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Differentially mutated subnetworks discovery.
Hajkarim MC, Upfal E, Vandin F. Hajkarim MC, et al. Among authors: upfal e. Algorithms Mol Biol. 2019 Mar 30;14:10. doi: 10.1186/s13015-019-0146-7. eCollection 2019. Algorithms Mol Biol. 2019. PMID: 30976291 Free PMC article.
On the Sample Complexity of Cancer Pathways Identification.
Vandin F, Raphael BJ, Upfal E. Vandin F, et al. Among authors: upfal e. J Comput Biol. 2016 Jan;23(1):30-41. doi: 10.1089/cmb.2015.0100. Epub 2015 Dec 8. J Comput Biol. 2016. PMID: 26645471 Free PMC article.
De novo discovery of mutated driver pathways in cancer.
Vandin F, Upfal E, Raphael BJ. Vandin F, et al. Among authors: upfal e. Genome Res. 2012 Feb;22(2):375-85. doi: 10.1101/gr.120477.111. Epub 2011 Jun 7. Genome Res. 2012. PMID: 21653252 Free PMC article.
Accurate computation of survival statistics in genome-wide studies.
Vandin F, Papoutsaki A, Raphael BJ, Upfal E. Vandin F, et al. Among authors: upfal e. PLoS Comput Biol. 2015 May 7;11(5):e1004071. doi: 10.1371/journal.pcbi.1004071. eCollection 2015 May. PLoS Comput Biol. 2015. PMID: 25950620 Free PMC article.
MADMX: a strategy for maximal dense motif extraction.
Grossi R, Pietracaprina A, Pisanti N, Pucci G, Upfal E, Vandin F. Grossi R, et al. Among authors: upfal e. J Comput Biol. 2011 Apr;18(4):535-45. doi: 10.1089/cmb.2010.0177. Epub 2011 Mar 21. J Comput Biol. 2011. PMID: 21417937
Finding driver pathways in cancer: models and algorithms.
Vandin F, Upfal E, Raphael BJ. Vandin F, et al. Among authors: upfal e. Algorithms Mol Biol. 2012 Sep 6;7(1):23. doi: 10.1186/1748-7188-7-23. Algorithms Mol Biol. 2012. PMID: 22954134 Free PMC article.