{"id":"https://openalex.org/W2131263703","doi":"https://doi.org/10.1093/bioinformatics/btt615","title":"Discriminative motif analysis of high-throughput dataset","display_name":"Discriminative motif analysis of high-throughput dataset","publication_year":2013,"publication_date":"2013-10-25","ids":{"openalex":"https://openalex.org/W2131263703","doi":"https://doi.org/10.1093/bioinformatics/btt615","mag":"2131263703","pmid":"https://pubmed.ncbi.nlm.nih.gov/24162561"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt615","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt615","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/6/775/48921639/bioinformatics_30_6_775.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/30/6/775/48921639/bioinformatics_30_6_775.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045133318","display_name":"Zizhen Yao","orcid":"https://orcid.org/0000-0002-9361-5607"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zizhen Yao","raw_affiliation_strings":["1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025688734","display_name":"Kyle L. MacQuarrie","orcid":"https://orcid.org/0000-0001-9624-7507"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyle L. MacQuarrie","raw_affiliation_strings":["1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113914122","display_name":"Abraham Fong","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abraham P. Fong","raw_affiliation_strings":["1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005088414","display_name":"Stephen J. Tapscott","orcid":"https://orcid.org/0000-0002-0319-0968"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen J. Tapscott","raw_affiliation_strings":["1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086685720","display_name":"Walter L. Ruzzo","orcid":"https://orcid.org/0000-0002-6260-2926"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walter L. Ruzzo","raw_affiliation_strings":["1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039040940","display_name":"Robert Gentleman","orcid":"https://orcid.org/0000-0003-4505-9893"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert C. Gentleman","raw_affiliation_strings":["1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 2Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, 3Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 4Department of Pediatrics, School of Medicine, 5Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, 6Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 7Department of Computer Science and Engineering, 8Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and 9Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045133318"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.5118,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.82357943,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"6","first_page":"775","last_page":"783"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8963000178337097,"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":0.8963000178337097,"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/T10885","display_name":"Gene expression and cancer classification","score":0.04149999842047691,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.02329999953508377,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/bioconductor","display_name":"Bioconductor","score":0.8033140897750854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7183595895767212},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.6825084090232849},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.6182417273521423},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5831602215766907},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5177554488182068},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5070207118988037},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.48539766669273376},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4641002416610718},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3478042483329773},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21133112907409668},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.13489940762519836},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1292436122894287},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10696029663085938},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07396253943443298}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8033140897750854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7183595895767212},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6825084090232849},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.6182417273521423},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5831602215766907},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5177554488182068},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5070207118988037},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.48539766669273376},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4641002416610718},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3478042483329773},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21133112907409668},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.13489940762519836},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1292436122894287},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10696029663085938},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07396253943443298},{"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt615","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt615","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/6/775/48921639/bioinformatics_30_6_775.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:24162561","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24162561","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:3323455","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3957073","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/btt615","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt615","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/6/775/48921639/bioinformatics_30_6_775.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":[{"display_name":"Reduced inequalities","score":0.7099999785423279,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G1705396944","display_name":null,"funder_award_id":"T32-CA-080416","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G616001722","display_name":null,"funder_award_id":"T32HD007183","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"},{"id":"https://openalex.org/G757553299","display_name":null,"funder_award_id":"R01AR 045113","funder_id":"https://openalex.org/F4320337362","funder_display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases"},{"id":"https://openalex.org/G863835797","display_name":null,"funder_award_id":"T32 GM 007266","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337362","display_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","ror":"https://ror.org/006zn3t30"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2131263703.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1214546200","https://openalex.org/W1499523727","https://openalex.org/W1966354073","https://openalex.org/W1972822540","https://openalex.org/W1998000745","https://openalex.org/W2003967338","https://openalex.org/W2008051478","https://openalex.org/W2028022357","https://openalex.org/W2032548898","https://openalex.org/W2061834804","https://openalex.org/W2062930223","https://openalex.org/W2068135787","https://openalex.org/W2072103265","https://openalex.org/W2072182762","https://openalex.org/W2095718954","https://openalex.org/W2097175728","https://openalex.org/W2097598963","https://openalex.org/W2098729669","https://openalex.org/W2115577355","https://openalex.org/W2124080033","https://openalex.org/W2125810118","https://openalex.org/W2139617657","https://openalex.org/W2141408320","https://openalex.org/W2144710927","https://openalex.org/W2148032724","https://openalex.org/W2160697532","https://openalex.org/W2161849959","https://openalex.org/W2582743722","https://openalex.org/W4299689471","https://openalex.org/W6628147189"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2952115151","https://openalex.org/W2073661767","https://openalex.org/W2380185347","https://openalex.org/W2370034659","https://openalex.org/W2159636084","https://openalex.org/W2117168988","https://openalex.org/W2103777723","https://openalex.org/W2748123750","https://openalex.org/W2610941444"],"abstract_inverted_index":{"MOTIVATION:":[0],"High-throughput":[1],"ChIP-seq":[2,73],"studies":[3,141],"typically":[4],"identify":[5,113],"thousands":[6],"of":[7,37,82,129,145,157,165,175],"peaks":[8],"for":[9,18,49,134],"a":[10,31,44],"single":[11,150],"transcription":[12],"factor":[13],"(TF).":[14],"It":[15],"is":[16,58,184],"common":[17,114],"traditional":[19],"motif":[20,101,122],"discovery":[21,102,164],"tools":[22],"to":[23,66,132,148],"predict":[24],"motifs":[25,52,79,168],"that":[26,57,119],"are":[27,36,197],"statistically":[28],"significant":[29],"against":[30],"na\u00efve":[32],"background":[33],"distribution":[34],"but":[35],"questionable":[38],"biological":[39,117],"relevance.":[40],"RESULTS:":[41],"We":[42,137],"describe":[43],"simple":[45],"yet":[46],"effective":[47,59],"algorithm":[48],"discovering":[50],"differential":[51],"between":[53],"two":[54,158],"sequence":[55],"datasets":[56,84],"in":[60,80,90,154,170],"eliminating":[61],"systematic":[62],"biases":[63],"and":[64,93,125],"scalable":[65],"large":[67],"datasets.":[68],"Tested":[69],"on":[70,106],"207":[71],"ENCODE":[72],"datasets,":[74,111],"our":[75,130,146],"method":[76,147],"identifies":[77],"correct":[78],"78%":[81],"the":[83,107,121,143,188],"with":[85,96],"known":[86],"motifs,":[87],"demonstrating":[88,142],"improvement":[89],"both":[91],"accuracy":[92],"efficiency":[94],"compared":[95],"DREME,":[97],"another":[98],"state-of-art":[99],"discriminative":[100],"tool.":[103],"More":[104],"interestingly,":[105],"remaining":[108],"more":[109],"challenging":[110],"we":[112,162],"technical":[115],"or":[116],"factors":[118],"compromise":[120],"search":[123],"results":[124],"use":[126],"advanced":[127],"features":[128],"tool":[131],"control":[133],"these":[135],"factors.":[136],"also":[138],"present":[139],"case":[140],"ability":[144],"detect":[149],"base":[151],"pair":[152],"differences":[153],"DNA":[155],"specificity":[156],"similar":[159],"TFs.":[160],"Lastly,":[161],"demonstrate":[163],"key":[166],"TF":[167],"involved":[169],"tissue":[171],"specification":[172],"by":[173],"examination":[174],"high-throughput":[176],"DNase":[177],"accessibility":[178],"data.":[179],"AVAILABILITY:":[180],"The":[181],"motifRG":[182],"package":[183],"publically":[185],"available":[186,198],"via":[187],"bioconductor":[189],"repository.":[190],"CONTACT:":[191],"yzizhen@fhcrc.org":[192],"SUPPLEMENTARY":[193],"INFORMATION:":[194],"Supplementary":[195],"data":[196],"at":[199],"Bioinformatics":[200],"online.":[201]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}