Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

Genetic Features of Aflatoxin-Associated Hepatocellular Carcinoma

(2017) Weilong Zhang et al.   GASTROENTEROLOGY

Molecular Classification of Hepatocellular Adenoma Associates With Risk Factors, Bleeding, and Malignant Transformation

(2017) Jean-Charles Nault et al.   GASTROENTEROLOGY

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

(2017) Dominik Glodzik et al.   NATURE GENETICS

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

(2016) Nicholas J. Haradhvala et al.   CELL

The nature of mutations induced by replication–transcription collisions

(2016) T. Sabari Sankar et al.   NATURE

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Tissue-specific mutation accumulation in human adult stem cells during life

(2016) Francis Blokzijl et al.   NATURE

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

(2016) Jaegil Kim et al.   NATURE GENETICS

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

Mutational signatures associated with tobacco smoking in human cancer

(2016) L. B. Alexandrov et al.   SCIENCE

The topography of mutational processes in breast cancer genomes

(2016) Sandro Morganella et al.   Nature Communications

Hepatocellular carcinoma

(2016) Josep M. Llovet et al.   Nature Reviews Disease Primers

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

(2015) Paz Polak et al.   NATURE

Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas

(2015) Jean-Charles Nault et al.   NATURE GENETICS

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

(2015) Kornelius Schulze et al.   NATURE GENETICS

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution

(2015) S. Kasar et al.   Nature Communications

Genomic Profiling of Hepatocellular Adenomas Reveals Recurrent FRK-Activating Mutations and the Mechanisms of Malignant Transformation

(2014) Camilla Pilati et al.   CANCER CELL

Genomic portrait of resectable hepatocellular carcinomas: Implications ofRB1andFGF19aberrations for patient stratification

(2014) Sung-Min Ahn et al.   HEPATOLOGY

Telomerase reverse transcriptase promoter mutation is an early somatic genetic alteration in the transformation of premalignant nodules in hepatocellular carcinoma on cirrhosis

(2014) Jean Charles Nault et al.   HEPATOLOGY

Epidemiology of hepatocellular carcinoma in the United States: Where are we? Where do we go?

(2014) Hashem B. El-Serag et al.   HEPATOLOGY

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

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

Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool

(2013) S. L. Poon et al.   Science Translational Medicine

High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions

(2013) Jean Charles Nault et al.   Nature Communications

Deciphering Signatures of Mutational Processes Operative in Human Cancer

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

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

(2013) Andrej Fischer et al.   GENOME BIOLOGY

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Automatic Relevance Determination in Nonnegative Matrix Factorization with the /spl beta/-Divergence

(2012) V. Y. F. Tan et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

(2012) Akihiro Fujimoto et al.   NATURE GENETICS

Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

(2012) Cécile Guichard et al.   NATURE GENETICS

Estimation of rearrangement phylogeny for cancer genomes

(2011) C. D. Greenman et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS