{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:44Z","timestamp":1787008484072,"version":"build-2736575974"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,9]],"date-time":"2018-08-09T00:00:00Z","timestamp":1533772800000},"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":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>isiKnock is a new software that automatically conducts in silico knockouts for mathematical models of signaling pathways. The software allows for the prediction of the behavior of biological systems after single or multiple knockout. The implemented algorithm applies transition invariants and the novel concept of Manatee invariants. A knockout matrix visualizes the results. The tool enables the analysis of dependencies, for example, in signal flows from the receptor activation to the cell response at steady state.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>isiKnock is an open-source tool, freely available at http:\/\/www.bioinformatik.uni-frankfurt.de\/tools\/isiKnock\/. It requires at least Java 8 and runs under Microsoft Windows, Linux, and Mac OS.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty700","type":"journal-article","created":{"date-parts":[[2018,8,8]],"date-time":"2018-08-08T07:09:52Z","timestamp":1533712192000},"page":"892-894","source":"Crossref","is-referenced-by-count":9,"title":["isiKnock:\n                    <i>in silico<\/i>\n                    knockouts in signaling pathways"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2789-5540","authenticated-orcid":false,"given":"Jennifer","family":"Hannig","sequence":"first","affiliation":[{"name":"Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany"},{"name":"Department of KITE - Kompetenzzentrum f\u00fcr Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5786-901X","authenticated-orcid":false,"given":"Heiko","family":"Giese","sequence":"additional","affiliation":[{"name":"Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00f6rje","family":"Schweizer","sequence":"additional","affiliation":[{"name":"Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonie","family":"Amstein","sequence":"additional","affiliation":[{"name":"Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f6rg","family":"Ackermann","sequence":"additional","affiliation":[{"name":"Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ina","family":"Koch","sequence":"additional","affiliation":[{"name":"Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,8,9]]},"reference":[{"key":"2023013107250534300_bty700-B1","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s12918-017-0448-7","article-title":"Manatees invariants reveal functional pathways in signaling networks","volume":"11","author":"Amstein","year":"2017","journal-title":"BMC Syst. Biol"},{"key":"2023013107250534300_bty700-B2","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1089\/cmb.2008.0177","article-title":"Modeling signal transduction in enzyme cascades with the concept of elementary flux modes","volume":"16","author":"Behre","year":"2009","journal-title":"J. Comput. Biol"},{"key":"2023013107250534300_bty700-B3","doi-asserted-by":"crossref","first-page":"341","DOI":"10.4161\/auto.7.3.14046","article-title":"The ubiquitin-binding adaptor proteins p62\/SQSTM1 and NDP52 are recruited independently to bacteria-associated microdomains to target Salmonella to the autophagy pathway","volume":"7","author":"Cemma","year":"2011","journal-title":"Autophagy"},{"key":"2023013107250534300_bty700-B4","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/bioinformatics\/btt165","article-title":"MonaLisa\u2014visualization and analysis of functional modules in biochemical networks","volume":"29","author":"Einloft","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013107250534300_bty700-B5","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1093\/bioinformatics\/btm560","article-title":"Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways","volume":"24","author":"Hardy","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013107250534300_bty700-B6","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013107250534300_bty700-B7","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1752-0509-1-2","article-title":"Structural and functional analysis of cellular networks with CellNetAnalyzer","volume":"1","author":"Klamt","year":"2007","journal-title":"BMC Syst. Biol"},{"key":"2023013107250534300_bty700-B8","volume-title":"Computational Biology","author":"Koch","year":"2011"},{"key":"2023013107250534300_bty700-B9","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"BoolNet\u2013an R package for generation, reconstruction and analysis of Boolean networks","volume":"26","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"key":"2023013107250534300_bty700-B10","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.biosystems.2009.04.008","article-title":"Logical modelling of regulatory networks with GINsim 2.3","volume":"97","author":"Naldi","year":"2009","journal-title":"Biosystems"},{"key":"2023013107250534300_bty700-B11","doi-asserted-by":"crossref","first-page":"e92481","DOI":"10.1371\/journal.pone.0092481","article-title":"Comprehensive logic based analyses of Toll-like receptor 4 signal transduction pathway","volume":"9","author":"Padwal","year":"2014","journal-title":"PLoS One"},{"key":"2023013107250534300_bty700-B12","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-7-482","article-title":"Application of Petri net based analysis techniques to signal transduction pathways","volume":"7","author":"Sackmann","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013107250534300_bty700-B13","doi-asserted-by":"crossref","first-page":"e1005200","DOI":"10.1371\/journal.pcbi.1005200","article-title":"In silico knockout studies of xenophagic capturing of Salmonella","volume":"12","author":"Scheidel","year":"2016","journal-title":"PLoS Comput. Biol"},{"key":"2023013107250534300_bty700-B14","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/73786","article-title":"A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks","volume":"18","author":"Schuster","year":"2000","journal-title":"Nat. Biotechnol"},{"key":"2023013107250534300_bty700-B15","volume-title":"INA\u2014Integrated Net Analyzer\u2014Version 2.2","author":"Starke","year":"1999"},{"key":"2023013107250534300_bty700-B16","doi-asserted-by":"crossref","first-page":"e1004338","DOI":"10.1371\/journal.pcbi.1004338","article-title":"Inference of network dynamics and metabolic interactions in the gut microbiome","volume":"11","author":"Steinway","year":"2015","journal-title":"PLoS Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/5\/892\/48965875\/bioinformatics_35_5_892.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/5\/892\/48965875\/bioinformatics_35_5_892.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T05:19:41Z","timestamp":1675142381000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/5\/892\/5068592"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,9]]},"references-count":16,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty700","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/313858","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3,1]]},"published":{"date-parts":[[2018,8,9]]}}}