{"id":"https://openalex.org/W1559434599","doi":"https://doi.org/10.1371/journal.pcbi.1003486","title":"Modular Composition of Gene Transcription Networks","display_name":"Modular Composition of Gene Transcription Networks","publication_year":2014,"publication_date":"2014-03-13","ids":{"openalex":"https://openalex.org/W1559434599","doi":"https://doi.org/10.1371/journal.pcbi.1003486","mag":"1559434599","pmid":"https://pubmed.ncbi.nlm.nih.gov/24626132"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003486","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003486","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003486&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":"book-chapter","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.1003486&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002692025","display_name":"Andr\u00e1s Gy\u00f6rgy","orcid":"https://orcid.org/0000-0001-8103-260X"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andras Gyorgy","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036095256","display_name":"Domitilla Del Vecchio","orcid":"https://orcid.org/0000-0001-6472-8576"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Domitilla Del Vecchio","raw_affiliation_strings":["Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5036095256"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.03856095,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"10","issue":"3","first_page":"e1003486","last_page":"e1003486"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9923999905586243,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9839000105857849,"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/modular-design","display_name":"Modular design","score":0.6443822383880615},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5754468441009521},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.553193211555481},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.5029613375663757},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5004267692565918},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.476977676153183},{"id":"https://openalex.org/keywords/interconnection","display_name":"Interconnection","score":0.4643004536628723},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.4522448778152466},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.33061790466308594},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2750525176525116},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.18516802787780762},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16381007432937622},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09989172220230103}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6443822383880615},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5754468441009521},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.553193211555481},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.5029613375663757},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5004267692565918},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.476977676153183},{"id":"https://openalex.org/C123745756","wikidata":"https://www.wikidata.org/wiki/Q1665949","display_name":"Interconnection","level":2,"score":0.4643004536628723},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.4522448778152466},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.33061790466308594},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2750525176525116},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.18516802787780762},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16381007432937622},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09989172220230103},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","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":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1003486","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003486","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003486&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:24626132","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24626132","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:doaj.org/article:fde5d1cd31fc4ecc9652274fa695c78e","is_oa":true,"landing_page_url":"https://doaj.org/article/fde5d1cd31fc4ecc9652274fa695c78e","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 3, p e1003486 (2014)","raw_type":"article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/86222","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/86222","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2936607","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3952816","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/961628","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Modular_Composition_of_Gene_Transcription_Networks_/961628","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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":"mag:1559434599","is_oa":false,"landing_page_url":"https://dspace.mit.edu/handle/1721.1/86222","pdf_url":null,"source":{"id":"https://openalex.org/S4306489179","display_name":"PLoS eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":"ebook platform"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"PLoS eBooks","raw_type":null}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003486","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003486","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003486&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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1559434599.pdf","grobid_xml":"https://content.openalex.org/works/W1559434599.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1590222219","https://openalex.org/W1599969036","https://openalex.org/W1606784130","https://openalex.org/W1971421925","https://openalex.org/W1985161570","https://openalex.org/W2003847712","https://openalex.org/W2010420771","https://openalex.org/W2014382043","https://openalex.org/W2016830368","https://openalex.org/W2018045523","https://openalex.org/W2023403198","https://openalex.org/W2037913229","https://openalex.org/W2038540528","https://openalex.org/W2039931639","https://openalex.org/W2041985017","https://openalex.org/W2056657629","https://openalex.org/W2061425021","https://openalex.org/W2071928210","https://openalex.org/W2071990853","https://openalex.org/W2081434722","https://openalex.org/W2081567538","https://openalex.org/W2106400237","https://openalex.org/W2107172834","https://openalex.org/W2110699703","https://openalex.org/W2111870329","https://openalex.org/W2114228460","https://openalex.org/W2117136688","https://openalex.org/W2119446631","https://openalex.org/W2123097315","https://openalex.org/W2129620576","https://openalex.org/W2129915447","https://openalex.org/W2132405406","https://openalex.org/W2132724170","https://openalex.org/W2132828256","https://openalex.org/W2133083422","https://openalex.org/W2134440848","https://openalex.org/W2134759932","https://openalex.org/W2134800568","https://openalex.org/W2136130117","https://openalex.org/W2136969641","https://openalex.org/W2138358136","https://openalex.org/W2140347764","https://openalex.org/W2144981232","https://openalex.org/W2147256329","https://openalex.org/W2148325536","https://openalex.org/W2148641266","https://openalex.org/W2153624566","https://openalex.org/W2159883877","https://openalex.org/W2161524167","https://openalex.org/W2166499263","https://openalex.org/W2170484057","https://openalex.org/W2171994731","https://openalex.org/W2316378629","https://openalex.org/W2500818914"],"related_works":["https://openalex.org/W2065151746","https://openalex.org/W2279309729","https://openalex.org/W2605301032","https://openalex.org/W2951749372","https://openalex.org/W2159848460","https://openalex.org/W2478826238","https://openalex.org/W2104948910","https://openalex.org/W2951077061","https://openalex.org/W2611824166","https://openalex.org/W3022401574","https://openalex.org/W2059942036","https://openalex.org/W1653689488","https://openalex.org/W2753758104","https://openalex.org/W2058618427","https://openalex.org/W31529398","https://openalex.org/W2004114069","https://openalex.org/W2963581134","https://openalex.org/W2791744956","https://openalex.org/W3210470230","https://openalex.org/W2950745592"],"abstract_inverted_index":{"Predicting":[0],"the":[1,11,52,115,122,142,153,167,185,198,202,215,235],"dynamic":[2,53,216],"behavior":[3,168,217],"of":[4,10,38,55,95,124,144,155,169,173,178,187,218,237,239],"a":[5,15,42,56,79,98,208,219],"large":[6],"network":[7,189],"from":[8,105,114],"that":[9,47,73,211],"composing":[12],"modules":[13,32,156,252],"is":[14,27,40,221],"central":[16],"problem":[17],"in":[18,49,157,253],"systems":[19],"and":[20,91,101,110,113,134,151,181,201,242],"synthetic":[21,254],"biology.":[22],"Yet,":[23],"this":[24],"predictive":[25],"ability":[26],"still":[28],"largely":[29],"missing":[30],"because":[31],"display":[33],"context-dependent":[34],"behavior.":[35],"One":[36],"cause":[37],"context-dependence":[39],"retroactivity,":[41],"phenomenon":[43],"similar":[44],"to":[45,60,222,233,243,248],"loading":[46,164],"influences":[48],"non-trivial":[50],"ways":[51],"performance":[54,186],"module":[57,220],"upon":[58],"connection":[59],"other":[61,225],"modules.":[62,146,174,226],"Here,":[63],"we":[64,159],"establish":[65,137,244],"an":[66,128,170],"analysis":[67],"framework":[68],"for":[69,76],"gene":[70],"transcription":[71],"networks":[72,241],"explicitly":[74],"accounts":[75],"retroactivity.":[77,93],"Specifically,":[78],"module's":[80,130],"key":[81],"properties":[82],"are":[83],"encoded":[84],"by":[85],"three":[86],"retroactivity":[87,120,136,183,250],"matrices:":[88],"internal,":[89,179],"scaling,":[90,180],"mixing":[92,135,182],"All":[94],"them":[96],"have":[97],"physical":[99],"interpretation":[100],"can":[102,160,229],"be":[103,230],"computed":[104],"macroscopic":[106],"parameters":[107],"(dissociation":[108],"constants":[109],"promoter":[111],"concentrations)":[112],"modules'":[116],"topology.":[117],"The":[118,132],"internal":[119],"quantifies":[121],"effect":[123],"intramodular":[125],"connections":[126,140],"on":[127,148,152,184],"isolated":[129],"dynamics.":[131],"scaling":[133],"how":[138,163,213],"intermodular":[139],"change":[141],"dynamics":[143,154],"connected":[145],"Based":[147],"these":[149],"matrices":[150],"isolation,":[158],"accurately":[161],"predict":[162],"will":[165],"affect":[166],"arbitrary":[171],"interconnection":[172,223],"We":[175,205],"illustrate":[176],"implications":[177],"recurrent":[188],"motifs,":[190],"including":[191],"negative":[192],"autoregulation,":[193],"combinatorial":[194],"regulation,":[195],"two-gene":[196],"clocks,":[197],"toggle":[199],"switch,":[200],"single-input":[203],"motif.":[204],"further":[206],"provide":[207],"quantitative":[209],"metric":[210,228],"determines":[212],"robust":[214],"with":[224],"This":[227],"employed":[231],"both":[232],"evaluate":[234],"extent":[236],"modularity":[238],"natural":[240],"concrete":[245],"design":[246],"guidelines":[247],"minimize":[249],"between":[251],"systems.":[255]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
