{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:44Z","timestamp":1772138084917,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2017,5,24]],"date-time":"2017-05-24T00:00:00Z","timestamp":1495584000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01-GM120033"],"award-info":[{"award-number":["R01-GM120033"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention Research Institute of Texas","doi-asserted-by":"publisher","award":["RP170387"],"award-info":[{"award-number":["RP170387"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001174","name":"Houston Endowment","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001174","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, CRISPRcloud, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, CRISPRcloud serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. Taken together, the framework described in this study is expected to accelerate development of web-based bioinformatics tool for handling all studies which include next generation sequencing data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>http:\/\/crispr.nrihub.org<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx335","type":"journal-article","created":{"date-parts":[[2017,5,23]],"date-time":"2017-05-23T07:09:33Z","timestamp":1495523373000},"page":"2963-2965","source":"Crossref","is-referenced-by-count":24,"title":["CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution"],"prefix":"10.1093","volume":"33","author":[{"given":"Hyun-Hwan","family":"Jeong","sequence":"first","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA"},{"name":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, TX, USA"}]},{"given":"Seon Young","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA"},{"name":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, TX, USA"}]},{"given":"Maxime W C","family":"Rousseaux","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA"},{"name":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, TX, USA"}]},{"given":"Huda Y","family":"Zoghbi","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA"},{"name":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, TX, USA"},{"name":"Department of Pediatrics, Howard Hughes Medical Institute, Houston, TX, USA"},{"name":"Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX, USA"}]},{"given":"Zhandong","family":"Liu","sequence":"additional","affiliation":[{"name":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, TX, USA"},{"name":"Department of Pediatrics, Howard Hughes Medical Institute, Houston, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,5,24]]},"reference":[{"key":"2023020206430618600_btx335-B1","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1016\/j.cell.2014.09.029","article-title":"Genome-scale CRISPR-mediated control of gene repression and activation","volume":"159","author":"Gilbert","year":"2014","journal-title":"Cell"},{"key":"2023020206430618600_btx335-B2","doi-asserted-by":"crossref","first-page":"e19760","DOI":"10.7554\/eLife.19760","article-title":"Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation","volume":"5","author":"Horlbeck","year":"2016","journal-title":"eLife"},{"key":"2023020206430618600_btx335-B3","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nature14136","article-title":"Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex","volume":"517","author":"Konermann","year":"2015","journal-title":"Nature"},{"key":"2023020206430618600_btx335-B4","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1186\/s13059-015-0843-6","article-title":"Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR","volume":"16","author":"Li","year":"2015","journal-title":"Genome Biol"},{"key":"2023020206430618600_btx335-B5","doi-asserted-by":"crossref","first-page":"550.","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023020206430618600_btx335-B6","doi-asserted-by":"crossref","first-page":"20380","DOI":"10.1073\/pnas.0810485105","article-title":"Highly parallel identification of essential genes in cancer cells","volume":"105","author":"Luo","year":"2008","journal-title":"Proc. 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