A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes

Proteogenomic Characterization of Endometrial Carcinoma

(2020) Yongchao Dou et al.   CELL

dbPepNeo: a manually curated database for human tumor neoantigen peptides

(2020) Xiaoxiu Tan et al.   Database-The Journal of Biological Databases and Curation

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Escape from nonsense-mediated decay associates with anti-tumor immunogenicity

(2020) Kevin Litchfield et al.   Nature Communications

Polycomb Group Proteins EZH2 and EED Directly Regulate Androgen Receptor in Advanced Prostate Cancer

(2019) Qipeng Liu et al.   INTERNATIONAL JOURNAL OF CANCER

Tissue-specificity in cancer: The rule, not the exception

(2019) Kevin M. Haigis et al.   SCIENCE

Identification, Characterization, and Regulatory Mechanisms of a Novel EGR1 Splicing Isoform

(2019) Vincenza Aliperti et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ScanNeo: identifying indel derived neoantigens using RNA-Seq data

(2019) Ting-You Wang et al.   BIOINFORMATICS

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes

(2019) Elizabeth J. Adams et al.   NATURE

Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer

(2019) Abhijit Parolia et al.   NATURE

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

(2019) David J. Clark et al.   CELL

pTuneos: prioritizing tumor neoantigens from next-generation sequencing data

(2019) Chi Zhou et al.   Genome Medicine

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

(2018) Zhenjia Wang et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Indel detection from DNA and RNA sequencing data with transIndel

(2018) Rendong Yang et al.   BMC GENOMICS

Systematic Functional Annotation of Somatic Mutations in Cancer

(2018) Patrick Kwok-Shing Ng et al.   CANCER CELL

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

(2018) David A. Quigley et al.   CELL

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

(2018) Maria Nattestad et al.   GENOME RESEARCH

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

(2018) Diana Miao et al.   SCIENCE

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

(2018) Michael Seiler et al.   Cell Reports

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

(2018) Kyle Ellrott et al.   Cell Systems

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

HGVS Recommendations for the Description of Sequence Variants: 2016 Update

(2016) Johan T. den Dunnen et al.   HUMAN MUTATION

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

The rules and impact of nonsense-mediated mRNA decay in human cancers

(2016) Rik G H Lindeboom et al.   NATURE GENETICS

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

(2016) Hannes L Röst et al.   NATURE METHODS

Lessons from non-canonical splicing

(2016) Christopher R. Sibley et al.   NATURE REVIEWS GENETICS

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

(2016) Morten Nielsen et al.   Genome Medicine

The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers

(2015) S. Legare et al.   CANCER RESEARCH

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

(2015) Yamile Marquez et al.   GENOME RESEARCH

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

(2015) Nathan J. Edwards et al.   JOURNAL OF PROTEOME RESEARCH

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung et al.   NATURE GENETICS

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+T cell epitopes

(2015) Diego Chowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Enter exitrons

(2015) Dorothee Staiger et al.   GENOME BIOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Michael S. Lawrence et al.   NATURE

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Fast and accurate read mapping with approximate seeds and multiple backtracking

(2013) Enrico Siragusa et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Hallmarks of alternative splicing in cancer

(2013) S Oltean et al.   ONCOGENE

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

(2013) M. J. Ellis et al.   Cancer Discovery

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models

(2010) Simon N. Wood   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Neurofilament Heavy Polypeptide Regulates the Akt-β-Catenin Pathway in Human Esophageal Squamous Cell Carcinoma

(2010) Myoung Sook Kim et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH