{"id":"https://openalex.org/W2532974794","doi":"https://doi.org/10.1371/journal.pcbi.1005146","title":"DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks","display_name":"DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks","publication_year":2016,"publication_date":"2016-10-19","ids":{"openalex":"https://openalex.org/W2532974794","doi":"https://doi.org/10.1371/journal.pcbi.1005146","mag":"2532974794","pmid":"https://pubmed.ncbi.nlm.nih.gov/27760135"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005146","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005146","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005146&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005146&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053240500","display_name":"Daifeng Wang","orcid":"https://orcid.org/0000-0001-9190-3704"},"institutions":[{"id":"https://openalex.org/I4210102711","display_name":"Stony Brook Medicine","ror":"https://ror.org/01882y777","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210102711"]},{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daifeng Wang","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, United States of America","Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9190-3704","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, United States of America","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook, New York, United States of America","institution_ids":["https://openalex.org/I4210102711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014834476","display_name":"Fei He","orcid":"https://orcid.org/0000-0002-1165-3248"},"institutions":[{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fei He","raw_affiliation_strings":["Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1165-3248","affiliations":[{"raw_affiliation_string":"Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America","institution_ids":["https://openalex.org/I200870766"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017591427","display_name":"Sergei Maslov","orcid":"https://orcid.org/0000-0002-3701-492X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I200870766","display_name":"Brookhaven National Laboratory","ror":"https://ror.org/02ex6cf31","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I200870766","https://openalex.org/I39565521","https://openalex.org/I4210142672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergei Maslov","raw_affiliation_strings":["Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America","Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3701-492X","affiliations":[{"raw_affiliation_string":"Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America","institution_ids":["https://openalex.org/I200870766"]},{"raw_affiliation_string":"Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Department of Computer Science, Yale University, New Haven, Connecticut, United States of America","Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America","Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5042321575"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8543,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.76682612,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"12","issue":"10","first_page":"e1005146","last_page":"e1005146"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9962999820709229,"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":0.9962999820709229,"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/T10676","display_name":"Genetics, Aging, and Longevity in Model Organisms","score":0.9940999746322632,"subfield":{"id":"https://openalex.org/subfields/1302","display_name":"Aging"},"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":0.9909999966621399,"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/biology","display_name":"Biology","score":0.6414341926574707},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6080455183982849},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5904422998428345},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5596122741699219},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5588210225105286},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5576211214065552},{"id":"https://openalex.org/keywords/drosophila-melanogaster","display_name":"Drosophila melanogaster","score":0.5242210626602173},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.47834083437919617},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.42779773473739624},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4206395745277405},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.24307668209075928}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6414341926574707},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6080455183982849},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5904422998428345},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5596122741699219},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5588210225105286},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5576211214065552},{"id":"https://openalex.org/C2780104201","wikidata":"https://www.wikidata.org/wiki/Q130888","display_name":"Drosophila melanogaster","level":3,"score":0.5242210626602173},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.47834083437919617},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.42779773473739624},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4206395745277405},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24307668209075928},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D025461","descriptor_name":"Feedback, Physiological","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D025461","descriptor_name":"Feedback, Physiological","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D025461","descriptor_name":"Feedback, Physiological","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1005146","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005146","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005146&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:27760135","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27760135","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:osti.gov:1627247","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1627247","pdf_url":"https://www.osti.gov/servlets/purl/1627247","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,"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:doaj.org/article:309e52bc73054fbab5801d434f060718","is_oa":false,"landing_page_url":"https://doaj.org/article/309e52bc73054fbab5801d434f060718","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 12, Iss 10, p e1005146 (2016)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/4046187","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/DREISS_Using_State-Space_Models_to_Infer_the_Dynamics_of_Gene_Expression_Driven_by_External_and_Internal_Regulatory_Networks/4046187","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:5070849","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5070849","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005146","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005146","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005146&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6299999952316284}],"awards":[{"id":"https://openalex.org/G7026991446","display_name":null,"funder_award_id":"U41 HG007355","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7816401740","display_name":null,"funder_award_id":"UL1 TR001863","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2532974794.pdf","grobid_xml":"https://content.openalex.org/works/W2532974794.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1594130515","https://openalex.org/W1979435105","https://openalex.org/W1982510939","https://openalex.org/W1994299883","https://openalex.org/W2011286119","https://openalex.org/W2014762516","https://openalex.org/W2015612505","https://openalex.org/W2026907845","https://openalex.org/W2033588416","https://openalex.org/W2038622868","https://openalex.org/W2038861887","https://openalex.org/W2046781332","https://openalex.org/W2064690543","https://openalex.org/W2074468058","https://openalex.org/W2084502634","https://openalex.org/W2089208780","https://openalex.org/W2094437016","https://openalex.org/W2110291976","https://openalex.org/W2117343824","https://openalex.org/W2119387367","https://openalex.org/W2122342005","https://openalex.org/W2135951244","https://openalex.org/W2138872672","https://openalex.org/W2146506956","https://openalex.org/W2155221318","https://openalex.org/W2155592813","https://openalex.org/W2157746260","https://openalex.org/W2158217645","https://openalex.org/W2164333136"],"related_works":["https://openalex.org/W2944994818","https://openalex.org/W2010571965","https://openalex.org/W3128451840","https://openalex.org/W2002709996","https://openalex.org/W4387092964","https://openalex.org/W2103471012","https://openalex.org/W2966064480","https://openalex.org/W2380236774","https://openalex.org/W2277277196","https://openalex.org/W2107149076"],"abstract_inverted_index":{"Gene":[0],"expression":[1,29,69,89,123,165,208,223,260],"is":[2,47,58,131,269],"controlled":[3,32,307],"by":[4,33,40,44,91,133,241,308],"the":[5,52,68,85,106,111,134,154,173,187,205,222,226,232,254,279],"combinatorial":[6],"effects":[7,175,189],"of":[8,70,87,183,190,210,225],"regulatory":[9,36,174,188,310],"factors":[10,19,23],"from":[11,177],"different":[12,264],"biological":[13],"subsystems":[14],"such":[15],"as":[16],"general":[17],"transcription":[18],"(TFs),":[20],"cellular":[21],"growth":[22,169],"and":[24,96,108,118,136,161,170,213],"microRNAs.":[25],"A":[26],"subsystem's":[27,120],"gene":[28,88,122,207],"may":[30],"be":[31,238],"its":[34,115],"internal":[35],"factors,":[37],"exclusively,":[38],"or":[39,43,61],"external":[41],"subsystems,":[42],"both.":[45],"It":[46],"thus":[48],"useful":[49],"to":[50,54,114,151,204,234,284],"distinguish":[51],"degree":[53,233],"which":[55,235],"a":[56,78,104,128,139],"subsystem":[57],"regulated":[59],"internally":[60,258],"externally-e.g.,":[62],"how":[63],"non-conserved,":[64],"species-specific":[65,245],"TFs":[66,195],"affect":[67],"conserved,":[71,227],"cross-species":[72],"genes":[73,229,273],"during":[74,216],"evolution.":[75],"We":[76,220,248],"developed":[77],"computational":[79],"method":[80],"(DREISS,":[81],"dreiss.gerteinlab.org)":[82],"for":[83,240,272],"analyzing":[84],"Dynamics":[86],"driven":[90,259,266],"Regulatory":[92],"networks,":[93],"both":[94],"External":[95],"Internal":[97],"based":[98],"on":[99],"State":[100],"Space":[101],"models.":[102],"Given":[103],"subsystem,":[105],"\"state\"":[107],"\"control\"":[109],"in":[110,282],"model":[112],"refer":[113],"own":[116],"(internal)":[117,243],"another":[119],"(external)":[121,246],"levels.":[124],"The":[125],"state":[126,135],"at":[127,138],"given":[129],"time":[130],"determined":[132],"control":[137],"previous":[140],"time.":[141],"Because":[142],"typical":[143],"time-series":[144,206],"data":[145],"do":[146],"not":[147],"have":[148,256],"enough":[149],"samples":[150],"fully":[152],"estimate":[153],"model's":[155],"parameters,":[156],"DREISS":[157,203],"uses":[158],"dimensionality":[159],"reduction,":[160],"identifies":[162],"canonical":[163],"temporal":[164],"trajectories":[166],"(e.g.,":[167,291],"degradation,":[168],"oscillation)":[171],"representing":[172],"emanating":[176],"various":[178],"subsystems.":[179],"To":[180],"demonstrate":[181],"capabilities":[182],"DREISS,":[184],"we":[185,201],"study":[186],"evolutionarily":[191,275],"conserved":[192],"vs.":[193],"divergent":[194],"across":[196],"distant":[197],"species.":[198],"In":[199],"particular,":[200],"applied":[202],"datasets":[209],"C.":[211],"elegans":[212],"D.":[214],"melanogaster":[215],"their":[217],"embryonic":[218],"development.":[219],"analyzed":[221],"dynamics":[224],"orthologous":[228,242],"(orthologs),":[230],"seeing":[231],"these":[236],"can":[237],"accounted":[239],"versus":[244],"TFs.":[247],"found":[249],"that":[250,296],"between":[251],"two":[252],"species,":[253],"orthologs":[255],"matched,":[257],"patterns":[261],"but":[262],"very":[263],"externally":[265],"ones.":[267],"This":[268,294],"particularly":[270],"true":[271],"with":[274,286],"ancient":[276,309],"functions":[277,290],"(e.g.":[278],"ribosomal":[280],"proteins),":[281],"contrast":[283],"those":[285],"more":[287],"recently":[288],"evolved":[289],"cell-cell":[292],"communication).":[293],"suggests":[295],"despite":[297],"striking":[298],"morphological":[299],"differences,":[300],"some":[301],"fundamental":[302],"embryonic-developmental":[303],"processes":[304],"are":[305],"still":[306],"systems.":[311]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
