Unsupervised detection of cancer driver mutations with parsimony-guided learning

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles

(2016) E. Kim et al.   Cancer Discovery

Extending P450 site-of-metabolism models with region-resolution data

(2015) Jed M. Zaretzki et al.   BIOINFORMATICS

do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations: Fig. 1.

(2015) Rajendra Kumar et al.   BIOINFORMATICS

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action

(2014) Michael P. Schroeder et al.   BIOINFORMATICS

Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma

(2014) Miwako Kakiuchi et al.   NATURE GENETICS

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Only three driver gene mutations are required for the development of lung and colorectal cancers

(2014) Cristian Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kin-Driver: a database of driver mutations in protein kinases

(2014) F. L. Simonetti et al.   Database-The Journal of Biological Databases and Curation

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features

(2013) Yong Mao et al.   PLoS One

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors

(2012) Bon-Kyoung Koo et al.   NATURE

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer

(2012) Ron Bose et al.   Cancer Discovery

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

(2012) Abel Gonzalez-Perez et al.   Genome Medicine

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

ARID1A, a Factor That Promotes Formation of SWI/SNF-Mediated Chromatin Remodeling, Is a Tumor Suppressor in Gynecologic Cancers

(2011) B. Guan et al.   CANCER RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Identifying cancer driver genes in tumor genome sequencing studies

(2010) Ahrim Youn et al.   BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH