{"id":"https://openalex.org/W4221032093","doi":"https://doi.org/10.1371/journal.pcbi.1009907","title":"IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data","display_name":"IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data","publication_year":2022,"publication_date":"2022-02-25","ids":{"openalex":"https://openalex.org/W4221032093","doi":"https://doi.org/10.1371/journal.pcbi.1009907","pmid":"https://pubmed.ncbi.nlm.nih.gov/35213533"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009907","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009907","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1009907","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027963882","display_name":"Tiam Heydari","orcid":"https://orcid.org/0000-0003-0465-8312"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Tiam Heydari","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]},{"raw_affiliation_string":"School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083909533","display_name":"Matthew A. Langley","orcid":"https://orcid.org/0000-0003-2890-5584"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Matthew A. Langley","raw_affiliation_strings":["Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090498221","display_name":"Cynthia L. Fisher","orcid":"https://orcid.org/0000-0001-6089-4868"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Cynthia L. Fisher","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]},{"raw_affiliation_string":"School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068186030","display_name":"Daniel Aguilar\u2010Hidalgo","orcid":"https://orcid.org/0000-0003-1366-9574"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Daniel Aguilar-Hidalgo","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]},{"raw_affiliation_string":"School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051549285","display_name":"Shreya Shukla","orcid":"https://orcid.org/0000-0001-5827-6059"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shreya Shukla","raw_affiliation_strings":["Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada","Notch Therapeutics, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Notch Therapeutics, Vancouver, British Columbia, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010749784","display_name":"Ayako Yachie\u2010Kinoshita","orcid":"https://orcid.org/0000-0003-2032-227X"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ayako Yachie-Kinoshita","raw_affiliation_strings":["Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106479385","display_name":"Michael R. Hughes","orcid":"https://orcid.org/0000-0002-7925-6070"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Michael Hughes","raw_affiliation_strings":["Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041571580","display_name":"Kelly M. McNagny","orcid":"https://orcid.org/0000-0003-4737-3499"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Kelly M. McNagny","raw_affiliation_strings":["Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada","School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026092817","display_name":"Peter W. Zandstra","orcid":"https://orcid.org/0000-0002-9568-733X"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Peter W. Zandstra","raw_affiliation_strings":["Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]},{"raw_affiliation_string":"School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5026092817"],"corresponding_institution_ids":["https://openalex.org/I141945490","https://openalex.org/I4210133112"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.1698,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.88093088,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"18","issue":"2","first_page":"e1009907","last_page":"e1009907"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9926000237464905,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9610999822616577,"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/executable","display_name":"Executable","score":0.9292255640029907},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6548033356666565},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6523755192756653},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5912330746650696},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.49008429050445557},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48919108510017395},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4518128037452698},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4256870746612549},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36314675211906433},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3376815915107727},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.18179312348365784},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17532134056091309},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15261340141296387},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08892065286636353}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.9292255640029907},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6548033356666565},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6523755192756653},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5912330746650696},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.49008429050445557},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48919108510017395},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4518128037452698},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4256870746612549},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36314675211906433},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3376815915107727},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.18179312348365784},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17532134056091309},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15261340141296387},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08892065286636353}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":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":"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":"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1009907","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009907","pdf_url":null,"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:35213533","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35213533","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:ac7a7750987c4461be0be648a96584c1","is_oa":true,"landing_page_url":"https://doaj.org/article/ac7a7750987c4461be0be648a96584c1","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":"PLoS Computational Biology, Vol 18, Iss 2, p e1009907 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8906617","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8906617","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1009907","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009907","pdf_url":null,"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":[{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2165548363","display_name":null,"funder_award_id":"Canada","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2629756198","display_name":null,"funder_award_id":"FRN 154283","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G3028888727","display_name":null,"funder_award_id":"RGPIN-2020-0","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3030655770","display_name":null,"funder_award_id":"Research Chair","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G3525686075","display_name":null,"funder_award_id":"RGPIN-2020","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G3969565085","display_name":null,"funder_award_id":"Foundation","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G4389354971","display_name":null,"funder_award_id":"Research","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G4515207065","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G5265193246","display_name":null,"funder_award_id":"Canada Research Chair","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G5439070872","display_name":null,"funder_award_id":"RGPIN-2020-06496","funder_id":"https://openalex.org/F4320321487","funder_display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G5784215521","display_name":null,"funder_award_id":"Chair","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6282788884","display_name":null,"funder_award_id":"Canadian Institutes of Health","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G727862659","display_name":null,"funder_award_id":"Canadian Institutes of Health Research (CIHR)","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G7443112882","display_name":null,"funder_award_id":"Foundation Grant","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G8105784103","display_name":null,"funder_award_id":"RGPIN-202","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G8284766523","display_name":null,"funder_award_id":"(NSERC)","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320308380","display_name":"Yale University","ror":"https://ror.org/03v76x132"},{"id":"https://openalex.org/F4320308943","display_name":"Microsoft Research","ror":"https://ror.org/00d0nc645"},{"id":"https://openalex.org/F4320321487","display_name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":85,"referenced_works":["https://openalex.org/W115452890","https://openalex.org/W1480909796","https://openalex.org/W1538274751","https://openalex.org/W1920024920","https://openalex.org/W1973770084","https://openalex.org/W1978031011","https://openalex.org/W2005529944","https://openalex.org/W2011346553","https://openalex.org/W2012931776","https://openalex.org/W2031285837","https://openalex.org/W2035444281","https://openalex.org/W2036283188","https://openalex.org/W2054470690","https://openalex.org/W2059817275","https://openalex.org/W2067060241","https://openalex.org/W2067088953","https://openalex.org/W2067131315","https://openalex.org/W2074081056","https://openalex.org/W2079296583","https://openalex.org/W2087634174","https://openalex.org/W2091854066","https://openalex.org/W2093227216","https://openalex.org/W2105372361","https://openalex.org/W2110213545","https://openalex.org/W2110259586","https://openalex.org/W2112138633","https://openalex.org/W2118524018","https://openalex.org/W2125987139","https://openalex.org/W2127218421","https://openalex.org/W2129795133","https://openalex.org/W2133254377","https://openalex.org/W2136453810","https://openalex.org/W2150729435","https://openalex.org/W2152505144","https://openalex.org/W2153868393","https://openalex.org/W2170505338","https://openalex.org/W2178062201","https://openalex.org/W2290826747","https://openalex.org/W2311221011","https://openalex.org/W2313486313","https://openalex.org/W2333997296","https://openalex.org/W2344681634","https://openalex.org/W2464730303","https://openalex.org/W2465917013","https://openalex.org/W2509957998","https://openalex.org/W2520858613","https://openalex.org/W2605463821","https://openalex.org/W2607076347","https://openalex.org/W2616922646","https://openalex.org/W2621589069","https://openalex.org/W2624618144","https://openalex.org/W2743748882","https://openalex.org/W2747877289","https://openalex.org/W2756796266","https://openalex.org/W2766222575","https://openalex.org/W2769933977","https://openalex.org/W2783975438","https://openalex.org/W2784588023","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2805619986","https://openalex.org/W2884030511","https://openalex.org/W2898762469","https://openalex.org/W2915813447","https://openalex.org/W2944018172","https://openalex.org/W2945949586","https://openalex.org/W2949237386","https://openalex.org/W2950214765","https://openalex.org/W2950372712","https://openalex.org/W2951799803","https://openalex.org/W2953942915","https://openalex.org/W2971758644","https://openalex.org/W2980698015","https://openalex.org/W2985827561","https://openalex.org/W2989744261","https://openalex.org/W2992151131","https://openalex.org/W2997831639","https://openalex.org/W3006301383","https://openalex.org/W3036206386","https://openalex.org/W3049671813","https://openalex.org/W3080162757","https://openalex.org/W3086060297","https://openalex.org/W3182034091","https://openalex.org/W4239993434","https://openalex.org/W4319591822"],"related_works":["https://openalex.org/W2350278424","https://openalex.org/W2071432835","https://openalex.org/W4239401009","https://openalex.org/W4234371507","https://openalex.org/W1628824497","https://openalex.org/W4299534542","https://openalex.org/W2053441600","https://openalex.org/W1990401748","https://openalex.org/W2047586841","https://openalex.org/W2141018266"],"abstract_inverted_index":{"The":[0],"increasing":[1],"availability":[2],"of":[3,47,58,70,98,106,115,123],"single-cell":[4],"RNA-sequencing":[5],"(scRNA-seq)":[6],"data":[7],"from":[8,22,39,79,104],"various":[9],"developmental":[10,51],"systems":[11],"provides":[12],"the":[13,56,68,91,116,121,152,159,165],"opportunity":[14],"to":[15,30,60,76,138,158,172],"infer":[16,94],"gene":[17,100,125,132],"regulatory":[18],"networks":[19],"(GRNs)":[20],"directly":[21,38],"data.":[23,41],"Herein":[24],"we":[25,73,128],"describe":[26,67],"IQCELL,":[27],"a":[28,169],"platform":[29,92,167],"infer,":[31,173],"simulate,":[32,174],"and":[33,53,83,88,175],"study":[34,176],"executable":[35,43,177],"logical":[36],"GRNs":[37,44,178],"scRNA-seq":[40,77],"Such":[42],"allow":[45],"simulation":[46],"fundamental":[48],"hypotheses":[49],"governing":[50],"programs":[52],"help":[54],"accelerate":[55],"design":[57],"strategies":[59],"control":[61],"stem":[62],"cell":[63,86],"fate.":[64],"We":[65,108,145],"first":[66],"architecture":[69],"IQCELL.":[71],"Next,":[72],"apply":[74],"IQCELL":[75,131,166],"datasets":[78],"early":[80],"mouse":[81],"T-cell":[82],"red":[84],"blood":[85],"development,":[87],"show":[89,111],"that":[90,112,135,147],"can":[93],"overall":[95],"over":[96],"74%":[97],"causal":[99],"interactions":[101],"previously":[102],"reported":[103],"decades":[105],"research.":[107],"will":[109],"also":[110],"dynamic":[113,180],"simulations":[114,149],"generated":[117],"GRN":[118,148],"qualitatively":[119],"recapitulate":[120],"effects":[122],"known":[124],"perturbations.":[126],"Finally,":[127],"implement":[129],"an":[130],"selection":[133],"pipeline":[134],"allows":[136],"us":[137],"identify":[139],"candidate":[140],"genes,":[141],"without":[142],"prior":[143],"knowledge.":[144],"demonstrate":[146],"based":[150],"on":[151],"inferred":[153],"set":[154],"yield":[155],"results":[156],"similar":[157],"original":[160],"curated":[161],"lists.":[162],"In":[163],"summary,":[164],"offers":[168],"versatile":[170],"tool":[171],"in":[179],"biological":[181],"systems.":[182]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":5}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}