{"id":"https://openalex.org/W4411163595","doi":"https://doi.org/10.1093/bioinformatics/btaf318","title":"BiGSM: Bayesian inference of gene regulatory network via sparse modelling","display_name":"BiGSM: Bayesian inference of gene regulatory network via sparse modelling","publication_year":2025,"publication_date":"2025-06-01","ids":{"openalex":"https://openalex.org/W4411163595","doi":"https://doi.org/10.1093/bioinformatics/btaf318","pmid":"https://pubmed.ncbi.nlm.nih.gov/40484997"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf318","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf318","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080331938","display_name":"Huanlong Qin","orcid":"https://orcid.org/0009-0005-7934-7633"},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Hang Qin","raw_affiliation_strings":["Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology , Stockholm 11428,","Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 11428, Sweden"],"affiliations":[{"raw_affiliation_string":"Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology , Stockholm 11428,","institution_ids":["https://openalex.org/I86987016"]},{"raw_affiliation_string":"Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 11428, Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018408470","display_name":"Mateusz Garbulowski","orcid":"https://orcid.org/0000-0002-2497-194X"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Mateusz Garbulowski","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , Solna 17121,","Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala 75123,","Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75123, Sweden","Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna 17121, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , Solna 17121,","institution_ids":["https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala 75123,","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75123, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna 17121, Sweden","institution_ids":["https://openalex.org/I2800139495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032432650","display_name":"Erik L. L. Sonnhammer","orcid":"https://orcid.org/0000-0002-9015-5588"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Erik L L Sonnhammer","raw_affiliation_strings":["Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , Solna 17121,","Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna 17121, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , Solna 17121,","institution_ids":["https://openalex.org/I2800139495"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna 17121, Sweden","institution_ids":["https://openalex.org/I2800139495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101692633","display_name":"Saikat Chatterjee","orcid":"https://orcid.org/0000-0003-2638-6047"},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Saikat Chatterjee","raw_affiliation_strings":["Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology , Stockholm 11428,","Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 11428, Sweden"],"affiliations":[{"raw_affiliation_string":"Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology , Stockholm 11428,","institution_ids":["https://openalex.org/I86987016"]},{"raw_affiliation_string":"Digital Futures, and School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 11428, Sweden","institution_ids":["https://openalex.org/I86987016"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080331938"],"corresponding_institution_ids":["https://openalex.org/I86987016"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11841231,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9975000023841858,"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":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9807000160217285,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9743000268936157,"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":0.7115346193313599},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6721404790878296},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5408388376235962},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5234375},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5229628682136536},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5107567310333252},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4869631230831146},{"id":"https://openalex.org/keywords/posterior-probability","display_name":"Posterior probability","score":0.4848940968513489},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.47462713718414307},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4576915204524994},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4248898923397064},{"id":"https://openalex.org/keywords/lasso","display_name":"Lasso (programming language)","score":0.4197234511375427},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4190298020839691}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7115346193313599},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6721404790878296},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5408388376235962},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5234375},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5229628682136536},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5107567310333252},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4869631230831146},{"id":"https://openalex.org/C57830394","wikidata":"https://www.wikidata.org/wiki/Q278079","display_name":"Posterior probability","level":3,"score":0.4848940968513489},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.47462713718414307},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4576915204524994},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4248898923397064},{"id":"https://openalex.org/C37616216","wikidata":"https://www.wikidata.org/wiki/Q3218363","display_name":"Lasso (programming language)","level":2,"score":0.4197234511375427},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4190298020839691},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf318","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40484997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40484997","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:DiVA.org:uu-561483","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-561483","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:europepmc.org:10964170","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12151459","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf318","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1972764318","https://openalex.org/W1990912589","https://openalex.org/W2025803032","https://openalex.org/W2050086663","https://openalex.org/W2057306408","https://openalex.org/W2071284784","https://openalex.org/W2076372398","https://openalex.org/W2076513103","https://openalex.org/W2099786058","https://openalex.org/W2106555403","https://openalex.org/W2122708083","https://openalex.org/W2139997707","https://openalex.org/W2143076232","https://openalex.org/W2148154358","https://openalex.org/W2150749732","https://openalex.org/W2152941516","https://openalex.org/W2157121418","https://openalex.org/W2383534773","https://openalex.org/W2608543022","https://openalex.org/W2757021802","https://openalex.org/W3013900499","https://openalex.org/W3030354362","https://openalex.org/W3134329288","https://openalex.org/W3142178348","https://openalex.org/W3186348651","https://openalex.org/W4212837655","https://openalex.org/W4212863985","https://openalex.org/W4281488864","https://openalex.org/W4300863446","https://openalex.org/W4323655246","https://openalex.org/W4390670020","https://openalex.org/W4402607747"],"related_works":["https://openalex.org/W2032094637","https://openalex.org/W2040227828","https://openalex.org/W2060045818","https://openalex.org/W2131935101","https://openalex.org/W2407375987","https://openalex.org/W856257623","https://openalex.org/W3049691116","https://openalex.org/W2505726097","https://openalex.org/W2950975704","https://openalex.org/W2010643158"],"abstract_inverted_index":{"Code":[0],"implemented":[1],"via":[2],"MATLAB":[3],"and":[4,11],"Python":[5],"are":[6],"available":[7],"at":[8,13],"Github:":[9],"https://github.com/SachLab/BiGSM":[10],"archived":[12],"zenodo.":[14]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
