{"id":"https://openalex.org/W2936606617","doi":"https://doi.org/10.1093/bioinformatics/btz198","title":"SArKS: <i>de novo</i> discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing","display_name":"SArKS: <i>de novo</i> discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing","publication_year":2019,"publication_date":"2019-03-20","ids":{"openalex":"https://openalex.org/W2936606617","doi":"https://doi.org/10.1093/bioinformatics/btz198","mag":"2936606617","pmid":"https://pubmed.ncbi.nlm.nih.gov/30903136"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz198","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz198","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7963082","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076478944","display_name":"Dennis Wylie","orcid":"https://orcid.org/0000-0003-0380-3549"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dennis C Wylie","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, University of Texas at Austin , Austin, TX, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056486525","display_name":"Hans A. Hofmann","orcid":"https://orcid.org/0000-0002-3335-330X"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hans A Hofmann","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, University of Texas at Austin , Austin, TX, USA","Department of Integrative Biology, University of Texas at Austin , Austin, TX, USA","Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin, TX, USA","Institute for Neuroscience, University of Texas at Austin , Austin, TX, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Department of Integrative Biology, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Institute for Neuroscience, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056678313","display_name":"Boris V. Zemelman","orcid":"https://orcid.org/0000-0003-2463-4887"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Boris V Zemelman","raw_affiliation_strings":["Center for Learning and Memory, University of Texas at Austin , Austin, TX, USA","Department of Neuroscience, University of Texas at Austin , Austin, TX, USA","Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin, TX, USA","Institute for Neuroscience, University of Texas at Austin , Austin, TX, USA"],"affiliations":[{"raw_affiliation_string":"Center for Learning and Memory, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Department of Neuroscience, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Institute for Neuroscience, University of Texas at Austin , Austin, TX, USA","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5056678313","https://openalex.org/A5076478944"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1705,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.50955939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"35","issue":"20","first_page":"3944","last_page":"3952"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10604","display_name":"RNA Research and Splicing","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/computational-biology","display_name":"Computational biology","score":0.5852155089378357},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.5554698705673218},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48597702383995056},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.4539508521556854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42484933137893677},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.41716691851615906},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3846703767776489},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3719440698623657}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5852155089378357},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.5554698705673218},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48597702383995056},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.4539508521556854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42484933137893677},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.41716691851615906},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3846703767776489},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3719440698623657},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz198","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz198","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"},{"id":"pmid:30903136","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30903136","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:pubmedcentral.nih.gov:7963082","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7963082","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7963082","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7963082","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1486659038","https://openalex.org/W1900337607","https://openalex.org/W1935339094","https://openalex.org/W1966354073","https://openalex.org/W1981140084","https://openalex.org/W1987079970","https://openalex.org/W1987122345","https://openalex.org/W1988599715","https://openalex.org/W1990381576","https://openalex.org/W2008027377","https://openalex.org/W2012597404","https://openalex.org/W2014677321","https://openalex.org/W2026593185","https://openalex.org/W2042392223","https://openalex.org/W2054984882","https://openalex.org/W2056002855","https://openalex.org/W2067899297","https://openalex.org/W2075996757","https://openalex.org/W2081146141","https://openalex.org/W2089912569","https://openalex.org/W2096139934","https://openalex.org/W2097175728","https://openalex.org/W2103777723","https://openalex.org/W2115761267","https://openalex.org/W2118393799","https://openalex.org/W2121307568","https://openalex.org/W2121356022","https://openalex.org/W2124793944","https://openalex.org/W2125598804","https://openalex.org/W2130564474","https://openalex.org/W2131263703","https://openalex.org/W2133446381","https://openalex.org/W2139425275","https://openalex.org/W2140952049","https://openalex.org/W2145091349","https://openalex.org/W2147794131","https://openalex.org/W2148014281","https://openalex.org/W2153561273","https://openalex.org/W2156733952","https://openalex.org/W2157009395","https://openalex.org/W2159164310","https://openalex.org/W2171787842","https://openalex.org/W2275033707","https://openalex.org/W2293652778","https://openalex.org/W2593848117","https://openalex.org/W4240157490"],"related_works":["https://openalex.org/W2073661767","https://openalex.org/W2143211236","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2103777723","https://openalex.org/W2159636084","https://openalex.org/W2610941444","https://openalex.org/W2117168988","https://openalex.org/W2154430121","https://openalex.org/W2605190264"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2019-04-25T00:00:00"}
