{"id":"https://openalex.org/W2101456936","doi":"https://doi.org/10.1093/bioinformatics/btn645","title":"Predicting the binding preference of transcription factors to individual DNA <i>k</i>-mers","display_name":"Predicting the binding preference of transcription factors to individual DNA <i>k</i>-mers","publication_year":2008,"publication_date":"2008-12-16","ids":{"openalex":"https://openalex.org/W2101456936","doi":"https://doi.org/10.1093/bioinformatics/btn645","mag":"2101456936","pmid":"https://pubmed.ncbi.nlm.nih.gov/19088121"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/8/1012/48989234/bioinformatics_25_8_1012.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/8/1012/48989234/bioinformatics_25_8_1012.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091052742","display_name":"Trevis M. Alleyne","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"Trevis M. Alleyne","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044078900","display_name":"Lourdes Pe\u00f1a\u2010Castillo","orcid":"https://orcid.org/0000-0002-0643-2547"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Lourdes Pe\u00f1a-Castillo","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027671746","display_name":"Gwena\u00ebl Badis","orcid":"https://orcid.org/0000-0003-2078-3076"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Gwenael Badis","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061751049","display_name":"Shaheynoor Talukder","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Shaheynoor Talukder","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104110846","display_name":"Michael F. Berger","orcid":"https://orcid.org/0000-0002-0760-7177"},"institutions":[{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Michael F. Berger","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023722989","display_name":"Andrew R. Gehrke","orcid":"https://orcid.org/0000-0002-6588-3890"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Andrew R. Gehrke","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008444707","display_name":"Anthony Philippakis","orcid":"https://orcid.org/0000-0001-6953-3794"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Anthony A. Philippakis","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064230419","display_name":"Martha L. Bulyk","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Martha L. Bulyk","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035010657","display_name":"Quaid Morris","orcid":"https://orcid.org/0000-0002-2760-6999"},"institutions":[{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Quaid D. Morris","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071531544","display_name":"Timothy R. Hughes","orcid":"https://orcid.org/0000-0002-8721-4719"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I4210092658","display_name":"Harvard\u2013MIT Division of Health Sciences and Technology","ror":"https://ror.org/00jjeh629","country_code":"US","type":"education","lineage":["https://openalex.org/I4210092658"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Timothy R. Hughes","raw_affiliation_strings":["1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, 2Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada, 3Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, 4Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, 5Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and 6Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I1283280774","https://openalex.org/I185261750","https://openalex.org/I4210092658"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5091052742"],"corresponding_institution_ids":["https://openalex.org/I1283280774","https://openalex.org/I136199984","https://openalex.org/I185261750","https://openalex.org/I4210092658"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6893,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.70174645,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"8","first_page":"1012","last_page":"1018"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9828000068664551,"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/T10604","display_name":"RNA Research and Splicing","score":0.9822999835014343,"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/inference","display_name":"Inference","score":0.7181448340415955},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6238283514976501},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6129542589187622},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5744800567626953},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5583321452140808},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5343897342681885},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5307707190513611},{"id":"https://openalex.org/keywords/preference","display_name":"Preference","score":0.48257675766944885},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.47840747237205505},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4536754786968231},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4140253961086273},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33017629384994507},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2777135968208313},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18748751282691956},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16661962866783142},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.11923813819885254}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7181448340415955},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6238283514976501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6129542589187622},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5744800567626953},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5583321452140808},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5343897342681885},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5307707190513611},{"id":"https://openalex.org/C2781249084","wikidata":"https://www.wikidata.org/wiki/Q908656","display_name":"Preference","level":2,"score":0.48257675766944885},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.47840747237205505},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4536754786968231},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4140253961086273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33017629384994507},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2777135968208313},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18748751282691956},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16661962866783142},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.11923813819885254},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btn645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/8/1012/48989234/bioinformatics_25_8_1012.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19088121","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19088121","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:dash.harvard.edu:1/10139267","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:10139267","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"},{"id":"pmh:oai:HAL:hal-03032780v1","is_oa":false,"landing_page_url":"https://hal.science/hal-03032780","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2009, 25 (8), pp.1012-1018. &#x27E8;10.1093/bioinformatics/btn645&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:dspace.mit.edu:1721.1/73182","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/73182","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Oxford","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:pubmedcentral.nih.gov:2666811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2666811","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":"doi:10.1093/bioinformatics/btn645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/8/1012/48989234/bioinformatics_25_8_1012.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2101456936.pdf","grobid_xml":"https://content.openalex.org/works/W2101456936.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W169392055","https://openalex.org/W1705407249","https://openalex.org/W1975036436","https://openalex.org/W1991105447","https://openalex.org/W1994122295","https://openalex.org/W1999755087","https://openalex.org/W2002285090","https://openalex.org/W2011039300","https://openalex.org/W2013382823","https://openalex.org/W2017071524","https://openalex.org/W2032975481","https://openalex.org/W2076849893","https://openalex.org/W2080152736","https://openalex.org/W2119743029","https://openalex.org/W2125810118","https://openalex.org/W2141885858","https://openalex.org/W2148711195","https://openalex.org/W2149006664","https://openalex.org/W2149769193","https://openalex.org/W2155181171","https://openalex.org/W2159412099","https://openalex.org/W2164599211","https://openalex.org/W2166277117","https://openalex.org/W2171153226","https://openalex.org/W2409636158","https://openalex.org/W2752128027","https://openalex.org/W2793129321","https://openalex.org/W2911964244","https://openalex.org/W4210400672","https://openalex.org/W6714462288"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W2090624569","https://openalex.org/W4321636575","https://openalex.org/W2357796999","https://openalex.org/W2045526782","https://openalex.org/W2379997263","https://openalex.org/W2367493320","https://openalex.org/W2131580913","https://openalex.org/W3083097828","https://openalex.org/W2125854412"],"abstract_inverted_index":{"We":[0,39],"employed":[1],"a":[2,41,79],"new":[3],"dataset":[4],"consisting":[5],"of":[6,10,30,43,52,74,85],"the":[7,27,53,65,72],"relative":[8],"preferences":[9],"mouse":[11],"homeodomains":[12,31],"for":[13,82],"all":[14],"eight-base":[15],"DNA":[16],"sequences":[17,36],"in":[18],"order":[19],"to":[20],"ask":[21],"how":[22],"well":[23,49],"we":[24],"can":[25],"predict":[26],"binding":[28],"profiles":[29],"when":[32],"only":[33],"their":[34],"protein":[35,54],"are":[37],"given.":[38],"evaluated":[40],"panel":[42],"standard":[44],"statistical":[45],"inference":[46],"techniques,":[47],"as":[48,50],"variations":[51],"features":[55],"considered.":[56],"Nearest":[57],"neighbour":[58],"among":[59,64],"functionally":[60],"important":[61],"residues":[62],"emerged":[63],"most":[66],"effective":[67],"methods.":[68],"Our":[69],"results":[70],"underscore":[71],"complexity":[73],"TF-DNA":[75],"recognition,":[76],"and":[77],"suggest":[78],"rational":[80],"approach":[81],"future":[83],"analyses":[84],"TF":[86],"families.":[87]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}
