{"id":"https://openalex.org/W4225366673","doi":"https://doi.org/10.1371/journal.pcbi.1009950","title":"Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level","display_name":"Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level","publication_year":2022,"publication_date":"2022-03-18","ids":{"openalex":"https://openalex.org/W4225366673","doi":"https://doi.org/10.1371/journal.pcbi.1009950","pmid":"https://pubmed.ncbi.nlm.nih.gov/35303737"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009950","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009950","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.1009950","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007012094","display_name":"An\u0111ela Davidovi\u0107","orcid":"https://orcid.org/0000-0001-7784-9270"},"institutions":[{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"An\u0111ela Davidovi\u0107","raw_affiliation_strings":["Department of Computational Biology, Institut Pasteur, Paris, France","D\u00e9partement de Biologie Computationnelle - Department of Computational Biology (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)"],"raw_orcid":"https://orcid.org/0000-0001-7784-9270","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Institut Pasteur, Paris, France","institution_ids":["https://openalex.org/I157536573"]},{"raw_affiliation_string":"D\u00e9partement de Biologie Computationnelle - Department of Computational Biology (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)","institution_ids":["https://openalex.org/I4210097156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081014991","display_name":"Remy Chait","orcid":"https://orcid.org/0000-0003-0876-3187"},"institutions":[{"id":"https://openalex.org/I157556583","display_name":"Institute of Science and Technology Austria","ror":"https://ror.org/03gnh5541","country_code":"AT","type":"education","lineage":["https://openalex.org/I157556583"]},{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["AT","GB"],"is_corresponding":false,"raw_author_name":"Remy Chait","raw_affiliation_strings":["Biosciences, Living Systems Institute, University of Exeter, Exeter, The United Kingdom","Institute of Science and Technology Austria, Klosterneuburg, Austria","IST Austria - Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria Am Campus 1 3400 Klosterneuburg Austria - Austria)","University of Exeter (Mail Room, The Old Library\r\nPrince of Wales Road\r\nExeter, Devon UK\r\nEX4 4SB - United Kingdom)"],"raw_orcid":"https://orcid.org/0000-0003-0876-3187","affiliations":[{"raw_affiliation_string":"Biosciences, Living Systems Institute, University of Exeter, Exeter, The United Kingdom","institution_ids":["https://openalex.org/I23923803"]},{"raw_affiliation_string":"Institute of Science and Technology Austria, Klosterneuburg, Austria","institution_ids":["https://openalex.org/I157556583"]},{"raw_affiliation_string":"IST Austria - Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria Am Campus 1 3400 Klosterneuburg Austria - Austria)","institution_ids":["https://openalex.org/I157556583"]},{"raw_affiliation_string":"University of Exeter (Mail Room, The Old Library\r\nPrince of Wales Road\r\nExeter, Devon UK\r\nEX4 4SB - United Kingdom)","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051551664","display_name":"Gr\u00e9gory Batt","orcid":"https://orcid.org/0000-0003-1697-139X"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]},{"id":"https://openalex.org/I4387153051","display_name":"INBIO : M\u00e9thodes exp\u00e9rimentales et computationnelles pour la mod\u00e9lisation des processus cellulaires","ror":"https://ror.org/01tnxwc41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I157536573","https://openalex.org/I204730241","https://openalex.org/I4387153051","https://openalex.org/I4405257605"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gregory Batt","raw_affiliation_strings":["Department of Computational Biology, Institut Pasteur, Paris, France","Inria Paris, Paris, France","D\u00e9partement de Biologie Computationnelle - Department of Computational Biology (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)","INBIO - InBio  - M\u00e9thodes Exp\u00e9rimentales et Computationnelles pour la Mod\u00e9lisation des Processus Cellulaires /  Experimental and Computational Methods for Modeling Cellular Processes (D\u00e9partement Biologie Computationnelle\r\n25-28 rue du Docteur Roux\r\n75724 Paris cedex 15 - France)"],"raw_orcid":"https://orcid.org/0000-0003-1697-139X","affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Institut Pasteur, Paris, France","institution_ids":["https://openalex.org/I157536573"]},{"raw_affiliation_string":"Inria Paris, Paris, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"D\u00e9partement de Biologie Computationnelle - Department of Computational Biology (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)","institution_ids":["https://openalex.org/I4210097156"]},{"raw_affiliation_string":"INBIO - InBio  - M\u00e9thodes Exp\u00e9rimentales et Computationnelles pour la Mod\u00e9lisation des Processus Cellulaires /  Experimental and Computational Methods for Modeling Cellular Processes (D\u00e9partement Biologie Computationnelle\r\n25-28 rue du Docteur Roux\r\n75724 Paris cedex 15 - France)","institution_ids":["https://openalex.org/I4387153051"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015991909","display_name":"Jakob Ruess","orcid":"https://orcid.org/0000-0003-1615-3282"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I4210097156","display_name":"Biologie Computationnelle, Quantitative et Synth\u00e9tique","ror":"https://ror.org/00pcqj134","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I39804081","https://openalex.org/I4210096427","https://openalex.org/I4210097156"]},{"id":"https://openalex.org/I4387153051","display_name":"INBIO : M\u00e9thodes exp\u00e9rimentales et computationnelles pour la mod\u00e9lisation des processus cellulaires","ror":"https://ror.org/01tnxwc41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I157536573","https://openalex.org/I204730241","https://openalex.org/I4387153051","https://openalex.org/I4405257605"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Jakob Ruess","raw_affiliation_strings":["Department of Computational Biology, Institut Pasteur, Paris, France","Inria Paris, Paris, France","D\u00e9partement de Biologie Computationnelle - Department of Computational Biology (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)","INBIO - InBio  - M\u00e9thodes Exp\u00e9rimentales et Computationnelles pour la Mod\u00e9lisation des Processus Cellulaires /  Experimental and Computational Methods for Modeling Cellular Processes (D\u00e9partement Biologie Computationnelle\r\n25-28 rue du Docteur Roux\r\n75724 Paris cedex 15 - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Institut Pasteur, Paris, France","institution_ids":["https://openalex.org/I157536573"]},{"raw_affiliation_string":"Inria Paris, Paris, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"D\u00e9partement de Biologie Computationnelle - Department of Computational Biology (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)","institution_ids":["https://openalex.org/I4210097156"]},{"raw_affiliation_string":"INBIO - InBio  - M\u00e9thodes Exp\u00e9rimentales et Computationnelles pour la Mod\u00e9lisation des Processus Cellulaires /  Experimental and Computational Methods for Modeling Cellular Processes (D\u00e9partement Biologie Computationnelle\r\n25-28 rue du Docteur Roux\r\n75724 Paris cedex 15 - France)","institution_ids":["https://openalex.org/I4387153051"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5015991909"],"corresponding_institution_ids":["https://openalex.org/I1326498283","https://openalex.org/I157536573","https://openalex.org/I4210097156","https://openalex.org/I4387153051"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2345,"currency":"EUR","value_usd":2529},"fwci":0.5208,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60860024,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"18","issue":"3","first_page":"e1009950","last_page":"e1009950"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9954000115394592,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9692999720573425,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/computer-science","display_name":"Computer science","score":0.6645435094833374},{"id":"https://openalex.org/keywords/kalman-filter","display_name":"Kalman filter","score":0.6231796145439148},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5754838585853577},{"id":"https://openalex.org/keywords/experimental-data","display_name":"Experimental data","score":0.49842286109924316},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4819926619529724},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.4481545686721802},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.4285683035850525},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.42636847496032715},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20067206025123596},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1994020640850067},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15815240144729614},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12344884872436523}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6645435094833374},{"id":"https://openalex.org/C157286648","wikidata":"https://www.wikidata.org/wiki/Q846780","display_name":"Kalman filter","level":2,"score":0.6231796145439148},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5754838585853577},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.49842286109924316},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4819926619529724},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.4481545686721802},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.4285683035850525},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.42636847496032715},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20067206025123596},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1994020640850067},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15815240144729614},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12344884872436523},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009950","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009950","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:35303737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35303737","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:HAL:hal-03625706v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-03625706","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"ISSN: 1553-734X","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1009950","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009950","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:e7dc8f57714a4606bd0b647eb1451fc7","is_oa":true,"landing_page_url":"https://doaj.org/article/e7dc8f57714a4606bd0b647eb1451fc7","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 3, p e1009950 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8967023","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8967023","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009950","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009950","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/G6744286077","display_name":null,"funder_award_id":"ANR-18-CE91-0002","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6876561401","display_name":null,"funder_award_id":"ANR-18","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1503248986","https://openalex.org/W1849560532","https://openalex.org/W1859064944","https://openalex.org/W1968856189","https://openalex.org/W1974475129","https://openalex.org/W1978319180","https://openalex.org/W1980774547","https://openalex.org/W1983431486","https://openalex.org/W1986206712","https://openalex.org/W1991780313","https://openalex.org/W2009710122","https://openalex.org/W2012100675","https://openalex.org/W2015655311","https://openalex.org/W2020684750","https://openalex.org/W2042321087","https://openalex.org/W2044278781","https://openalex.org/W2053644777","https://openalex.org/W2066594542","https://openalex.org/W2081970839","https://openalex.org/W2085061065","https://openalex.org/W2088020133","https://openalex.org/W2101958901","https://openalex.org/W2122028584","https://openalex.org/W2138163236","https://openalex.org/W2155202381","https://openalex.org/W2156541178","https://openalex.org/W2158912722","https://openalex.org/W2161304688","https://openalex.org/W2164343005","https://openalex.org/W2198863405","https://openalex.org/W2262285937","https://openalex.org/W2323723611","https://openalex.org/W2500539065","https://openalex.org/W2507618556","https://openalex.org/W2517280042","https://openalex.org/W2531578105","https://openalex.org/W2764169974","https://openalex.org/W2767587403","https://openalex.org/W2769086206","https://openalex.org/W2804461679","https://openalex.org/W3099969635","https://openalex.org/W3104744823","https://openalex.org/W3123235823","https://openalex.org/W3139406751","https://openalex.org/W3160612437","https://openalex.org/W4282941149"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W1580685205","https://openalex.org/W2760382975","https://openalex.org/W3191856393","https://openalex.org/W2349716249","https://openalex.org/W2370409284","https://openalex.org/W1780459493","https://openalex.org/W2949893228","https://openalex.org/W2001928443","https://openalex.org/W2278941722"],"abstract_inverted_index":{"Understanding":[0],"and":[1,16,30,42,59,95,114,178,214,218,260,267],"characterising":[2],"biochemical":[3],"processes":[4,22],"inside":[5],"single":[6,244],"cells":[7,99,160],"requires":[8],"experimental":[9,40,91,228],"platforms":[10,41],"that":[11,90,96],"allow":[12],"one":[13,173],"to":[14,28,48,55,72,100,150,168,174,179,255,276],"perturb":[15],"observe":[17],"the":[18,34,88,130,141,166,189,195,198,209,232,282],"dynamics":[19],"of":[20,75,98,122,129,194,201,211,235,281],"such":[21],"as":[23,25,157,159],"well":[24],"computational":[26,199],"methods":[27,71,149],"build":[29],"parameterise":[31,277],"models":[32,78],"from":[33,79,183,226],"collected":[35],"data.":[36],"Recent":[37],"progress":[38],"with":[39,66,135,247],"optogenetics":[43],"has":[44],"made":[45],"it":[46],"possible":[47],"expose":[49],"each":[50],"cell":[51],"in":[52,186,208,242],"an":[53,56,240,248],"experiment":[54,241],"individualised":[57],"input":[58,106,216],"automatically":[60],"record":[61],"cellular":[62],"responses":[63,97],"over":[64],"days":[65],"fine":[67],"time":[68,265],"resolution.":[69],"However,":[70],"infer":[73,180],"parameters":[74,182],"stochastic":[76,279],"kinetic":[77],"single-cell":[80,123],"longitudinal":[81,124],"data":[82,92,125,184,224],"have":[83],"generally":[84],"been":[85],"developed":[86],"under":[87],"assumption":[89],"is":[93,219],"sparse":[94],"at":[101,262],"most":[102],"a":[103,136,151,169,278],"few":[104],"different":[105,116,215,257],"perturbations":[107,217],"can":[108],"be":[109],"observed.":[110],"Here,":[111],"we":[112,238],"investigate":[113],"compare":[115],"approaches":[117],"for":[118,223],"calculating":[119],"parameter":[120,269],"likelihoods":[121,177],"based":[126,271],"on":[127,139,272],"approximations":[128,193],"chemical":[131],"master":[132],"equation":[133],"(CME)":[134],"particular":[137],"focus":[138],"coupling":[140,165],"linear":[142],"noise":[143],"approximation":[144],"(LNA)":[145],"or":[146],"moment":[147],"closure":[148],"Kalman":[152,170],"filter.":[153],"We":[154],"show":[155],"that,":[156],"long":[158],"are":[161,253],"measured":[162,261],"sufficiently":[163],"frequently,":[164],"LNA":[167,190],"filter":[171],"allows":[172],"accurately":[175],"approximate":[176],"model":[181,280],"even":[185],"cases":[187],"where":[188],"provides":[191],"poor":[192],"CME.":[196],"Furthermore,":[197],"cost":[200],"filtering-based":[202],"iterative":[203,273],"likelihood":[204,274],"evaluation":[205,275],"scales":[206],"advantageously":[207],"number":[210],"measurement":[212],"times":[213],"thus":[220],"ideally":[221],"suited":[222],"obtained":[225],"modern":[227],"platforms.":[229],"To":[230],"demonstrate":[231],"practical":[233],"usefulness":[234],"these":[236],"results,":[237],"perform":[239],"which":[243],"cells,":[245],"equipped":[246],"optogenetic":[249],"gene":[250],"expression":[251],"system,":[252],"exposed":[254],"various":[256],"light-input":[258],"sequences":[259],"several":[263],"hundred":[264],"points":[266],"use":[268],"inference":[270],"system.":[283]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}