Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma

Proteogenomic Characterization of Endometrial Carcinoma

(2020) Yongchao Dou et al.   CELL

Insights into the origin of intrahepatic cholangiocarcinoma from mouse models

(2020) Yan Zhu et al.   HEPATOLOGY

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

Molecular targeted therapies: Ready for “prime time” in biliary tract cancer

(2020) Angela Lamarca et al.   JOURNAL OF HEPATOLOGY

Ivosidenib in IDH1-mutant, chemotherapy-refractory cholangiocarcinoma (ClarIDHy): a multicentre, randomised, double-blind, placebo-controlled, phase 3 study

(2020) Ghassan K Abou-Alfa et al.   LANCET ONCOLOGY

Pemigatinib for previously treated, locally advanced or metastatic cholangiocarcinoma: a multicentre, open-label, phase 2 study

(2020) Ghassan K Abou-Alfa et al.   LANCET ONCOLOGY

A Phase 2 Multi-institutional Study of Nivolumab for Patients With Advanced Refractory Biliary Tract Cancer

(2020) Richard D. Kim et al.   JAMA Oncology

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Cholangiocarcinoma 2020: the next horizon in mechanisms and management

(2020) Jesus M. Banales et al.   Nature Reviews Gastroenterology & Hepatology

Biological Mechanisms and Clinical Significance of BAP1 Mutations in Human Cancer

(2020) Michele Carbone et al.   Cancer Discovery

dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

(2020) Daniel G Bunis et al.   BIOINFORMATICS

Mutated nucleophosmin 1 as immunotherapy target in acute myeloid leukemia

(2019) Dyantha I. van der Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma

(2019) Ying Jiang et al.   NATURE

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Raddeanin A promotes apoptosis and ameliorates 5-fluorouracil resistance in cholangiocarcinoma cells

(2019) Shuang-Shuang Guo et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Dysbiosis signatures of the microbial profile in tissue from bladder cancer

(2019) Fei Liu et al.   Cancer Medicine

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

(2019) Qiang Gao et al.   CELL

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

(2019) David J. Clark et al.   CELL

Monocarboxylate transporter 4 (MCT4) is a high affinity transporter capable of exporting lactate in high-lactate microenvironments

(2019) Yasna Contreras-Baeza et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of four immune subtypes characterized by distinct composition and functions of tumor microenvironment in intrahepatic cholangiocarcinoma

(2019) Sylvie Job et al.   HEPATOLOGY

Heterogeneous immunogenomic features and distinct escape mechanisms in multifocal hepatocellular carcinoma

(2019) Liang-qing Dong et al.   JOURNAL OF HEPATOLOGY

Biological Role and Therapeutic Potential of IDH Mutations in Cancer

(2018) Matthew S. Waitkus et al.   CANCER CELL

Revolutionizing Precision Oncology through Collaborative Proteogenomics and Data Sharing

(2018) Henry Rodriguez et al.   CELL

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Comprehensive molecular profiling of intra- and extrahepatic cholangiocarcinomas: potential targets for intervention

(2018) Maeve A Lowery et al.   CLINICAL CANCER RESEARCH

Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations

(2018) Christopher P. Wardell et al.   JOURNAL OF HEPATOLOGY

Spatial and temporal clonal evolution of intrahepatic cholangiocarcinoma

(2018) Liang-Qing Dong et al.   JOURNAL OF HEPATOLOGY

MCT4 Expression Is a Potential Therapeutic Target in Colorectal Cancer with Peritoneal Carcinomatosis

(2018) Hee Kyung Kim et al.   MOLECULAR CANCER THERAPEUTICS

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

(2018) Qingsong Gao et al.   Cell Reports

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

(2018) Francis Blokzijl et al.   Genome Medicine

Guidelines for Diagnosis and Treatment of Primary Liver Cancer in China (2017 Edition)

(2018) Jian Zhou et al.   Liver Cancer

P53-induced miR-30e-5p inhibits colorectal cancer invasion and metastasis by targeting ITGA6 and ITGB1

(2017) Sara Laudato et al.   INTERNATIONAL JOURNAL OF CANCER

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Cholangiocarcinoma — evolving concepts and therapeutic strategies

(2017) Sumera Rizvi et al.   Nature Reviews Clinical Oncology

DGIdb 3.0: a redesign and expansion of the drug–gene interaction database

(2017) Kelsy C Cotto et al.   NUCLEIC ACIDS RESEARCH

Oncogenic K-Ras upregulates ITGA6 expression via FOSL1 to induce anoikis resistance and synergizes with αV-Class integrins to promote EMT

(2017) K Zhang et al.   ONCOGENE

Host Genetics and Gut Microbiome: Challenges and Perspectives

(2017) Alexander Kurilshikov et al.   TRENDS IN IMMUNOLOGY

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

(2017) Apinya Jusakul et al.   Cancer Discovery

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH -Mutant Molecular Profiles

(2017) Farshad Farshidfar et al.   Cell Reports

Synthetic Lethal Vulnerabilities in KRAS -Mutant Cancers

(2017) Andrew J. Aguirre et al.   Cold Spring Harbor Perspectives in Medicine

High expression of hexokinase domain containing 1 is associated with poor prognosis and aggressive phenotype in hepatocarcinoma

(2016) Zijian Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases

(2016) Ying-Nan P. Chen et al.   NATURE

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

(2016) E. Stronen et al.   SCIENCE

Tumor-Suppressor Functions of the TP53 Pathway

(2016) Brandon J. Aubrey et al.   Cold Spring Harbor Perspectives in Medicine

Expanding the UniFrac Toolbox

(2016) Ruth G. Wong et al.   PLoS One

Genomic spectra of biliary tract cancer

(2015) Hiromi Nakamura et al.   NATURE GENETICS

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

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

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

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1

(2015) Cong Guo et al.   Nature Communications

Massive parallel sequencing uncovers actionable FGFR2–PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma

(2015) Daniela Sia et al.   Nature Communications

CopywriteR: DNA copy number detection from off-target sequence data

(2015) Thomas Kuilman et al.   GENOME BIOLOGY

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Executive Summary: Heart Disease and Stroke Statistics—2014 Update

(2014) Alan S. Go et al.   CIRCULATION

Activating FGFR2-RAS-BRAF Mutations in Ameloblastoma

(2014) N. A. Brown et al.   CLINICAL CANCER RESEARCH

IMGT®, the international ImMunoGeneTics information system® 25 years on

(2014) Marie-Paule Lefranc et al.   NUCLEIC ACIDS RESEARCH

Mutational landscape of intrahepatic cholangiocarcinoma

(2014) Shanshan Zou et al.   Nature Communications

MCT4 Defines a Glycolytic Subtype of Pancreatic Cancer with Poor Prognosis and Unique Metabolic Dependencies

(2014) GuemHee Baek et al.   Cell Reports

Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer

(2013) Gong-Hua Li et al.   BIOINFORMATICS

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma

(2013) Yasuhito Arai et al.   HEPATOLOGY

Grb2 controls phosphorylation of FGFR2 by inhibiting receptor kinase and Shp2 phosphatase activity

(2013) Zamal Ahmed et al.   JOURNAL OF CELL BIOLOGY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas

(2013) Yuchen Jiao et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Enhanced Expression of Fibroblast Growth Factor Receptor 2 IIIc Promotes Human Pancreatic Cancer Cell Proliferation

(2012) Toshiyuki Ishiwata et al.   AMERICAN JOURNAL OF PATHOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Inhibition of Basal FGF Receptor Signaling by Dimeric Grb2

(2012) Chi-Chuan Lin et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Transcriptomic profiling reveals hepatic stem-like gene signatures and interplay of miR-200c and epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma

(2012) Naoki Oishi et al.   HEPATOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

p38 Inhibition ameliorates skin and skull abnormalities in Fgfr2 Beare-Stevenson mice

(2012) Yingli Wang et al.   JOURNAL OF CLINICAL INVESTIGATION

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2012) Ethan Cerami et al.   Cancer Discovery

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Ptpn11/Shp2 Acts as a Tumor Suppressor in Hepatocellular Carcinogenesis

(2011) Emilie A. Bard-Chapeau et al.   CANCER CELL

Genomic and Genetic Characterization of Cholangiocarcinoma Identifies Therapeutic Targets for Tyrosine Kinase Inhibitors

(2011) Jesper B. Andersen et al.   GASTROENTEROLOGY

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

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

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Molecular evolution of the vertebrate hexokinase gene family: Identification of a conserved fifth vertebrate hexokinase gene

(2007) David M. Irwin et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics