Pharmacologic modulation of RNA splicing enhances anti-tumor immunity

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

(2020) James D. Thomas et al.   NATURE GENETICS

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study

(2020) Aurélien Marabelle et al.   LANCET ONCOLOGY

Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia

(2019) Eric Wang et al.   CANCER CELL

Proteomics profiling of arginine methylation defines PRMT5 substrate specificity

(2019) Daniele Musiani et al.   Science Signaling

Anti-tumor Activity of the Type I PRMT Inhibitor, GSK3368715, Synergizes with PRMT5 Inhibition through MTAP Loss

(2019) Andrew Fedoriw et al.   CANCER CELL

Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation

(2019) Jia Yi Fong et al.   CANCER CELL

The Splicing Modulator GEX1A Exhibits Potent Anti-Leukemic Activity Both in Vitro and In Vivo through Inducing an MCL1 Splice-Switch in Pre-Clinical Models of Acute Myeloid Leukemia

(2019) Mark Sellin et al.   BLOOD

H3B-8800, an orally available small-molecule splicing modulator, induces lethality in spliceosome-mutant cancers

(2018) Michael Seiler et al.   NATURE MEDICINE

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

(2018) Reyka G. Jayasinghe et al.   Cell Reports

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

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

(2018) André Kahles et al.   CANCER CELL

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

A tissue-based draft map of the murine MHC class I immunopeptidome

(2018) Heiko Schuster et al.   Scientific Data

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

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

MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies

(2017) J. Patrick Murphy et al.   JOURNAL OF PROTEOME RESEARCH

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15

(2017) Ting Han et al.   SCIENCE

TNFα blockade overcomes resistance to anti-PD-1 in experimental melanoma

(2017) Florie Bertrand et al.   Nature Communications

Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases

(2015) Mohammad S. Eram et al.   ACS Chemical Biology

A selective inhibitor of PRMT5 with in vivo and in vitro potency in MCL models

(2015) Elayne Chan-Penebre et al.   Nature Chemical Biology

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Dose-Response Analysis Using R

(2015) Christian Ritz et al.   PLoS One

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

Sample processing obscures cancer-specific alterations in leukemic transcriptomes

(2014) Heidi Dvinge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A

(2013) C. G. Hubert et al.   GENES & DEVELOPMENT

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Synergistic Effect of CTLA-4 Blockade and Cancer Chemotherapy in the Induction of Anti-Tumor Immunity

(2013) W. Joost Lesterhuis et al.   PLoS One

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

A cell-based MHC stabilization assay for the detection of peptide binding to the canine classical class I molecule, DLA-88

(2012) Peter Ross et al.   VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Biological validation that SF3b is a target of the antitumor macrolide pladienolide

(2011) Akira Yokoi et al.   FEBS Journal

Bayesian hypothesis testing for psychologists: A tutorial on the Savage–Dickey method

(2010) Eric-Jan Wagenmakers et al.   COGNITIVE PSYCHOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The cytolytic molecules Fas ligand and TRAIL are required for murine thymic graft-versus-host disease

(2009) Il-Kang Na et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2009) Ben Langmead et al.   GENOME BIOLOGY