{"id":"https://openalex.org/W2154782854","doi":"https://doi.org/10.1093/bioinformatics/bts212","title":"A single source <i>k</i>-shortest paths algorithm to infer regulatory pathways in a gene network","display_name":"A single source <i>k</i>-shortest paths algorithm to infer regulatory pathways in a gene network","publication_year":2012,"publication_date":"2012-06-09","ids":{"openalex":"https://openalex.org/W2154782854","doi":"https://doi.org/10.1093/bioinformatics/bts212","mag":"2154782854","pmid":"https://pubmed.ncbi.nlm.nih.gov/22689778"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i49/16906115/bts212.pdf","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i49/16906115/bts212.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012461924","display_name":"Yu-Keng Shih","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu-Keng Shih","raw_affiliation_strings":["Department of Computer Science and Engineering, the Ohio State University, Columbus, OH, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, the Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100755351","display_name":"Srinivasan Parthasarathy","orcid":"https://orcid.org/0000-0002-6062-6449"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Srinivasan Parthasarathy","raw_affiliation_strings":["Department of Computer Science and Engineering, the Ohio State University, Columbus, OH, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, the Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100755351"],"corresponding_institution_ids":["https://openalex.org/I52357470"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6267,"has_fulltext":false,"cited_by_count":40,"citation_normalized_percentile":{"value":0.90509368,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"12","first_page":"i49","last_page":"i58"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.998199999332428,"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":0.9969000220298767,"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","display_name":"Gene regulatory network","score":0.7623215913772583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7253627777099609},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6946011185646057},{"id":"https://openalex.org/keywords/extant-taxon","display_name":"Extant taxon","score":0.5107386112213135},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4740821123123169},{"id":"https://openalex.org/keywords/intuition","display_name":"Intuition","score":0.4348008632659912},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36199337244033813},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35563063621520996},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28899866342544556},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2329799234867096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16174429655075073},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10794806480407715}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7623215913772583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7253627777099609},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6946011185646057},{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.5107386112213135},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4740821123123169},{"id":"https://openalex.org/C132010649","wikidata":"https://www.wikidata.org/wiki/Q189222","display_name":"Intuition","level":2,"score":0.4348008632659912},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36199337244033813},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35563063621520996},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28899866342544556},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2329799234867096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16174429655075073},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10794806480407715},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i49/16906115/bts212.pdf","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"},{"id":"pmid:22689778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22689778","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:europepmc.org:2378064","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3371844","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/i49/16906115/bts212.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2154782854.pdf","grobid_xml":"https://content.openalex.org/works/W2154782854.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1841073402","https://openalex.org/W1967490380","https://openalex.org/W1970543907","https://openalex.org/W2003652380","https://openalex.org/W2010134474","https://openalex.org/W2011282943","https://openalex.org/W2012852001","https://openalex.org/W2019136808","https://openalex.org/W2051382614","https://openalex.org/W2059456342","https://openalex.org/W2062727958","https://openalex.org/W2063961010","https://openalex.org/W2072306817","https://openalex.org/W2074443723","https://openalex.org/W2080182143","https://openalex.org/W2097636810","https://openalex.org/W2103017472","https://openalex.org/W2113654464","https://openalex.org/W2122867585","https://openalex.org/W2124168655","https://openalex.org/W2126717546","https://openalex.org/W2129112644","https://openalex.org/W2130790725","https://openalex.org/W2146264532","https://openalex.org/W2147356380","https://openalex.org/W2150182123","https://openalex.org/W2163485494","https://openalex.org/W2166606182","https://openalex.org/W2167064216","https://openalex.org/W2167654789","https://openalex.org/W2170937146","https://openalex.org/W2277605219","https://openalex.org/W4285719527","https://openalex.org/W6663348246","https://openalex.org/W6677889054"],"related_works":["https://openalex.org/W2402755139","https://openalex.org/W4249944690","https://openalex.org/W2353808877","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W4385727351","https://openalex.org/W4306798985","https://openalex.org/W4385417763"],"abstract_inverted_index":{"All":[0],"data":[1],"and":[2],"codes":[3],"are":[4],"freely":[5],"available":[6],"upon":[7],"request.":[8]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
