{"id":"https://openalex.org/W3036077871","doi":"https://doi.org/10.1093/bioinformatics/btaa576","title":"Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference","display_name":"Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference","publication_year":2020,"publication_date":"2020-06-11","ids":{"openalex":"https://openalex.org/W3036077871","doi":"https://doi.org/10.1093/bioinformatics/btaa576","mag":"3036077871","pmid":"https://pubmed.ncbi.nlm.nih.gov/33026066"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa576","doi":"https://doi.org/10.1093/bioinformatics/btaa576","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa576","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/464479","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062730839","display_name":"Pierre-Cyril Aubin-Frankowski","orcid":"https://orcid.org/0000-0001-7992-8335","observed_orcids":["https://orcid.org/0000-0001-7992-8335"]},"institutions":[{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I4405253156","display_name":"Centre de Bio-Informatique","ror":"https://ror.org/00c00ys31","country_code":"FR","type":"facility","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I4405253156","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Pierre-Cyril Aubin-Frankowski","raw_affiliation_strings":["MINES ParisTech, PSL Research University, CBIO \u2013 Centre for Computational Biology , F-75006 Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MINES ParisTech, PSL Research University, CBIO \u2013 Centre for Computational Biology , F-75006 Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I4405253156","https://openalex.org/I70768539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064770739","display_name":"Jean\u2010Philippe Vert","orcid":"https://orcid.org/0000-0001-9510-8441","observed_orcids":["https://orcid.org/0000-0001-9510-8441"]},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I4405253156","display_name":"Centre de Bio-Informatique","ror":"https://ror.org/00c00ys31","country_code":"FR","type":"facility","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I4405253156","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]}],"countries":["FR","US"],"is_corresponding":true,"raw_author_name":"Jean-Philippe Vert","raw_affiliation_strings":["Google Research , Brain team, 75009 Paris, France","MINES ParisTech, PSL Research University, CBIO \u2013 Centre for Computational Biology , F-75006 Paris, France"],"raw_orcid":"https://orcid.org/0000-0001-9510-8441","affiliations":[{"raw_affiliation_string":"Google Research , Brain team, 75009 Paris, France","institution_ids":["https://openalex.org/I1291425158"]},{"raw_affiliation_string":"MINES ParisTech, PSL Research University, CBIO \u2013 Centre for Computational Biology , F-75006 Paris, France","institution_ids":["https://openalex.org/I2746051580","https://openalex.org/I4405253156","https://openalex.org/I70768539"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062730839","https://openalex.org/A5064770739"],"corresponding_institution_ids":["https://openalex.org/I1291425158","https://openalex.org/I2746051580","https://openalex.org/I4405253156","https://openalex.org/I70768539"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":4.6453,"has_fulltext":false,"cited_by_count":116,"citation_normalized_percentile":{"value":0.96831431,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"36","issue":"18","first_page":"4774","last_page":"4780"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9014000296592712,"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":0.9014000296592712,"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":0.09709999710321426,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":9.999999747378752e-05,"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/gene-regulatory-network-inference","display_name":"gene regulatory network inference","score":0.9940000176429749},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.9539999961853027},{"id":"https://openalex.org/keywords/linear-differential-equations","display_name":"linear differential equations","score":0.7450000047683716},{"id":"https://openalex.org/keywords/sparse-regression","display_name":"sparse regression","score":0.7310000061988831},{"id":"https://openalex.org/keywords/cell-differentiation","display_name":"cell differentiation","score":0.7089999914169312},{"id":"https://openalex.org/keywords/cell-cycle","display_name":"cell cycle","score":0.6980000138282776}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7792714834213257},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6803487539291382},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.5568839311599731},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4718359112739563},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4572874903678894},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.45698028802871704},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.45346227288246155},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.41926825046539307},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.4157974123954773},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38405361771583557},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.3271275460720062},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31143200397491455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18659710884094238},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18430554866790771},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1615842878818512},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1071060299873352},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa576","doi":"https://doi.org/10.1093/bioinformatics/btaa576","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa576","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/464479","doi":"https://doi.org/10.1101/464479","is_oa":true,"landing_page_url":"https://doi.org/10.1101/464479","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:33026066","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33026066","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,"listed_in":[],"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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:HAL:hal-03114385v1","doi":null,"is_oa":false,"landing_page_url":"https://hal.science/hal-03114385","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2020, &#x27E8;10.1101/464479&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1101/464479","doi":"https://doi.org/10.1101/464479","is_oa":true,"landing_page_url":"https://doi.org/10.1101/464479","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1543475572","https://openalex.org/W1580018887","https://openalex.org/W1792532087","https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W1987320425","https://openalex.org/W1988391018","https://openalex.org/W1990930479","https://openalex.org/W2023887100","https://openalex.org/W2065427389","https://openalex.org/W2076513103","https://openalex.org/W2106555403","https://openalex.org/W2110503722","https://openalex.org/W2125258701","https://openalex.org/W2129905934","https://openalex.org/W2136453810","https://openalex.org/W2138265962","https://openalex.org/W2151611345","https://openalex.org/W2177432730","https://openalex.org/W2178888844","https://openalex.org/W2231058499","https://openalex.org/W2338756998","https://openalex.org/W2347567240","https://openalex.org/W2416402039","https://openalex.org/W2511896561","https://openalex.org/W2526724898","https://openalex.org/W2562162676","https://openalex.org/W2594807826","https://openalex.org/W2612568060","https://openalex.org/W2616922646","https://openalex.org/W2757234574","https://openalex.org/W2766437506","https://openalex.org/W2783644856","https://openalex.org/W2891678790","https://openalex.org/W2948300330","https://openalex.org/W2952535935","https://openalex.org/W3047141442","https://openalex.org/W6754519919"],"related_works":["https://openalex.org/W7116703160","https://openalex.org/W4281559042","https://openalex.org/W3019620359","https://openalex.org/W4409570092","https://openalex.org/W3159703342","https://openalex.org/W4391126196","https://openalex.org/W7159065274","https://openalex.org/W4213344226","https://openalex.org/W3182728713","https://openalex.org/W7155516157"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"offers":[5],"new":[6,50],"possibilities":[7],"to":[8,35,40,92],"infer":[9],"gene":[10],"regulatory":[11],"network":[12],"(GRNs)":[13],"for":[14,54,115],"biological":[15],"processes":[16],"involving":[17],"a":[18,49,64,87,98,110],"notion":[19],"of":[20,71,76,83,127],"time,":[21],"such":[22],"as":[23],"cell":[24,27,84],"differentiation":[25],"or":[26],"cycles.":[28],"It":[29],"also":[30],"raises":[31],"many":[32],"challenges":[33],"due":[34],"the":[36,41,69,81,94],"destructive":[37],"measurements":[38],"inherent":[39],"technology.":[42],"RESULTS:":[43],"In":[44],"this":[45],"work,":[46],"we":[47],"propose":[48],"method":[51,114],"named":[52],"GRISLI":[53,62,108,128],"de":[55],"novo":[56],"GRN":[57,96,116],"inference":[58],"from":[59,74,118],"scRNA-seq":[60,72,119],"data.":[61,120],"infers":[63],"velocity":[65],"vector":[66],"field":[67],"in":[68],"space":[70],"data":[73,106,136],"profiles":[75],"individual":[77],"cells,":[78],"and":[79],"models":[80],"dynamics":[82],"trajectories":[85],"with":[86,97],"linear":[88],"ordinary":[89],"differential":[90],"equation":[91],"reconstruct":[93],"underlying":[95],"sparse":[99],"regression":[100],"procedure.":[101],"We":[102],"show":[103],"on":[104],"real":[105],"that":[107],"outperforms":[109],"recently":[111],"proposed":[112],"state-of-the-art":[113],"reconstruction":[117],"AVAILABILITY":[121],"AND":[122],"IMPLEMENTATION:":[123],"The":[124],"MATLAB":[125],"code":[126],"is":[129],"available":[130,138],"at:":[131],"https://github.com/PCAubin/GRISLI.":[132],"SUPPLEMENTARY":[133],"INFORMATION:":[134],"Supplementary":[135],"are":[137],"at":[139],"Bioinformatics":[140],"online.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":23},{"year":2022,"cited_by_count":25},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2020-06-25T00:00:00"}
