{"id":"https://openalex.org/W2130398729","doi":"https://doi.org/10.1093/bioinformatics/btp681","title":"Tmod: toolbox of motif discovery","display_name":"Tmod: toolbox of motif discovery","publication_year":2009,"publication_date":"2009-12-10","ids":{"openalex":"https://openalex.org/W2130398729","doi":"https://doi.org/10.1093/bioinformatics/btp681","mag":"2130398729","pmid":"https://pubmed.ncbi.nlm.nih.gov/20007740"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp681","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp681","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/405/570601/btp681.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/26/3/405/570601/btp681.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101492860","display_name":"Hanchang Sun","orcid":"https://orcid.org/0000-0003-2397-5081"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hanchang Sun","raw_affiliation_strings":["1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334810","display_name":"Yuan Yuan","orcid":"https://orcid.org/0000-0003-4706-7897"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Yuan","raw_affiliation_strings":["1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100612174","display_name":"Yibo Wu","orcid":"https://orcid.org/0000-0003-0076-8784"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yibo Wu","raw_affiliation_strings":["1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100387512","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0001-7158-913X"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Liu","raw_affiliation_strings":["1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012820890","display_name":"Jun S. Liu","orcid":"https://orcid.org/0000-0002-4450-7239"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun S. Liu","raw_affiliation_strings":["1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108195531","display_name":"Hongwei Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongwei Xie","raw_affiliation_strings":["1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Automatic Control, College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan 410073, China and 2 Department of Statistics, Harvard University, Cambridge, MA 02138-2931, USA","institution_ids":["https://openalex.org/I170215575"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101492860"],"corresponding_institution_ids":["https://openalex.org/I170215575"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9407,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.74685146,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"3","first_page":"405","last_page":"407"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9789999723434448,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9789999723434448,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9692999720573425,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9663000106811523,"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/toolbox","display_name":"Toolbox","score":0.8739985823631287},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.8069701194763184},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6039215326309204},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5187970995903015},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.46305227279663086},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33799198269844055},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.21320131421089172},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18142461776733398}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8739985823631287},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.8069701194763184},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6039215326309204},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5187970995903015},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.46305227279663086},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33799198269844055},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.21320131421089172},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18142461776733398},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp681","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp681","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/405/570601/btp681.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:20007740","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20007740","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:2033142","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2815662","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:dash.harvard.edu:1/33719948","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:33719948","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"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":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp681","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp681","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/3/405/570601/btp681.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/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2130398729.pdf","grobid_xml":"https://content.openalex.org/works/W2130398729.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1975924111","https://openalex.org/W1998300401","https://openalex.org/W2003967338","https://openalex.org/W2062872358","https://openalex.org/W2067524083","https://openalex.org/W2073727170","https://openalex.org/W2073850887","https://openalex.org/W2077013196","https://openalex.org/W2084908610","https://openalex.org/W2089783852","https://openalex.org/W2096139934","https://openalex.org/W2101835893","https://openalex.org/W2115761267","https://openalex.org/W2121356022","https://openalex.org/W2126468786","https://openalex.org/W2141224484","https://openalex.org/W2141408320","https://openalex.org/W2147415348","https://openalex.org/W2148014281","https://openalex.org/W2154165587","https://openalex.org/W2158266834","https://openalex.org/W2158962723","https://openalex.org/W2162111678","https://openalex.org/W2167190345","https://openalex.org/W2167713786","https://openalex.org/W2168157737","https://openalex.org/W2610493035","https://openalex.org/W6635200387","https://openalex.org/W6669145357"],"related_works":["https://openalex.org/W2068663075","https://openalex.org/W2797837731","https://openalex.org/W4286950177","https://openalex.org/W4285337522","https://openalex.org/W3203498468","https://openalex.org/W2464866501","https://openalex.org/W2289852464","https://openalex.org/W4282836492","https://openalex.org/W3011348691","https://openalex.org/W2788261136"],"abstract_inverted_index":{"Tmod":[0],"is":[1],"available":[2],"for":[3],"download":[4],"at":[5],"http://www.fas.harvard.edu/~junliu/Tmod/.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
