Whole-genome reconstruction and mutational signatures in gastric cancer

A comprehensive survey of genomic alterations in gastric cancer reveals systematic patterns of molecular exclusivity and co-occurrence among distinct therapeutic targets

(2012) Niantao Deng et al.   GUT

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

(2012) Zhi Jiang Zang et al.   NATURE GENETICS

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

(2011) A. M. Hillmer et al.   GENOME RESEARCH

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

(2011) Kai Wang et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Activation-Induced Cytidine Deaminase Targets DNA at Sites of RNA Polymerase II Stalling by Interaction with Spt5

(2010) Rushad Pavri et al.   CELL

Helicobacter pylori-induced activation-induced cytidine deaminase expression and carcinogenesis

(2010) Hiroyuki Marusawa et al.   CURRENT OPINION IN IMMUNOLOGY

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Do microsatellite instability profiles really differ between colorectal and endometrial tumors?

(2009) Ana M. Ferreira et al.   GENES CHROMOSOMES & CANCER

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

(2009) Stefan M. Woerner et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY