{"id":"https://openalex.org/W2076149854","doi":"https://doi.org/10.1186/1752-0509-8-s3-s1","title":"A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets","display_name":"A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets","publication_year":2014,"publication_date":"2014-10-22","ids":{"openalex":"https://openalex.org/W2076149854","doi":"https://doi.org/10.1186/1752-0509-8-s3-s1","mag":"2076149854","pmid":"https://pubmed.ncbi.nlm.nih.gov/25350697"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-8-s3-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s3-s1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S3-S1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S3-S1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112150417","display_name":"Lizhi Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Li-Zhi Liu","raw_affiliation_strings":["Department of Mechanical Engineering, University of Saskatchewan, 57 Campus Drive, S7N 5A9 Saskatoon, Canada","Dept. of Mechanical Eng., Univ. of Saskatchewan, Saskatoon, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, University of Saskatchewan, 57 Campus Drive, S7N 5A9 Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]},{"raw_affiliation_string":"Dept. of Mechanical Eng., Univ. of Saskatchewan, Saskatoon, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091157395","display_name":"Fang\u2010Xiang Wu","orcid":"https://orcid.org/0000-0002-4593-9332"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Fang-Xiang Wu","raw_affiliation_strings":["Division of Biomedical Engineering; University of Saskatchewan; Saskatoon Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Engineering; University of Saskatchewan; Saskatoon Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"last","author":{"id":null,"display_name":"Wen-Jun Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Wen-Jun Zhang","raw_affiliation_strings":["Division of Biomedical Engineering; University of Saskatchewan; Saskatoon Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Engineering; University of Saskatchewan; Saskatoon Canada","institution_ids":["https://openalex.org/I32625721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5112150417"],"corresponding_institution_ids":["https://openalex.org/I32625721"],"apc_list":null,"apc_paid":null,"fwci":2.4188,"has_fulltext":true,"cited_by_count":49,"citation_normalized_percentile":{"value":0.89178208,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"8","issue":"S3","first_page":"S1","last_page":"S1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6819000244140625,"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/T10885","display_name":"Gene expression and cancer classification","score":0.6819000244140625,"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":0.26350000500679016,"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":0.008700000122189522,"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/systems-biology","display_name":"Systems biology","score":0.671230673789978},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6183270215988159},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6007893681526184},{"id":"https://openalex.org/keywords/lasso","display_name":"Lasso (programming language)","score":0.5742774605751038},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4771161377429962},{"id":"https://openalex.org/keywords/group","display_name":"Group (periodic table)","score":0.46423664689064026},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4094504714012146},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3749632239341736},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25988250970840454},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21224573254585266}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.671230673789978},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6183270215988159},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6007893681526184},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.5742774605751038},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4771161377429962},{"id":"https://openalex.org/C2781311116","wikidata":"https://www.wikidata.org/wiki/Q83306","display_name":"Group (periodic table)","level":2,"score":0.46423664689064026},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4094504714012146},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3749632239341736},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25988250970840454},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21224573254585266},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"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":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-8-s3-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s3-s1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S3-S1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:25350697","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25350697","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4243122","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4243122","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-8-s3-s1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-s3-s1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-S3-S1","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2076149854.pdf","grobid_xml":"https://content.openalex.org/works/W2076149854.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1540764732","https://openalex.org/W1554944419","https://openalex.org/W1965169081","https://openalex.org/W1966546718","https://openalex.org/W1974442150","https://openalex.org/W1981276685","https://openalex.org/W1993279375","https://openalex.org/W2001334414","https://openalex.org/W2008358153","https://openalex.org/W2027146421","https://openalex.org/W2057682568","https://openalex.org/W2061749710","https://openalex.org/W2067931273","https://openalex.org/W2073661114","https://openalex.org/W2095622082","https://openalex.org/W2106555403","https://openalex.org/W2106927126","https://openalex.org/W2120748206","https://openalex.org/W2126874285","https://openalex.org/W2135029798","https://openalex.org/W2138019504","https://openalex.org/W2159495578","https://openalex.org/W2161409973","https://openalex.org/W2163296862","https://openalex.org/W2163485494","https://openalex.org/W2168215278","https://openalex.org/W2562162676","https://openalex.org/W2999905431","https://openalex.org/W3105120000","https://openalex.org/W3143596294","https://openalex.org/W3146116728"],"related_works":["https://openalex.org/W5284979","https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2032799661","https://openalex.org/W4245853730","https://openalex.org/W2884256268","https://openalex.org/W2131025197","https://openalex.org/W2171763327","https://openalex.org/W2154615478","https://openalex.org/W2031892952"],"abstract_inverted_index":{"BACKGROUND:":[0],"As":[1],"an":[2,150],"abstract":[3],"mapping":[4],"of":[5,28,48,69,157,181,210,228,245,257],"the":[6,10,46,101,115,131,142,147,155,205,221,229,234,238,242,246,255,258,271],"gene":[7,12,29,34,53,62,71,87,123,266],"regulations":[8],"in":[9,42,146,208,262],"cell,":[11],"regulatory":[13,30,72],"network":[14,63,73,118,178],"is":[15,37,83,111,164,170,188],"important":[16],"to":[17,113,129,133,172,175,190,241,273],"both":[18,191,211],"biological":[19,49],"research":[20,40],"study":[21],"and":[22,161,194,218,250,269],"practical":[23],"applications.":[24],"The":[25,67,185,225,248],"reverse":[26],"engineering":[27],"networks":[31],"from":[32,120,237],"microarray":[33],"expression":[35,54,88,124,267],"data":[36,89,252],"a":[38,60,70,177],"challenging":[39],"problem":[41,144],"systems":[43],"biology.":[44],"With":[45],"development":[47],"technologies,":[50],"multiple":[51,80,121,264],"time-course":[52,122,265],"datasets":[55,125,193,268],"might":[56],"be":[57,75,91],"collected":[58],"for":[59],"specific":[61],"under":[64,213,220],"different":[65],"circumstances.":[66],"inference":[68,102],"can":[74],"improved":[76],"by":[77],"integrating":[78,263],"these":[79],"datasets.":[81,197],"It":[82,198],"also":[84],"known":[85],"that":[86,200,233],"may":[90,99],"contaminated":[92],"with":[93,183],"large":[94,134,274],"errors":[95,275],"or":[96,136,276],"outliers,":[97],"which":[98,153],"affect":[100],"results.":[103],"RESULTS:":[104],"A":[105,166],"novel":[106],"method,":[107,149],"Huber":[108,201,259],"group":[109,202,206,260],"LASSO,":[110],"proposed":[112,148,186],"infer":[114],"same":[116],"underlying":[117],"topology":[119,179],"as":[126,128],"well":[127],"take":[130],"robustness":[132],"error":[135],"outliers":[137],"into":[138],"account.":[139],"To":[140],"solve":[141],"optimization":[143],"involved":[145],"efficient":[151],"algorithm":[152,230,239],"combines":[154],"ideas":[156],"auxiliary":[158],"function":[159],"minimization":[160],"block":[162],"descent":[163],"developed.":[165],"stability":[167],"selection":[168],"method":[169,174,187],"adapted":[171],"our":[173],"find":[176],"consisting":[180],"edges":[182],"scores.":[184],"applied":[189],"simulation":[192,249],"real":[195,251],"experimental":[196],"shows":[199,232],"LASSO":[203,207,261],"outperforms":[204],"terms":[209],"areas":[212,219],"receiver":[214],"operating":[215],"characteristic":[216],"curves":[217],"precision-recall":[222],"curves.":[223],"CONCLUSIONS:":[224],"convergence":[226],"analysis":[227],"theoretically":[231],"sequence":[235],"generated":[236],"converges":[240],"optimal":[243],"solution":[244],"problem.":[247],"examples":[253],"demonstrate":[254],"effectiveness":[256],"improving":[270],"resistance":[272],"outliers.":[277]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}