{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:20Z","timestamp":1740185120487,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,1,8]],"date-time":"2021-01-08T00:00:00Z","timestamp":1610064000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>KNIT is a web application that provides a hierarchical, directed graph on how a set of genes is connected to a particular gene of interest. Its primary aim is to aid researchers in discerning direct from indirect effects that a gene might have on the expression of other genes and molecular pathways, a very common problem in omics analysis. As such, KNIT provides deep contextual information for experiments where gene or protein expression might be changed, such as gene knock-out and overexpression experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>KNIT is publicly available at http:\/\/knit.ims.bio. It is implemented with Django and Nuxtjs, with all major browsers supported.<\/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\/btaa1107","type":"journal-article","created":{"date-parts":[[2021,1,3]],"date-time":"2021-01-03T20:06:52Z","timestamp":1609704412000},"page":"276-278","source":"Crossref","is-referenced-by-count":1,"title":["Interactive gene networks with KNIT"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5708-8400","authenticated-orcid":false,"given":"D S","family":"Magruder","sequence":"first","affiliation":[{"name":"Institute for Medical Systems Biology, bAIome \u2013 Center for Biomedical AI, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf , 20246 Hamburg, Germany"},{"name":"Genevention GmbH , 37079 Goettingen, Germany"}]},{"given":"A M","family":"Liebhoff","sequence":"additional","affiliation":[{"name":"Institute for Medical Systems Biology, bAIome \u2013 Center for Biomedical AI, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf , 20246 Hamburg, Germany"}]},{"given":"J","family":"Bethune","sequence":"additional","affiliation":[{"name":"Institute for Medical Systems Biology, bAIome \u2013 Center for Biomedical AI, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf , 20246 Hamburg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4366-5662","authenticated-orcid":false,"given":"S","family":"Bonn","sequence":"additional","affiliation":[{"name":"Institute for Medical Systems Biology, bAIome \u2013 Center for Biomedical AI, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf , 20246 Hamburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,1,8]]},"reference":[{"key":"2023051510593324800_btaa1107-B1","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1186\/1471-2105-7-497","article-title":"cPath: open source software for collecting, storing, and querying biological pathways","volume":"7","author":"Cerami","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023051510593324800_btaa1107-B2","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway Commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023051510593324800_btaa1107-B3","doi-asserted-by":"crossref","first-page":"D684","DOI":"10.1093\/nar\/gkm795","article-title":"STITCH: interaction networks of chemicals and proteins","volume":"36","author":"Kuhn","year":"2008","journal-title":"Nucleic Acids Res"},{"year":"2017","author":"Madkour","key":"2023051510593324800_btaa1107-B4"},{"key":"2023051510593324800_btaa1107-B5","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s1-s4","article-title":"GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function","volume":"9","author":"Mostafavi","year":"2008","journal-title":"Genome Biol"},{"key":"2023051510593324800_btaa1107-B6","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1016\/j.bbadis.2019.04.010","article-title":"Cardiac myocyte KLF5 regulates body weight via alteration of cardiac FGF21","volume":"1865","author":"Pol","year":"2019","journal-title":"Biochim. 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