{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:39:59Z","timestamp":1767962399538,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary:CompleteMOTIFs (cMOTIFs) is an integrated web tool developed to facilitate systematic discovery of overrepresented transcription factor binding motifs from high-throughput chromatin immunoprecipitation experiments. Comprehensive annotations and Boolean logic operations on multiple peak locations enable users to focus on genomic regions of interest for de novo motif discovery using tools such as MEME, Weeder and ChIPMunk. The pipeline incorporates a scanning tool for known motifs from TRANSFAC and JASPAR databases, and performs an enrichment test using local or precalculated background models that significantly improve the motif scanning result. Furthermore, using the cMOTIFs pipeline, we demonstrated that multiple transcription factors could cooperatively bind to the upstream of important stem cell differentiation regulators.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/cmotifs.tchlab.org<\/jats:p>\n               <jats:p>Contact: \u00a0sekwon.kong@childrens.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq707","type":"journal-article","created":{"date-parts":[[2010,12,24]],"date-time":"2010-12-24T03:10:15Z","timestamp":1293160215000},"page":"715-717","source":"Crossref","is-referenced-by-count":43,"title":["CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments"],"prefix":"10.1093","volume":"27","author":[{"given":"Lakshmi","family":"Kuttippurathu","sequence":"first","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Hsing","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongchao","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas L.","family":"Maskell","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyungjoon","family":"Lee","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aibin","family":"He","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William T.","family":"Pu","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sek Won","family":"Kong","sequence":"additional","affiliation":[{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, 2Department of Cardiology, Children's Hospital Boston, Boston, MA 02115, USA, 3School of Computer Engineering, Nanyang Technological University, Singapore 639798 and 4Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,23]]},"reference":[{"key":"2023012511571430800_B1","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"2023012511571430800_B2","doi-asserted-by":"crossref","first-page":"D102","DOI":"10.1093\/nar\/gkm955","article-title":"JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update","volume":"36","author":"Bryne","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012511571430800_B3","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"2023012511571430800_B4","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/bioinformatics\/btl567","article-title":"Using GOstats to test gene lists for GO term association","volume":"23","author":"Falcon","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012511571430800_B5","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/nrg2636","article-title":"Insights from genomic profiling of transcription factors","volume":"10","author":"Farnham","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2023012511571430800_B6","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol."},{"key":"2023012511571430800_B7","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","article-title":"Identifying DNA and protein patterns with statistically significant alignments of multiple sequences","volume":"15","author":"Hertz","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012511571430800_B8","doi-asserted-by":"crossref","first-page":"2622","DOI":"10.1093\/bioinformatics\/btq488","article-title":"Deep and wide digging for binding motifs in ChIP-Seq data","volume":"26","author":"Kulakovskiy","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511571430800_B9","doi-asserted-by":"crossref","first-page":"2170","DOI":"10.1016\/j.patrec.2009.10.009","article-title":"CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units","volume":"31","author":"Liu","year":"2010","journal-title":"Pattern Recognit. Lett."},{"key":"2023012511571430800_B10","doi-asserted-by":"crossref","first-page":"W253","DOI":"10.1093\/nar\/gkm272","article-title":"STAMP: a web tool for exploring DNA-binding motif similarities","volume":"35","author":"Mahony","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012511571430800_B11","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012511571430800_B12","doi-asserted-by":"crossref","first-page":"W199","DOI":"10.1093\/nar\/gkh465","article-title":"Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes","volume":"32","author":"Pavesi","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012511571430800_B13","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genomewide studies","volume":"100","author":"Storey","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511571430800_B14","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1093\/bioinformatics\/btp681","article-title":"Tmod: toolbox of motif discovery","volume":"26","author":"Sun","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511571430800_B15","doi-asserted-by":"crossref","first-page":"W119","DOI":"10.1093\/nar\/gkn304","article-title":"RSAT: regulatory sequence analysis tools","volume":"36","author":"Thomas-Chollier","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012511571430800_B16","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/nbt1053","article-title":"Assessing computational tools for the discovery of transcription factor binding sites","volume":"23","author":"Tompa","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023012511571430800_B17","doi-asserted-by":"crossref","first-page":"e1000562","DOI":"10.1371\/journal.pcbi.1000562","article-title":"Discovery of regulatory elements is improved by a discriminatory approach","volume":"5","author":"Valen","year":"2009","journal-title":"PLoS. Comput. Biol."},{"key":"2023012511571430800_B18","article-title":"GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments","author":"van Heeringen","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511571430800_B19","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/nrg1315","article-title":"Applied bioinformatics for the identification of regulatory elements","volume":"5","author":"Wasserman","year":"2004","journal-title":"Nat. Rev. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/5\/715\/48866565\/bioinformatics_27_5_715.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/5\/715\/48866565\/bioinformatics_27_5_715.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:38:12Z","timestamp":1674650292000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/5\/715\/263043"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12,23]]},"references-count":19,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2011,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq707","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,3,1]]},"published":{"date-parts":[[2010,12,23]]}}}