C
Chris Sander
Researcher at Harvard University
Publications - 730
Citations - 273726
Chris Sander is an academic researcher from Harvard University. The author has contributed to research in topics: Large Hadron Collider & Protein structure. The author has an hindex of 178, co-authored 713 publications receiving 233287 citations. Previous affiliations of Chris Sander include Purdue University & University of Leeds.
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Journal ArticleDOI
CAST: an iterative algorithm for the complexity analysis of sequence tracts
Vasilis J. Promponas,Anton J. Enright,Sophia Tsoka,David P. Kreil,Christophe Leroy,Stavros J. Hamodrakas,Chris Sander,Christos A. Ouzounis +7 more
TL;DR: A novel algorithm for low-complexity region detection and selective masking based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties that is sufficient for masking database query sequences without generating false positives.
Journal ArticleDOI
Computational approaches to identify functional genetic variants in cancer genomes.
Abel Gonzalez-Perez,Ville Mustonen,Boris Reva,Graham R. S. Ritchie,Pau Creixell,Rachel Karchin,Miguel Vazquez,J. Lynn Fink,Karin S. Kassahn,John V. Pearson,Gary D. Bader,Paul C. Boutros,Lakshmi Muthuswamy,B. F. Francis Ouellette,Jüri Reimand,Rune Linding,Tatsuhiro Shibata,Alfonso Valencia,Adam Butler,Serge Dronov,Paul Flicek,Nick B. Shannon,Hannah Carter,Li Ding,Chris Sander,Josh M. Stuart,Lincoln Stein,Nuria Lopez-Bigas +27 more
TL;DR: The result of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy is presented, and computational techniques to annotate somatic variants and predict their impact on cancer phenotype are recommended.
Journal ArticleDOI
Functional Copy-Number Alterations in Cancer
Barry S. Taylor,Jordi Barretina,Jordi Barretina,Nicholas D. Socci,Penelope DeCarolis,Marc Ladanyi,Matthew Meyerson,Matthew Meyerson,Samuel Singer,Chris Sander +9 more
TL;DR: A comprehensive computational approach to robustly map chromosomal alterations in tumor samples and assess their functional importance in cancer is presented, applicable to high-resolution genomic data.
Correlated Mutations and Residue Contacts
TL;DR: A simple and general method to analyze correlations in mutational behavior between different positions in a multiple se- quence alignment and predict contact maps for each of 11 pro- tein families and compare the result with the contacts determined by crystallography.
Journal ArticleDOI
Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
Özgün Babur,Mithat Gönen,Bulent Arman Aksoy,Nikolaus Schultz,Giovanni Ciriello,Chris Sander,Emek Demir +6 more
TL;DR: A novel method is presented for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles, using a mutual exclusivity criterion that ensures that each gene in the group significantly contributes to the Mutual exclusivity pattern.