Maftools: efficient and comprehensive analysis of somatic variants in cancer

Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients

(2018) De-Chen Lin et al.   GASTROENTEROLOGY

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

(2018) Kyle Ellrott et al.   Cell Systems

Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas

(2017) De-Chen Lin et al.   GUT

Integrated genomic characterization of oesophageal carcinoma

(2017)   NATURE

Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes

(2017) Luis Zapata et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance

(2016) Maria Secrier et al.   NATURE GENETICS

Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma

(2016) Jia-Jie Hao et al.   NATURE GENETICS

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels

(2016) Matteo D’Antonio et al.   Cell Reports

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

(2015) C. Swanton et al.   Cancer Discovery

Voltage-gated Na+ Channel Activity Increases Colon Cancer Transcriptional Activity and Invasion Via Persistent MAPK Signaling

(2015) Carrie D. House et al.   Scientific Reports

changepoint: AnRPackage for Changepoint Analysis

(2015) Rebecca Killick et al.   Journal of Statistical Software

ErbB targeting inhibitors repress cell migration of esophageal squamous cell carcinoma and adenocarcinoma cells by distinct signaling pathways

(2014) Christiane D. Fichter et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genomic and molecular characterization of esophageal squamous cell carcinoma

(2014) De-Chen Lin et al.   NATURE GENETICS

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

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

(2013) David Tamborero et al.   BIOINFORMATICS

From human genome to cancer genome: The first decade

(2013) D. A. Wheeler et al.   GENOME RESEARCH

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

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

(2013) Austin M Dulak et al.   NATURE GENETICS

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

(2013) Benjamin JM Taylor et al.   eLife

EMu: probabilistic inference of mutational processes and their localization in the cancer genome

(2013) Andrej Fischer et al.   GENOME BIOLOGY

AID/APOBEC cytosine deaminase induces genome-wide kataegis

(2012) Artem G Lada et al.   Biology Direct

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

MuSiC: Identifying mutational significance in cancer genomes

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

Voltage-gated sodium channels at 60: structure, function and pathophysiology

(2012) William A. Catterall   JOURNAL OF PHYSIOLOGY-LONDON

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Functional impact bias reveals cancer drivers

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

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

PathScan: a tool for discerning mutational significance in groups of putative cancer genes

(2011) Michael C. Wendl et al.   BIOINFORMATICS

De novo discovery of mutated driver pathways in cancer

(2011) F. Vandin et al.   GENOME RESEARCH

Sodium ion channel mutations in glioblastoma patients correlate with shorter survival

(2011) Avadhut D Joshi et al.   Molecular Cancer

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Acute Myeloid Leukemia WithIDH1orIDH2Mutation

(2010) Keyur P. Patel et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Therapeutic Targeting of the DNA Mismatch Repair Pathway

(2010) S. A. Martin et al.   CLINICAL CANCER RESEARCH

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Combinatorial patterns of somatic gene mutations in cancer

(2008) Chen-Hsiang Yeang et al.   FASEB JOURNAL