{"id":"https://openalex.org/W7117552449","doi":"https://doi.org/10.1186/s12859-025-06354-3","title":"DANSE: a pipeline for dynamic modelling of time-series multi-omics data","display_name":"DANSE: a pipeline for dynamic modelling of time-series multi-omics data","publication_year":2025,"publication_date":"2025-12-30","ids":{"openalex":"https://openalex.org/W7117552449","doi":"https://doi.org/10.1186/s12859-025-06354-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/41469543"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06354-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06354-3","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06354-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Lucas F. Jansen Klomp","orcid":null},"institutions":[{"id":"https://openalex.org/I94624287","display_name":"University of Twente","ror":"https://ror.org/006hf6230","country_code":"NL","type":"education","lineage":["https://openalex.org/I94624287"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Lucas F. Jansen Klomp","raw_affiliation_strings":["Department of Applied Mathematics, Faculty of Electrical Engineering, Computer Science, Mathematics, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands. l.f.jansenklomp@utwente.nl","Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands. l.f.jansenklomp@utwente.nl"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Faculty of Electrical Engineering, Computer Science, Mathematics, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands. l.f.jansenklomp@utwente.nl","institution_ids":["https://openalex.org/I94624287","https://openalex.org/I94624287"]},{"raw_affiliation_string":"Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands. l.f.jansenklomp@utwente.nl","institution_ids":["https://openalex.org/I94624287","https://openalex.org/I94624287"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101539993","display_name":"Xin Yan","orcid":"https://orcid.org/0000-0002-5053-5447"},"institutions":[{"id":"https://openalex.org/I94624287","display_name":"University of Twente","ror":"https://ror.org/006hf6230","country_code":"NL","type":"education","lineage":["https://openalex.org/I94624287"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Xinqi Yan","raw_affiliation_strings":["Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands","institution_ids":["https://openalex.org/I94624287"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086616064","display_name":"Rebecca R. Snabel","orcid":"https://orcid.org/0000-0001-8053-1191"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]},{"id":"https://openalex.org/I4210109357","display_name":"Radboud Institute for Molecular Life Sciences","ror":"https://ror.org/01yb10j39","country_code":"NL","type":"facility","lineage":["https://openalex.org/I145872427","https://openalex.org/I4210109357"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Rebecca R. Snabel","raw_affiliation_strings":["Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, Houtlaan, 6525XZ, Nijmegen, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, Houtlaan, 6525XZ, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I4210109357","https://openalex.org/I2802934949"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121586497","display_name":"Gert Jan C. Veenstra","orcid":null},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]},{"id":"https://openalex.org/I2802934949","display_name":"Radboud University Medical Center","ror":"https://ror.org/05wg1m734","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2802934949"]},{"id":"https://openalex.org/I4210109357","display_name":"Radboud Institute for Molecular Life Sciences","ror":"https://ror.org/01yb10j39","country_code":"NL","type":"facility","lineage":["https://openalex.org/I145872427","https://openalex.org/I4210109357"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Gert Jan C. Veenstra","raw_affiliation_strings":["Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, Houtlaan, 6525XZ, Nijmegen, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, Houtlaan, 6525XZ, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I145872427","https://openalex.org/I4210109357","https://openalex.org/I2802934949"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121543547","display_name":"Hil G. E. Meijer","orcid":null},"institutions":[{"id":"https://openalex.org/I94624287","display_name":"University of Twente","ror":"https://ror.org/006hf6230","country_code":"NL","type":"education","lineage":["https://openalex.org/I94624287"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Hil G. E. Meijer","raw_affiliation_strings":["Department of Applied Mathematics, Faculty of Electrical Engineering, Computer Science, Mathematics, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Faculty of Electrical Engineering, Computer Science, Mathematics, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands","institution_ids":["https://openalex.org/I94624287"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061489108","display_name":"Janine N. Post","orcid":"https://orcid.org/0000-0002-6645-6583"},"institutions":[{"id":"https://openalex.org/I94624287","display_name":"University of Twente","ror":"https://ror.org/006hf6230","country_code":"NL","type":"education","lineage":["https://openalex.org/I94624287"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Janine N. Post","raw_affiliation_strings":["Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands. j.n.post@utwente.nl"],"affiliations":[{"raw_affiliation_string":"Developmental BioEngineering, Faculty of Science and Technology, University of Twente, Drienerlolaan, 7522NB, Enschede, The Netherlands. j.n.post@utwente.nl","institution_ids":["https://openalex.org/I94624287"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I94624287"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.62552117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8891000151634216,"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":0.8891000151634216,"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/T10885","display_name":"Gene expression and cancer classification","score":0.027899999171495438,"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":0.026399999856948853,"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/pipeline","display_name":"Pipeline (software)","score":0.7595000267028809},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4778999984264374},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.46140000224113464},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.44670000672340393},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.44530001282691956},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4025000035762787},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.3716999888420105},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.34470000863075256},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.3384000062942505}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7595000267028809},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7372999787330627},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4778999984264374},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.46140000224113464},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.44670000672340393},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44530001282691956},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42640000581741333},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4025000035762787},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3849000036716461},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3716999888420105},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.34470000863075256},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.3384000062942505},{"id":"https://openalex.org/C155702961","wikidata":"https://www.wikidata.org/wiki/Q5318975","display_name":"Dynamic factor","level":2,"score":0.33730000257492065},{"id":"https://openalex.org/C13540734","wikidata":"https://www.wikidata.org/wiki/Q5318996","display_name":"Dynamic network analysis","level":2,"score":0.32100000977516174},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.3199000060558319},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3118000030517578},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2849000096321106},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.28139999508857727},{"id":"https://openalex.org/C173396325","wikidata":"https://www.wikidata.org/wiki/Q1501275","display_name":"Gene knockdown","level":3,"score":0.2791000008583069},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2736999988555908},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.27309998869895935},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.25699999928474426},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.25429999828338623},{"id":"https://openalex.org/C82142266","wikidata":"https://www.wikidata.org/wiki/Q3456604","display_name":"Dynamic Bayesian network","level":3,"score":0.25369998812675476},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2524999976158142}],"mesh":[],"locations_count":9,"locations":[{"id":"doi:10.1186/s12859-025-06354-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06354-3","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41469543","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41469543","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:ris.utwente.nl:openaire_cris_publications/4d3fa1f7-24a1-4d44-b723-4e2f218fa879","is_oa":true,"landing_page_url":"https://research.utwente.nl/en/publications/4d3fa1f7-24a1-4d44-b723-4e2f218fa879","pdf_url":null,"source":{"id":"https://openalex.org/S4406922991","display_name":"University of Twente Research Information","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Jansen Klomp, L F, Yan, X, Snabel, R R, Veenstra, G J C, Meijer, H G E & Post, J N 2026, 'DANSE : A pipeline for dynamic modelling of time-series multi-omics data', BMC bioinformatics, vol. 27, no. 1, 28. https://doi.org/10.1186/s12859-025-06354-3","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:ris.utwente.nl:publications/4d3fa1f7-24a1-4d44-b723-4e2f218fa879","is_oa":true,"landing_page_url":"https://research.utwente.nl/files/522913234/s12859-025-06354-3.pdf","pdf_url":"https://ris.utwente.nl/ws/files/522913234/s12859-025-06354-3.pdf","source":{"id":"https://openalex.org/S4406922991","display_name":"University of Twente Research Information","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jansen Klomp, L F, Yan, X, Snabel, R R, Veenstra, G J C, Meijer, H G E & Post, J N 2026, 'DANSE : A pipeline for dynamic modelling of time-series multi-omics data', BMC bioinformatics, vol. 27, no. 1, 28. https://doi.org/10.1186/s12859-025-06354-3","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:doi:10.6084/m9.figshare.c.8281422","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Collection"},{"id":"pmh:oai:doaj.org/article:28657c29761c48178e333744ed346f37","is_oa":true,"landing_page_url":"https://doaj.org/article/28657c29761c48178e333744ed346f37","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-22 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11667598","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12859988","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:pubmedcentral.nih.gov:12859988","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12859988/","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:repository.ubn.ru.nl:2066/328829","is_oa":false,"landing_page_url":"https://hdl.handle.net/2066/328829","pdf_url":null,"source":{"id":"https://openalex.org/S4306401067","display_name":"Radboud Repository (Radboud University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145872427","host_organization_name":"Radboud University Nijmegen","host_organization_lineage":["https://openalex.org/I145872427"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06354-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06354-3","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.43131223320961,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G6247533343","display_name":null,"funder_award_id":"OCENW.GROOT.2019.079","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G781596827","display_name":null,"funder_award_id":"OCENW.XL21.XL21.067","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1870167959","https://openalex.org/W1972773888","https://openalex.org/W1980253661","https://openalex.org/W1984883254","https://openalex.org/W1993323315","https://openalex.org/W2041898322","https://openalex.org/W2054286320","https://openalex.org/W2060200034","https://openalex.org/W2061425021","https://openalex.org/W2076513103","https://openalex.org/W2099951294","https://openalex.org/W2103017472","https://openalex.org/W2111452249","https://openalex.org/W2120835467","https://openalex.org/W2128555837","https://openalex.org/W2144738674","https://openalex.org/W2146512944","https://openalex.org/W2161121464","https://openalex.org/W2163296115","https://openalex.org/W2189918007","https://openalex.org/W2267423417","https://openalex.org/W2311415470","https://openalex.org/W2343910187","https://openalex.org/W2461230718","https://openalex.org/W2616922646","https://openalex.org/W2623261195","https://openalex.org/W2789634291","https://openalex.org/W2803928488","https://openalex.org/W2907043693","https://openalex.org/W2927507212","https://openalex.org/W2951799803","https://openalex.org/W2952535935","https://openalex.org/W2964695565","https://openalex.org/W2968327171","https://openalex.org/W2970876998","https://openalex.org/W2997831639","https://openalex.org/W3013118364","https://openalex.org/W3086251959","https://openalex.org/W3093153369","https://openalex.org/W3096305291","https://openalex.org/W3133716533","https://openalex.org/W3177876754","https://openalex.org/W3178951523","https://openalex.org/W3186788670","https://openalex.org/W3210860076","https://openalex.org/W4294216483","https://openalex.org/W4313332909","https://openalex.org/W4324145615","https://openalex.org/W4362521890","https://openalex.org/W4366351220","https://openalex.org/W4378212544","https://openalex.org/W4382022265","https://openalex.org/W4384198561","https://openalex.org/W4387774515","https://openalex.org/W4389141343","https://openalex.org/W4389379124","https://openalex.org/W4405231264","https://openalex.org/W4405515317","https://openalex.org/W4408022513","https://openalex.org/W4414037215"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"time-dependent":[1,44],"intracellular":[2],"processes,":[3,46],"such":[4],"as":[5],"cell":[6,152],"differentiation,":[7],"is":[8,158],"key":[9,41,104],"to":[10,26,108,124],"developing":[11],"new":[12],"therapies":[13],"for":[14,96,139,145,162],"a":[15,67,77,88,92,100,159,167],"wide":[16],"range":[17],"of":[18,36,43,87,99,103,118,142,177],"diseases.":[19],"Models":[20,132],"that":[21,128,150,170],"connect":[22],"transcription":[23,70,105],"factor":[24,71],"activity":[25],"dynamic":[27,78,175],"expression":[28],"patterns":[29],"are":[30],"rare,":[31],"despite":[32],"the":[33,49,97,110,116,140,174],"increased":[34],"availability":[35],"time-series":[37],"data.":[38,181],"To":[39],"identify":[40],"regulators":[42],"biological":[45,112],"we":[47],"present":[48],"pipeline":[50,65,120],"DANSE:":[51],"Dynamics":[52],"inference":[53],"Algorithm":[54],"on":[55,81],"Networks":[56],"Specified":[57],"by":[58,121],"Enhancers.":[59],"Starting":[60],"from":[61],"multi-omics":[62,178],"data,":[63],"our":[64,119],"constructs":[66],"data-driven":[68,168],"mechanistic":[69,93],"(TF)":[72],"network":[73,90],"and":[74,91],"subsequently":[75],"defines":[76],"model":[79,94],"based":[80],"this":[82,155],"TF":[83,89],"network.":[84],"The":[85],"combination":[86],"allows":[95],"identification":[98],"small":[101],"set":[102],"factors":[106],"predicted":[107],"drive":[109],"modelled":[111],"process.":[113],"We":[114],"showcase":[115],"result":[117],"applying":[122],"DANSE":[123,135,157],"two":[125],"different":[126],"datasets":[127],"describe":[129],"iPSC":[130],"differentiation.":[131],"constructed":[133],"using":[134],"suggest":[136],"testable":[137],"hypotheses":[138,165],"perturbation":[141],"gene":[143],"expression,":[144],"example,":[146],"knockdown":[147],"or":[148],"overexpression,":[149],"influence":[151],"fate.":[153],"In":[154],"way,":[156],"powerful":[160],"tool":[161],"generating":[163],"novel":[164],"in":[166],"manner":[169],"take":[171],"into":[172],"account":[173],"nature":[176],"time":[179],"series":[180]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-12-30T00:00:00"}