Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma

EASL Clinical Practice Guidelines: Management of hepatocellular carcinoma

(2018) Peter R. Galle et al.   JOURNAL OF HEPATOLOGY

Hepatocellular carcinoma

(2018) Alejandro Forner et al.   LANCET

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Identification of an Immune-specific Class of Hepatocellular Carcinoma, Based on Molecular Features

(2017) Daniela Sia et al.   GASTROENTEROLOGY

TiO2 with Tandem Fractionation (TAFT): An Approach for Rapid, Deep, Reproducible, and High-Throughput Phosphoproteome Analysis

(2017) Liangliang Ren et al.   JOURNAL OF PROTEOME RESEARCH

SREBP-regulated lipid metabolism: convergent physiology — divergent pathophysiology

(2017) Hitoshi Shimano et al.   Nature Reviews Endocrinology

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

GOLM1 Modulates EGFR/RTK Cell-Surface Recycling to Drive Hepatocellular Carcinoma Metastasis

(2016) Qing-Hai Ye et al.   CANCER CELL

TSC1/2 mutations define a molecular subset of HCC with aggressive behaviour and treatment implication

(2016) Daniel W H Ho et al.   GUT

Abrogating cholesterol esterification suppresses growth and metastasis of pancreatic cancer

(2016) J Li et al.   ONCOGENE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Untargeted UPLC-MS Profiling Pipeline to Expand Tissue Metabolome Coverage: Application to Cardiovascular Disease

(2015) Panagiotis A. Vorkas et al.   ANALYTICAL CHEMISTRY

Inactivation of Hippo Pathway Is Significantly Associated with Poor Prognosis in Hepatocellular Carcinoma

(2015) B. H. Sohn et al.   CLINICAL CANCER RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Kornelius Schulze et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Advances in targeted therapies for hepatocellular carcinoma in the genomic era

(2015) Josep M. Llovet et al.   Nature Reviews Clinical Oncology

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Cholesteryl Ester Accumulation Induced by PTEN Loss and PI3K/AKT Activation Underlies Human Prostate Cancer Aggressiveness

(2014) Shuhua Yue et al.   Cell Metabolism

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

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

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies

(2013) Xing Hua et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

(2013) Jing-Woei Li et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Mutations in TP53, CTNNB1 and PIK3CA genes in hepatocellular carcinoma associated with hepatitis B and hepatitis C virus infections

(2013) Maria Lina Tornesello et al.   GENOMICS

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Wnt-Pathway Activation in Two Molecular Classes of Hepatocellular Carcinoma and Experimental Modulation by Sorafenib

(2012) A. Lachenmayer et al.   CLINICAL CANCER RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

(2012) Marija Milacic et al.   Cancers

A Unique Metastasis Gene Signature Enables Prediction of Tumor Relapse in Early-Stage Hepatocellular Carcinoma Patients

(2010) S. Roessler et al.   CANCER RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment

(2010) Yujin Hoshida   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Integrative Transcriptome Analysis Reveals Common Molecular Subclasses of Human Hepatocellular Carcinoma

(2009) Y. Hoshida et al.   CANCER RESEARCH

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Focal Gains of VEGFA and Molecular Classification of Hepatocellular Carcinoma

(2008) D. Y. Chiang et al.   CANCER RESEARCH

Transforming growth factor-β gene expression signature in mouse hepatocytes predicts clinical outcome in human cancer

(2008) Cédric Coulouarn et al.   HEPATOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH