{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T03:20:49Z","timestamp":1778642449282,"version":"3.51.4"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation.<\/jats:p>\n               <jats:p>Availability: The BINOCh open source Python package is freely available at http:\/\/liulab.dfci.harvard.edu\/BINOCh under the FreeBSD license.<\/jats:p>\n               <jats:p>Contact: \u00a0cliff@jimmy.harvard.edu; xsliu@jimmy.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr279","type":"journal-article","created":{"date-parts":[[2011,5,7]],"date-time":"2011-05-07T00:34:56Z","timestamp":1304728496000},"page":"1867-1868","source":"Crossref","is-referenced-by-count":25,"title":["BINOCh: binding inference from nucleosome occupancy changes"],"prefix":"10.1093","volume":"27","author":[{"given":"Clifford A.","family":"Meyer","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health and 2Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Housheng H.","family":"He","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health and 2Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA"},{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health and 2Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Myles","family":"Brown","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health and 2Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"X. Shirley","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health and 2Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,5,5]]},"reference":[{"key":"2023012512014600200_B1","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nprot.2008.195","article-title":"Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors","volume":"4","author":"Berger","year":"2009","journal-title":"Nat. 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