{"id":"https://openalex.org/W2998917483","doi":"https://doi.org/10.1093/bioinformatics/btaa032","title":"Inference of gene regulatory networks based on nonlinear ordinary differential equations","display_name":"Inference of gene regulatory networks based on nonlinear ordinary differential equations","publication_year":2020,"publication_date":"2020-01-15","ids":{"openalex":"https://openalex.org/W2998917483","doi":"https://doi.org/10.1093/bioinformatics/btaa032","mag":"2998917483"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa032","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa032","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,"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"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060457543","display_name":"Baoshan Ma","orcid":"https://orcid.org/0000-0003-1629-1968"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Baoshan Ma","raw_affiliation_strings":["College of Information Science and Technology, Dalian Maritime University , Dalian 116026, China"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Dalian Maritime University , Dalian 116026, China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013473604","display_name":"Mingkun Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingkun Fang","raw_affiliation_strings":["College of Information Science and Technology, Dalian Maritime University , Dalian 116026, China"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Dalian Maritime University , Dalian 116026, China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056001377","display_name":"Xiangtian Jiao","orcid":null},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtian Jiao","raw_affiliation_strings":["College of Information Science and Technology, Dalian Maritime University , Dalian 116026, China"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Dalian Maritime University , Dalian 116026, China","institution_ids":["https://openalex.org/I43313876"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060457543"],"corresponding_institution_ids":["https://openalex.org/I43313876"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.0081,"has_fulltext":false,"cited_by_count":78,"citation_normalized_percentile":{"value":0.92204657,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"36","issue":"19","first_page":"4885","last_page":"4893"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962000250816345,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9940999746322632,"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/computer-science","display_name":"Computer science","score":0.7229134440422058},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7075996994972229},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6841057538986206},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.6001295447349548},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5458205342292786},{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.5288152694702148},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.5008578300476074},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48216575384140015},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4622056484222412},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4100727438926697},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3710872232913971},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3382227122783661},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29499703645706177},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.24655476212501526},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16769182682037354},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16199904680252075},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14653223752975464},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12942400574684143}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7229134440422058},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7075996994972229},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6841057538986206},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.6001295447349548},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5458205342292786},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.5288152694702148},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.5008578300476074},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48216575384140015},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4622056484222412},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4100727438926697},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3710872232913971},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3382227122783661},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29499703645706177},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.24655476212501526},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16769182682037354},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16199904680252075},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14653223752975464},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12942400574684143},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btaa032","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa032","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,"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"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G244748139","display_name":null,"funder_award_id":"61471078","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1971144865","https://openalex.org/W1973260612","https://openalex.org/W1986688807","https://openalex.org/W1993418188","https://openalex.org/W1999902057","https://openalex.org/W2003003919","https://openalex.org/W2023348596","https://openalex.org/W2037544231","https://openalex.org/W2043652309","https://openalex.org/W2054286320","https://openalex.org/W2076513103","https://openalex.org/W2095073726","https://openalex.org/W2101792624","https://openalex.org/W2108579152","https://openalex.org/W2109384743","https://openalex.org/W2115108153","https://openalex.org/W2125508747","https://openalex.org/W2126345910","https://openalex.org/W2139997707","https://openalex.org/W2143076232","https://openalex.org/W2154297838","https://openalex.org/W2160533336","https://openalex.org/W2161922735","https://openalex.org/W2232370058","https://openalex.org/W2280966365","https://openalex.org/W2303875941","https://openalex.org/W2498761000","https://openalex.org/W2518309745","https://openalex.org/W2555391902","https://openalex.org/W2561175740","https://openalex.org/W2757021802","https://openalex.org/W2791183315","https://openalex.org/W2803928488","https://openalex.org/W2899545492","https://openalex.org/W2900099657","https://openalex.org/W2952535935","https://openalex.org/W2963189776","https://openalex.org/W2968131803","https://openalex.org/W3104499332"],"related_works":["https://openalex.org/W3082668976","https://openalex.org/W2517973022","https://openalex.org/W1543121148","https://openalex.org/W1580703421","https://openalex.org/W2996841952","https://openalex.org/W2618518959","https://openalex.org/W2231364979","https://openalex.org/W4295745414","https://openalex.org/W4382202915","https://openalex.org/W2469875185"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Gene":[2],"regulatory":[3,8,74,117],"networks":[4],"(GRNs)":[5],"capture":[6],"the":[7,14,25,43,64,72,127,147,162,165,170,196],"interactions":[9],"between":[10],"genes,":[11],"resulting":[12],"from":[13,37,87],"fundamental":[15],"biological":[16],"process":[17],"of":[18,27,42,71,96,137,157],"transcription":[19],"and":[20,32,89,108,131,139,180,188,199],"translation.":[21],"In":[22,77],"some":[23],"cases,":[24],"topology":[26],"GRNs":[28,45,86],"is":[29,123,193,200],"not":[30],"known,":[31],"has":[33],"to":[34,51,103,113],"be":[35],"inferred":[36],"gene":[38,106,134],"expression":[39,135],"data.":[40,56],"Most":[41],"existing":[44],"reconstruction":[46],"algorithms":[47,154],"are":[48,208],"either":[49],"applied":[50],"time-series":[52,58,88],"data":[53,59,68,91,207],"or":[54],"steady-state":[55,67,90],"Although":[57],"include":[60],"more":[61],"information":[62,205],"about":[63],"system":[65],"dynamics,":[66],"imply":[69],"stability":[70],"underlying":[73],"networks.":[75],"Results":[76],"this":[78],"article,":[79],"we":[80],"propose":[81],"a":[82,97,183],"method":[83,122,149,175,192],"for":[84],"inferring":[85],"jointly.":[92],"We":[93],"make":[94],"use":[95],"non-linear":[98],"ordinary":[99],"differential":[100],"equations":[101],"framework":[102],"model":[104],"dynamic":[105],"regulation":[107],"an":[109],"importance":[110],"measurement":[111],"strategy":[112],"infer":[114],"all":[115],"putative":[116],"links":[118],"efficiently.":[119],"The":[120,190],"proposed":[121,148,191],"evaluated":[124],"extensively":[125],"on":[126,143,164],"artificial":[128],"DREAM4":[129],"dataset":[130],"two":[132],"real":[133],"datasets":[136,166],"yeast":[138],"Escherichia":[140],"coli.":[141],"Based":[142],"public":[144],"benchmark":[145],"datasets,":[146],"outperforms":[150],"other":[151],"popular":[152],"inference":[153],"in":[155,195],"terms":[156],"overall":[158],"score.":[159],"By":[160],"comparing":[161],"performance":[163],"with":[167],"different":[168],"scales,":[169],"results":[171],"show":[172],"that":[173],"our":[174],"still":[176],"keeps":[177],"good":[178],"robustness":[179],"accuracy":[181],"at":[182,210],"low":[184],"computational":[185],"complexity.":[186],"Availability":[187],"implementation":[189],"written":[194],"Python":[197],"language,":[198],"available":[201,209],"at:":[202],"https://github.com/lab319/GRNs_nonlinear_ODEs":[203],"Supplementary":[204,206],"Bioinformatics":[211],"online.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":3}],"updated_date":"2026-03-05T09:29:38.588285","created_date":"2020-01-23T00:00:00"}