{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T11:33:16Z","timestamp":1774265596113,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis and exploration platform. We present here new functionality and workflows that open the door to performing next-generation sequencing analysis using the KNIME framework.<\/jats:p>\n               <jats:p>Availability: All sources and compiled code are available via the KNIME update mechanism. Example workflows and descriptions are available through http:\/\/tech.knime.org\/community\/next-generation-sequencing.<\/jats:p>\n               <jats:p>Contact: \u00a0bernd.jagla@pasteur.fr<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr478","type":"journal-article","created":{"date-parts":[[2011,8,28]],"date-time":"2011-08-28T00:36:05Z","timestamp":1314491765000},"page":"2907-2909","source":"Crossref","is-referenced-by-count":33,"title":["Extending KNIME for next-generation sequencing data analysis"],"prefix":"10.1093","volume":"27","author":[{"given":"Bernd","family":"Jagla","sequence":"first","affiliation":[{"name":"1 Departement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, Plate-forme Transcriptome et Epig\u00e9nome, 25 Rue du Docteur Roux, F-75015 Paris, France and 2KNIME.com AG - Technoparkstr. 1 - 8005 Z\u00fcrich, Switzerland"}]},{"given":"Bernd","family":"Wiswedel","sequence":"additional","affiliation":[{"name":"1 Departement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, Plate-forme Transcriptome et Epig\u00e9nome, 25 Rue du Docteur Roux, F-75015 Paris, France and 2KNIME.com AG - Technoparkstr. 1 - 8005 Z\u00fcrich, Switzerland"}]},{"given":"Jean-Yves","family":"Copp\u00e9e","sequence":"additional","affiliation":[{"name":"1 Departement G\u00e9nomes et G\u00e9n\u00e9tique, Institut Pasteur, Plate-forme Transcriptome et Epig\u00e9nome, 25 Rue du Docteur Roux, F-75015 Paris, France and 2KNIME.com AG - Technoparkstr. 1 - 8005 Z\u00fcrich, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2011,8,27]]},"reference":[{"key":"2023012512014064000_B1","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1007\/978-3-540-78246-9_38","article-title":"KNIME: The Konstanz Information Miner","volume-title":"Data Analysis, Machine Learning and Applications: Studies in Classification, Data Analysis, and Knowledge Organization","author":"Berthold","year":"2008"},{"key":"2023012512014064000_B2","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1093\/bioinformatics\/btq282","article-title":"geWorkbench: an open source platform for integrative genomics","volume":"26","author":"Floratos","year":"2010","journal-title":"Bioinformatics"},{"issue":"Suppl. 2","key":"2023012512014064000_B3","doi-asserted-by":"crossref","first-page":"W677","DOI":"10.1093\/nar\/gkq429","article-title":"myExperiment: a repository and social network for the sharing of bioinformatics workflows","volume":"38","author":"Goble","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512014064000_B4","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":"2023012512014064000_B5","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1093\/nar\/gkl320","article-title":"Taverna: a tool for building and running workflows of services","volume":"24","author":"Hull","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512014064000_B6","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012512014064000_B7","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512014064000_B8","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/bioinformatics\/btr040","article-title":"Conveyor : a workflow engine for bioinformatic analyses","volume":"27","author":"Linke","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512014064000_B9","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1002\/cpe.994","article-title":"Scientific workflow management and the Kepler system. Grid systems","volume":"18","author":"Lud\u00e4scher","year":"2006","journal-title":"Concurr. Comput. Pract. Exp."},{"key":"2023012512014064000_B10","doi-asserted-by":"crossref","first-page":"3005","DOI":"10.1093\/bioinformatics\/btp493","article-title":"Mobyle: a new full web bioinformatics framework","volume":"25","author":"N\u00e9ron","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512014064000_B11","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512014064000_B12","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2907\/48874080\/bioinformatics_27_20_2907.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2907\/48874080\/bioinformatics_27_20_2907.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:12:33Z","timestamp":1674655953000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/20\/2907\/201998"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,8,27]]},"references-count":12,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2011,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr478","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,10,15]]},"published":{"date-parts":[[2011,8,27]]}}}