TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

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

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

Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma

(2014) John C Castle et al.   BMC GENOMICS

Translation of genomics-guided RNA-based personalised cancer vaccines: towards the bedside

(2014) V Boisguérin et al.   BRITISH JOURNAL OF CANCER

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA-Binding Properties of Tumor Neoepitopes in Humans

(2014) E. F. Fritsch et al.   Cancer Immunology Research

A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines

(2014) Sebastian Boegel et al.   OncoImmunology

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

Infection of Xenotransplanted Human Cell Lines by Murine Retroviruses: A Lesson Brought Back to Light by XMRV

(2013) Heidi A. Hempel et al.   Frontiers in Oncology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Exploiting the Mutanome for Tumor Vaccination

(2012) J. C. Castle et al.   CANCER RESEARCH

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles

(2008) K. Boller et al.   JOURNAL OF GENERAL VIROLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Molecular cloning and functional characterization of the human endogenous retrovirus K113

(2008) Nadine Beimforde et al.   VIROLOGY