Comparison of algorithms for the detection of cancer drivers at subgene resolution

3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets

(2017) Jianjiong Gao et al.   Genome Medicine

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

(2017) William Poole et al.   PLoS Computational Biology

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development

(2016) Bálint Mészáros et al.   Biology Direct

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer

(2016) Giorgio E. M. Melloni et al.   BMC BIOINFORMATICS

Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure

(2016) Collin Tokheim et al.   CANCER RESEARCH

Protein-structure-guided discovery of functional mutations across 19 cancer types

(2016) Beifang Niu et al.   NATURE GENETICS

Phenotypic Characterization of a Comprehensive Set of MAPK1 /ERK2 Missense Mutants

(2016) Lisa Brenan et al.   Cell Reports

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein–protein interfaces: Fig. 1.

(2015) Miguel Vázquez et al.   BIOINFORMATICS

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

(2015) Jimmy Van den Eynden et al.   BMC BIOINFORMATICS

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

(2015) Pau Creixell et al.   CELL

‘Latent drivers’ expand the cancer mutational landscape

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GermlinePARP4mutations in patients with primary thyroid and breast cancers

(2015) Yuji Ikeda et al.   ENDOCRINE-RELATED CANCER

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

(2015) Matthew T Chang et al.   NATURE BIOTECHNOLOGY

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

(2015) Carlos L Araya et al.   NATURE GENETICS

dSysMap: exploring the edgetic role of disease mutations

(2015) Roberto Mosca et al.   NATURE METHODS

Effect of Mutation Order on Myeloproliferative Neoplasms

(2015) Christina A. Ortmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

PDBFlex: exploring flexibility in protein structures

(2015) Thomas Hrabe et al.   NUCLEIC ACIDS RESEARCH

Comprehensive assessment of cancer missense mutation clustering in protein structures

(2015) Atanas Kamburov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

(2015) Eduard Porta-Pardo et al.   PLoS Computational Biology

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

(2015) Martin L. Miller et al.   Cell Systems

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

(2014) Eduard Porta-Pardo et al.   BIOINFORMATICS

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations

(2014) Gregory A Ryslik et al.   BMC BIOINFORMATICS

A spatial simulation approach to account for protein structure when identifying non-random somatic mutations

(2014) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

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

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

Cancer3D: understanding cancer mutations through protein structures

(2014) Eduard Porta-Pardo et al.   NUCLEIC ACIDS RESEARCH

The UCSC Cancer Genomics Browser: update 2015

(2014) Mary Goldman et al.   NUCLEIC ACIDS RESEARCH

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

(2013) David Tamborero et al.   BIOINFORMATICS

Utilizing protein structure to identify non-random somatic mutations

(2013) Gregory A Ryslik et al.   BMC BIOINFORMATICS

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

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

(2013) Michael S. Lawrence et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

The Continuum Model of Selection in Human Tumors: General Paradigm or Niche Product?

(2012) S. Leedham et al.   CANCER RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Functional impact bias reveals cancer drivers

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

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Statistical method on nonrandom clustering with application to somatic mutations in cancer

(2010) Jingjing Ye et al.   BMC BIOINFORMATICS

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology