4.8 Article

Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

The Reactome Pathway Knowledgebase

Antonio Fabregat et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Li Ding et al.

Article Biochemistry & Molecular Biology

Comprehensive Characterization of Cancer Driver Genes and Mutations

Matthew H. Bailey et al.

Article Biochemistry & Molecular Biology

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

Katherine A. Hoadley et al.

Article Genetics & Heredity

The long tail of oncogenic drivers in prostate cancer

Joshua Armenia et al.

NATURE GENETICS (2018)

Review Biochemistry & Molecular Biology

Classifying BRAF alterations in cancer: new rational therapeutic strategies for actionable mutations

Matthew Dankner et al.

ONCOGENE (2018)

Article Biochemistry & Molecular Biology

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

Kyle Ellrott et al.

CELL SYSTEMS (2018)

Article Biochemistry & Molecular Biology

Expansion of the Gene Ontology knowledgebase and resources

S. Carbon et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

COSMIC: somatic cancer genetics at high-resolution

Simon A. Forbes et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

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

Eduard Porta-Pardo et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples

Thomas A. Peterson et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemical Research Methods

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R. Conway et al.

BIOINFORMATICS (2017)

Article Biochemical Research Methods

Leveraging protein quaternary structure to identify oncogenic driver mutations

Gregory A. Ryslik et al.

BMC BIOINFORMATICS (2016)

Article Genetics & Heredity

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

Beifang Niu et al.

NATURE GENETICS (2016)

Article Biochemical Research Methods

The development of cryo-EM into a mainstream structural biology technique

Eva Nogales

NATURE METHODS (2016)

Article Biochemistry & Molecular Biology

Localized structural frustration for evaluating the impact of sequence variants

Sushant Kumar et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Pharmacology & Pharmacy

Targeting therapeutic liabilities engendered by PIK3R1 mutations for cancer treatment

Lydia W. T. Cheung et al.

PHARMACOGENOMICS (2016)

Article Biochemistry & Molecular Biology

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation

Declan Clarke et al.

STRUCTURE (2016)

Article Biochemical Research Methods

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

Jimmy Van den Eynden et al.

BMC BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

'Latent drivers' expand the cancer mutational landscape

Ruth Nussinov et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Comprehensive assessment of cancer missense mutation clustering in protein structures

Atanas Kamburov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemical Research Methods

Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

Fan Yang et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemical Research Methods

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

Eduard Porta-Pardo et al.

PLOS COMPUTATIONAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

Martin L. Miller et al.

CELL SYSTEMS (2015)

Article Biochemistry & Molecular Biology

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

Simon A. Forbes et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

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

Eduard Porta-Pardo et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Gregory A. Ryslik et al.

BMC BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Gregory A. Ryslik et al.

BMC BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

Discovery and saturation analysis of cancer genes across 21 tumour types

Michael S. Lawrence et al.

NATURE (2014)

Article Genetics & Heredity

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

Martin Kircher et al.

NATURE GENETICS (2014)

Review Genetics & Heredity

Expanding the computational toolbox for mining cancer genomes

Li Ding et al.

NATURE REVIEWS GENETICS (2014)

Article Chemistry, Physical

The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

Chung-Jung Tsai et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)

Article Multidisciplinary Sciences

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

Amie J. Radenbaugh et al.

PLOS ONE (2014)

Article Biochemical Research Methods

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

David Tamborero et al.

BIOINFORMATICS (2013)

Review Biochemistry & Molecular Biology

Allostery in Disease and in Drug Discovery

Ruth Nussinov et al.

Review Biochemistry & Molecular Biology

Lessons from the Cancer Genome

Levi A. Garraway et al.

Article Biochemistry & Molecular Biology

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

Jueri Reimand et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Multidisciplinary Sciences

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

Michael S. Lawrence et al.

NATURE (2013)

Article Biotechnology & Applied Microbiology

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

Kristian Cibulskis et al.

NATURE BIOTECHNOLOGY (2013)

Editorial Material Genetics & Heredity

The Cancer Genome Atlas Pan-Cancer analysis project

John N. Weinstein et al.

NATURE GENETICS (2013)

Article Multidisciplinary Sciences

Comprehensive identification of mutational cancer driver genes across 12 tumor types

David Tamborero et al.

SCIENTIFIC REPORTS (2013)

Article Multidisciplinary Sciences

The mutational landscape of phosphorylation signaling in cancer

Jueri Reimand et al.

SCIENTIFIC REPORTS (2013)

Article Biochemical Research Methods

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

David E. Larson et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

Nai-Jyuan Wang et al.

BMC GENOMICS (2012)

Article Biochemistry & Molecular Biology

MuSiC: Identifying mutational significance in cancer genomes

Nathan D. Dees et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

Functional impact bias reveals cancer drivers

Abel Gonzalez-Perez et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Review Multidisciplinary Sciences

Exploring the Genomes of Cancer Cells: Progress and Promise

Michael R. Stratton

SCIENCE (2011)

Article Multidisciplinary Sciences

Proteoglycan-Specific Molecular Switch for RPTPσ Clustering and Neuronal Extension

Charlotte H. Coles et al.

SCIENCE (2011)

Article Biochemical Research Methods

Binding Leverage as a Molecular Basis for Allosteric Regulation

Simon Mitternacht et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemical Research Methods

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

Jingjing Ye et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Detection of nonneutral substitution rates on mammalian phylogenies

Katherine S. Pollard et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

International network of cancer genome projects

Thomas J. Hudson et al.

NATURE (2010)

Article Biochemical Research Methods

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

Daniel C. Koboldt et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

The role of dynamic conformational ensembles in biomolecular recognition

David D. Boehr et al.

NATURE CHEMICAL BIOLOGY (2009)

Article Multidisciplinary Sciences

The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers

Selvaraju Veeriah et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Dynamical networks in tRNA: protein complexes

Anurag Sethi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Multidisciplinary Sciences

Dynamic personalities of proteins

Katherine Henzler-Wildman et al.

NATURE (2007)

Article Biochemical Research Methods

Genetic progression and the waiting time to cancer

Niko Beerenwinkel et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Multidisciplinary Sciences

Patterns of somatic mutation in human cancer genomes

Christopher Greenman et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Residues crucial for maintaining short paths in network communication mediate signaling in proteins

Antonio del Sol et al.

MOLECULAR SYSTEMS BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Quantifying allosteric effects in proteins

DM Ming et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Review Biochemistry & Molecular Biology

A systems biology perspective on protein structural dynamics and signal transduction

F Rousseau et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)

Review Oncology

A census of human cancer genes

PA Futreal et al.

NATURE REVIEWS CANCER (2004)

Review Oncology

Roles of heparan-sulphate glycosaminoglycans in cancer

R Sasisekharan et al.

NATURE REVIEWS CANCER (2002)

Article Multidisciplinary Sciences

Mutations of the BRAF gene in human cancer

H Davies et al.

NATURE (2002)

Article Multidisciplinary Sciences

Community structure in social and biological networks

M Girvan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)