Computational approaches for the identification of cancer genes and pathways

CM Dimitrakopoulos… - … Reviews: Systems Biology …, 2017 - Wiley Online Library
High‐throughput DNA sequencing techniques enable large‐scale measurement of somatic
mutations in tumors. Cancer genomics research aims at identifying all cancer‐related genes …

[HTML][HTML] Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

BJ Raphael, JR Dobson, L Oesper, F Vandin - Genome medicine, 2014 - Springer
High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the
measurement of the somatic mutations that drive cancer development. However, the …

Deciphering oncogenic drivers: from single genes to integrated pathways

J Chen, M Sun, B Shen - Briefings in bioinformatics, 2015 - academic.oup.com
Technological advances in next-generation sequencing have uncovered a wide spectrum of
aberrations in cancer genomes. The extreme diversity in cancer mutations necessitates …

Algorithms for detecting significantly mutated pathways in cancer

F Vandin, E Upfal, BJ Raphael - Annual International Conference on …, 2010 - Springer
Recent genome sequencing studies have shown that the somatic mutations that drive
cancer development are distributed across a large number of genes. This mutational …

Algorithms for detecting significantly mutated pathways in cancer

F Vandin, E Upfal, BJ Raphael - Journal of Computational Biology, 2011 - liebertpub.com
Recent genome sequencing studies have shown that the somatic mutations that drive
cancer development are distributed across a large number of genes. This mutational …

Pathway and network analysis of cancer genomes

Nature methods, 2015 - nature.com
Genomic information on tumors from 50 cancer types cataloged by the International Cancer
Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently …

Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing

J Zhang, J Liu, J Sun, C Chen, G Foltz… - Briefings in …, 2014 - academic.oup.com
Distinguishing driver mutations from passenger mutations is critical to the understanding of
the molecular mechanisms of carcinogenesis and for identifying prognostic and diagnostic …

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

F Cheng, J Zhao, Z Zhao - Briefings in bioinformatics, 2016 - academic.oup.com
Cancer is often driven by the accumulation of genetic alterations, including single nucleotide
variants, small insertions or deletions, gene fusions, copy-number variations, and large …

[HTML][HTML] MUFFINN: cancer gene discovery via network analysis of somatic mutation data

A Cho, JE Shim, E Kim, F Supek, B Lehner, I Lee - Genome biology, 2016 - Springer
A major challenge for distinguishing cancer-causing driver mutations from inconsequential
passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here …

[HTML][HTML] Finding driver pathways in cancer: models and algorithms

F Vandin, E Upfal, BJ Raphael - Algorithms for Molecular Biology, 2012 - Springer
Background Cancer sequencing projects are now measuring somatic mutations in large
numbers of cancer genomes. A key challenge in interpreting these data is to distinguish …