Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

Differential DNA mismatch repair underlies mutation rate variation across the human genome

(2015) Fran Supek et al.   NATURE

Lagging-strand replication shapes the mutational landscape of the genome

(2015) Martin A. M. Reijns et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

e-Driver: a novel method to identify protein regions driving cancer

(2014) Eduard Porta-Pardo et al.   BIOINFORMATICS

Structure of the BRAF-MEK Complex Reveals a Kinase Activity Independent Role for BRAF in MAPK Signaling

(2014) Jacob R. Haling et al.   CANCER CELL

A Common Cancer-Associated DNA Polymerase   Mutation Causes an Exceptionally Strong Mutator Phenotype, Indicating Fidelity Defects Distinct from Loss of Proofreading

(2014) D. P. Kane et al.   CANCER RESEARCH

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

(2014) Andrew L. Wolfe et al.   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Activation of diverse signalling pathways by oncogenic PIK3CA mutations

(2014) Xinyan Wu et al.   Nature Communications

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant

(2014) Paraskevi Gkeka et al.   PLoS Computational Biology

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

(2013) David Tamborero et al.   BIOINFORMATICS

Histone H3.3 Mutations: A Variant Path to Cancer

(2013) Benjamin T.K. Yuen et al.   CANCER CELL

The p90 RSK Family Members: Common Functions and Isoform Specificity

(2013) R. Lara et al.   CANCER RESEARCH

Overexpression of Rab25 contributes to metastasis of bladder cancer through induction of epithelial–mesenchymal transition and activation of Akt/GSK-3β/Snail signaling

(2013) Jiaxing Zhang et al.   CARCINOGENESIS

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

(2013) A. Malhotra et al.   GENOME RESEARCH

Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer

(2013) Eva Budinska et al.   JOURNAL OF PATHOLOGY

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Hidden specificity in an apparently nonspecific RNA-binding protein

(2013) Ulf-Peter Guenther et al.   NATURE

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

TCPA: a resource for cancer functional proteomics data

(2013) Jun Li et al.   NATURE METHODS

Interaction-based discovery of functionally important genes in cancers

(2013) Dario Ghersi et al.   NUCLEIC ACIDS RESEARCH

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

SMAD2, SMAD3 and SMAD4 Mutations in Colorectal Cancer

(2012) N. I. Fleming et al.   CANCER RESEARCH

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

The DNA damage response and cancer therapy

(2012) Christopher J. Lord et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

miRmap: Comprehensive prediction of microRNA target repression strength

(2012) Charles E. Vejnar et al.   NUCLEIC ACIDS RESEARCH

Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110  (PIK3CA)

(2012) J. E. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Python for Scientists and Engineers

(2011) K. Jarrod Millman et al.   COMPUTING IN SCIENCE & ENGINEERING

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis

(2011) Gina M. DeNicola et al.   NATURE

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis

(2011) Y-P Mei et al.   ONCOGENE

Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes

(2011) Can Cenik et al.   PLoS Genetics

Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs

(2010) M. Schnall-Levin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

(2009) Gozde Kar et al.   PLoS Computational Biology

Helical domain and kinase domain mutations in p110  of phosphatidylinositol 3-kinase induce gain of function by different mechanisms

(2008) L. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE