0219720022500214","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039669097","display_name":"Gatis Melkus","orcid":"https://orcid.org/0000-0002-3077-6809"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Gatis Melkus","raw_affiliation_strings":["Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051714710","display_name":"K\u0101rlis \u010cer\u0101ns","orcid":"https://orcid.org/0000-0002-0154-5294"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Karlis Cerans","raw_affiliation_strings":["Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085237554","display_name":"K\u0101rlis Freivalds","orcid":"https://orcid.org/0000-0003-2684-559X"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Karlis Freivalds","raw_affiliation_strings":["Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064697845","display_name":"Lelde L\u0101ce","orcid":"https://orcid.org/0000-0001-7650-2355"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Lelde Lace","raw_affiliation_strings":["Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009490243","display_name":"Darta Zajakina","orcid":null},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":false,"raw_author_name":"Darta Zajakina","raw_affiliation_strings":["Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia","institution_ids":["https://openalex.org/I91123046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035792920","display_name":"Juris V\u012bksna","orcid":"https://orcid.org/0000-0003-2283-2978"},"institutions":[{"id":"https://openalex.org/I91123046","display_name":"University of Latvia","ror":"https://ror.org/05g3mes96","country_code":"LV","type":"education","lineage":["https://openalex.org/I91123046"]}],"countries":["LV"],"is_corresponding":true,"raw_author_name":"Juris Viksna","raw_affiliation_strings":["Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia"],"affiliations":[{"raw_affiliation_string":"Institute of Mathematics and Computer Science, University of Latvia, Rainis Boulevard 29, Riga LV-1459, Latvia","institution_ids":["https://openalex.org/I91123046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035792920"],"corresponding_institution_ids":["https://openalex.org/I91123046"],"apc_list":null,"apc_paid":null,"fwci":0.0858,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.42519404,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"20","issue":"05","first_page":"2250021","last_page":"2250021"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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":0.9977999925613403,"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/lysogenic-cycle","display_name":"Lysogenic cycle","score":0.9368416666984558},{"id":"https://openalex.org/keywords/lytic-cycle","display_name":"Lytic cycle","score":0.8760468363761902},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.7357089519500732},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5859320163726807},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5333955883979797},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5311647057533264},{"id":"https://openalex.org/keywords/lysogen","display_name":"Lysogen","score":0.5243604183197021},{"id":"https://openalex.org/keywords/lambda-phage","display_name":"Lambda phage","score":0.49117061495780945},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45801252126693726},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40816962718963623},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39085066318511963},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35680270195007324},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3381170630455017},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2497512698173523},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12019956111907959},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.09491991996765137},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.0934397280216217}],"concepts":[{"id":"https://openalex.org/C136199206","wikidata":"https://www.wikidata.org/wiki/Q1148110","display_name":"Lysogenic cycle","level":5,"score":0.9368416666984558},{"id":"https://openalex.org/C182615771","wikidata":"https://www.wikidata.org/wiki/Q1369386","display_name":"Lytic cycle","level":3,"score":0.8760468363761902},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.7357089519500732},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5859320163726807},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5333955883979797},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5311647057533264},{"id":"https://openalex.org/C48292096","wikidata":"https://www.wikidata.org/wiki/Q6710264","display_name":"Lysogen","level":5,"score":0.5243604183197021},{"id":"https://openalex.org/C2781135666","wikidata":"https://www.wikidata.org/wiki/Q615868","display_name":"Lambda phage","level":5,"score":0.49117061495780945},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45801252126693726},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40816962718963623},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39085066318511963},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35680270195007324},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3381170630455017},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2497512698173523},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12019956111907959},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.09491991996765137},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0934397280216217},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008242","descriptor_name":"Lysogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008242","descriptor_name":"Lysogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008242","descriptor_name":"Lysogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720022500214","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720022500214","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:36102744","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36102744","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":{"id":"doi:10.1142/s0219720022500214","is_oa":true,"landing_page_url":"https://doi.org/10.1142/s0219720022500214","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3066116365","display_name":null,"funder_award_id":"lzp-2019/1-0432","funder_id":"https://openalex.org/F4320323269","funder_display_name":"Latvijas Zin\u0101tnes Padome"}],"funders":[{"id":"https://openalex.org/F4320323269","display_name":"Latvijas Zin\u0101tnes Padome","ror":"https://ror.org/02ar66p97"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W164184961","https://openalex.org/W1535220465","https://openalex.org/W1569236477","https://openalex.org/W1973110798","https://openalex.org/W1979230873","https://openalex.org/W1980570931","https://openalex.org/W1983099607","https://openalex.org/W1986373777","https://openalex.org/W1987122230","https://openalex.org/W1998356614","https://openalex.org/W2004463571","https://openalex.org/W2018238833","https://openalex.org/W2022624450","https://openalex.org/W2047279254","https://openalex.org/W2065782501","https://openalex.org/W2077720193","https://openalex.org/W2099362734","https://openalex.org/W2114518254","https://openalex.org/W2119580810","https://openalex.org/W2127820082","https://openalex.org/W2136559804","https://openalex.org/W2152533774","https://openalex.org/W2168167613","https://openalex.org/W2296076055","https://openalex.org/W2555913743","https://openalex.org/W2566997984","https://openalex.org/W2586943721","https://openalex.org/W2621589069","https://openalex.org/W2947628476"],"related_works":["https://openalex.org/W2768112850","https://openalex.org/W1988397740","https://openalex.org/W4255734500","https://openalex.org/W2403522141","https://openalex.org/W2034347319","https://openalex.org/W2271288605","https://openalex.org/W1969790171","https://openalex.org/W1607264707","https://openalex.org/W2102105094","https://openalex.org/W4293833705"],"abstract_inverted_index":{"We":[0],"present":[1],"hybrid":[2,175,179],"system-based":[3],"gene":[4,43],"regulatory":[5,44,193],"network":[6],"models":[7,50,55,69,91],"for":[8,114,197],"lambda,":[9],"HK022,":[10,46],"and":[11,34,47,63,74,134,195,203],"Mu":[12,48,160],"bacteriophages":[13],"together":[14],"with":[15],"dynamics":[16,202],"analysis":[17,199],"of":[18,59,132,150,159,200],"the":[19,41,68,85,90,121,171],"modeled":[20,86],"networks.":[21,87],"The":[22],"proposed":[23],"lambda":[24],"phage":[25,49,161],"model":[26,120,177,201],"LPH2":[27,119],"is":[28,162],"based":[29],"on":[30,129],"an":[31],"earlier":[32],"work":[33],"incorporates":[35],"more":[36],"recent":[37],"biological":[38,116],"assumptions":[39],"about":[40],"underlying":[42],"mechanism,":[45],"are":[51,76,112],"new.":[52],"All":[53],"three":[54],"provide":[56],"accurate":[57],"representations":[58],"experimentally":[60],"observed":[61],"lytic":[62,102],"lysogenic":[64,104],"behavioral":[65,105],"cycles.":[66],"Importantly,":[67],"also":[70,163],"imply":[71],"that":[72,81,97,111,174],"lysis":[73],"lysogeny":[75],"<i>the":[77],"only</i>":[78],"stable":[79,204],"behaviors":[80],"can":[82,182],"occur":[83],"in":[84],"In":[88,169],"addition,":[89],"allow":[92],"to":[93,100,186],"derive":[94],"switching":[95,157],"conditions":[96],"irrevocably":[98],"lead":[99],"either":[101],"or":[103],"cycle":[106],"as":[107,109],"well":[108],"constraints":[110,123],"required":[113],"their":[115],"feasibility.":[117],"For":[118],"feasibility":[122],"place":[124],"two":[125],"mutually":[126],"independent":[127],"requirements":[128],"comparative":[130],"order":[131],"cro":[133],"cI":[135],"protein":[136],"binding":[137],"site":[138],"affinities.":[139],"However,":[140],"HK022":[141],"model,":[142],"while":[143],"broadly":[144],"similar,":[145],"does":[146],"not":[147],"require":[148],"any":[149],"these":[151],"constraints.":[152],"Biologically":[153],"very":[154],"different":[155],"lysis-lysogeny":[156],"mechanism":[158],"accurately":[164],"reproduced":[165],"by":[166],"its":[167],"model.":[168],"general":[170],"results":[172],"show":[173],"system":[176,180],"(HSM)":[178],"framework":[181],"be":[183],"successfully":[184],"applied":[185],"modeling":[187],"small":[188],"([Formula:":[189],"see":[190],"text]":[191],"gene)":[192],"networks":[194],"used":[196],"comprehensive":[198],"behavior":[205],"regions.":[206]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
