{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T03:21:27Z","timestamp":1787714487439,"version":"build-2784847793"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,8,19]],"date-time":"2014-08-19T00:00:00Z","timestamp":1408406400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12918-014-0099-x","type":"journal-article","created":{"date-parts":[[2014,8,18]],"date-time":"2014-08-18T05:38:41Z","timestamp":1408340321000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":59,"title":["KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape"],"prefix":"10.1186","volume":"8","author":[{"given":"Nicolas","family":"Alcaraz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josch","family":"Pauling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richa","family":"Batra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eudes","family":"Barbosa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Junge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne GL","family":"Christensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasco","family":"Azevedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henrik J","family":"Ditzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Baumbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,8,19]]},"reference":[{"key":"99_CR1","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1752-0509-1-8","volume":"1","author":"I Ulitsky","year":"2007","unstructured":"Ulitsky I, Shamir R: Identification of functional modules using network topology and high-throughput data. BMC Syst Biol. 2007, 1: 8-10.1186\/1752-0509-1-8.","journal-title":"BMC Syst Biol"},{"issue":"Suppl 1","key":"99_CR2","doi-asserted-by":"crossref","first-page":"S233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","volume":"18","author":"T Ideker","year":"2002","unstructured":"Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002, 18 (Suppl 1): S233-S240. 10.1093\/bioinformatics\/18.suppl_1.S233.","journal-title":"Bioinformatics"},{"key":"99_CR3","doi-asserted-by":"crossref","first-page":"e13367","DOI":"10.1371\/journal.pone.0013367","volume":"5","author":"I Ulitsky","year":"2010","unstructured":"Ulitsky I, Krishnamurthy A, Karp RM, Shamir R: DEGAS: de novo discovery of dysregulated pathways in human diseases. PLoS One. 2010, 5: e13367-10.1371\/journal.pone.0013367.","journal-title":"PLoS One"},{"key":"99_CR4","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1145\/2330163.2330188","volume-title":"GECCO","author":"J Baumbach","year":"2012","unstructured":"Baumbach J, Friedrich T, Kotzing T, Krohmer A, M\u00fcller J, Pauling J: Efficient Algorithms for Extracting Biological key Pathways With Global Constraints Categories and Subject Descriptors. GECCO. 2012, ACM, Philadelphia, Pennsylvania, USA, 169-176."},{"key":"99_CR5","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1093\/bioinformatics\/btt576","volume":"30","author":"H Sun","year":"2014","unstructured":"Sun H, Wang H, Zhu R, Tang K, Gong Q, Cui J, Cao Z, Liu Q: iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. Bioinformatics. 2014, 30: 737-739. 10.1093\/bioinformatics\/btt576.","journal-title":"Bioinformatics"},{"key":"99_CR6","doi-asserted-by":"crossref","first-page":"9622","DOI":"10.1093\/nar\/gkt752","volume":"41","author":"S Sass","year":"2013","unstructured":"Sass S, Buettner F, Mueller NS, Theis FJ: A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res. 2013, 41: 9622-9633. 10.1093\/nar\/gkt752.","journal-title":"Nucleic Acids Res"},{"key":"99_CR7","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13: 2498-2504. 10.1101\/gr.1239303.","journal-title":"Genome Res"},{"key":"99_CR8","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1080\/15427951.2011.604548","volume":"7","author":"N Alcaraz","year":"2011","unstructured":"Alcaraz N, K\u00fcc\u00fck H, Weile J, Wipat A, Baumbach J: KeyPathwayMiner: detecting case-specific biological pathways using expression data. Internet Math. 2011, 7: 299-313. 10.1080\/15427951.2011.604548.","journal-title":"Internet Math"},{"key":"99_CR9","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1039\/c2ib00133k","volume":"4","author":"N Alcaraz","year":"2012","unstructured":"Alcaraz N, Friedrich T, Kotzing T, Krohmer A, Muller J, Pauling J, Baumbach J: Efficient key pathway mining: combining networks and OMICS data. Integr Biol (Camb). 2012, 4: 756-764. 10.1039\/c2ib00133k.","journal-title":"Integr Biol (Camb)"},{"key":"99_CR10","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1093\/bioinformatics\/btt138","volume":"29","author":"S Lotia","year":"2013","unstructured":"Lotia S, Montojo J, Dong Y, Bader GD, Pico AR: Cytoscape app store. Bioinformatics. 2013, 29: 1350-1351. 10.1093\/bioinformatics\/btt138.","journal-title":"Bioinformatics"},{"key":"99_CR11","doi-asserted-by":"crossref","unstructured":"Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012, 487: 330-337. 10.1038\/nature11252.","DOI":"10.1038\/nature11252"},{"key":"99_CR12","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/nrgastro.2011.173","volume":"8","author":"VV Lao","year":"2011","unstructured":"Lao VV, Grady WM: Epigenetics and colorectal cancer. Nat Rev Gastroenterol Hepatol. 2011, 8: 686-700. 10.1038\/nrgastro.2011.173.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"99_CR13","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","volume":"37","author":"TS Keshava Prasad","year":"2009","unstructured":"Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A: Human protein reference database\u20132009 update. Nucleic Acids Res. 2009, 37: D767-D772. 10.1093\/nar\/gkn892.","journal-title":"Nucleic Acids Res"},{"key":"99_CR14","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1053\/j.gastro.2011.05.010","volume":"141","author":"J Zhang","year":"2011","unstructured":"Zhang J, Roberts TM, Shivdasani RA: Targeting PI3K signaling as a therapeutic approach for colorectal cancer. Gastroenterology. 2011, 141: 50-61. 10.1053\/j.gastro.2011.05.010.","journal-title":"Gastroenterology"},{"key":"99_CR15","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1200\/JCO.2009.25.3641","volume":"28","author":"KD Courtney","year":"2010","unstructured":"Courtney KD, Corcoran RB, Engelman JA: The PI3K pathway as drug target in human cancer. J Clin Oncol. 2010, 28: 1075-1083. 10.1200\/JCO.2009.25.3641.","journal-title":"J Clin Oncol"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-014-0099-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-014-0099-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-014-0099-x","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,13]],"date-time":"2019-08-13T22:51:43Z","timestamp":1565736703000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-014-0099-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,8,19]]},"references-count":15,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["99"],"URL":"https:\/\/doi.org\/10.1186\/s12918-014-0099-x","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,8,19]]},"article-number":"99"}}