Integrated Analysis of Whole Genome and Transcriptome Sequencing Reveals Diverse Transcriptomic Aberrations Driven by Somatic Genomic Changes in Liver Cancers

Next-Generation Sequencing Reveals Deep Intronic Cryptic ABCC8 and HADH Splicing Founder Mutations Causing Hyperinsulinism by Pseudoexon Activation

(2012) Sarah E. Flanagan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

(2012) J. Liu et al.   GENOME RESEARCH

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

(2012) Z. Jiang et al.   GENOME RESEARCH

The transcriptional landscape and mutational profile of lung adenocarcinoma

(2012) J.-S. Seo et al.   GENOME RESEARCH

Proteomic Investigations Reveal a Role for RNA Processing Factor THRAP3 in the DNA Damage Response

(2012) Petra Beli et al.   MOLECULAR CELL

Exome sequencing of hepatitis B virus–associated hepatocellular carcinoma

(2012) Jian Huang et al.   NATURE GENETICS

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

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

(2012) Wing-Kin Sung 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

Genome Sequencing Identifies a Basis for Everolimus Sensitivity

(2012) G. Iyer et al.   SCIENCE

Chronic Activation of mTOR Complex 1 Is Sufficient to Cause Hepatocellular Carcinoma in Mice

(2012) S. Menon et al.   Science Signaling

Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach

(2012) Dong Ding et al.   PLoS Genetics

DNA Methylation Suppresses Expression of the Urea Cycle Enzyme Carbamoyl Phosphate Synthetase 1 (CPS1) in Human Hepatocellular Carcinoma

(2011) Hongyan Liu et al.   AMERICAN JOURNAL OF PATHOLOGY

An HNF4α-miRNA Inflammatory Feedback Circuit Regulates Hepatocellular Oncogenesis

(2011) Maria Hatziapostolou et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

Hepatocellular Carcinoma

(2011) Hashem B. El-Serag   NEW ENGLAND JOURNAL OF MEDICINE

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Hepatocyte Nuclear Factor 4  Suppresses the Development of Hepatocellular Carcinoma

(2010) B.-F. Ning et al.   CANCER RESEARCH

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

(2010) C. J. David et al.   GENES & DEVELOPMENT

Signatures of mutation and selection in the cancer genome

(2010) Graham R. Bignell et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS