{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T05:54:35Z","timestamp":1776232475111,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T00:00:00Z","timestamp":1479254400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000009","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R00GM95713"],"award-info":[{"award-number":["R00GM95713"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000009","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01NS89676"],"award-info":[{"award-number":["R01NS89676"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["307711"],"award-info":[{"award-number":["307711"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>UV cross-linking and immunoprecipitation (CLIP), followed by high-throughput sequencing, is a powerful biochemical assay that maps in vivo protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The software is implemented in Perl. The source code and detailed documentation are available at http:\/\/zhanglab.c2b2.columbia.edu\/index.php\/CTK.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw653","type":"journal-article","created":{"date-parts":[[2016,10,11]],"date-time":"2016-10-11T15:05:32Z","timestamp":1476198332000},"page":"566-567","source":"Crossref","is-referenced-by-count":186,"title":["CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data"],"prefix":"10.1093","volume":"33","author":[{"given":"Ankeeta","family":"Shah","sequence":"first","affiliation":[{"name":"Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA"}]},{"given":"Yingzhi","family":"Qian","sequence":"additional","affiliation":[{"name":"Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA"}]},{"given":"Sebastien M","family":"Weyn-Vanhentenryck","sequence":"additional","affiliation":[{"name":"Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA"}]},{"given":"Chaolin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,11,16]]},"reference":[{"key":"2023020204421109800_btw653-B1","doi-asserted-by":"crossref","first-page":"R18","DOI":"10.1186\/gb-2014-15-1-r18","article-title":"PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis","volume":"15","author":"Chen","year":"2014","journal-title":"Genome Biol"},{"key":"2023020204421109800_btw653-B2","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1002\/wrna.31","article-title":"HITS-CLIP: panoramic views of protein\u2013RNA regulation in living cells","volume":"1","author":"Darnell","year":"2010","journal-title":"Wiley Interdiscip. 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