Translating Immunopeptidomics to Immunotherapy-Decision-Making for Patient and Personalized Target Selection

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

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

The Potential and Challenges of Exploiting the Vast But Dynamic Neoepitope Landscape for Immunotherapy

(2017) Els M. E. Verdegaal et al.   Frontiers in Immunology

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system

(2015) Antonis Koussounadis et al.   Scientific Reports

Translating DRiPs: MHC class I immunosurveillance of pathogens and tumors

(2014) L. C. Anton et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations

(2014) Faviel F. González-Galarza et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Sangtae Kim et al.   Nature Communications

MHC Class I Antigen Processing and Presenting Machinery: Organization, Function, and Defects in Tumor Cells

(2013) P. Leone et al.   JNCI-Journal of the National Cancer Institute

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

(2013) Michael S. Lawrence et al.   NATURE

The regulatory landscape for actively personalized cancer immunotherapies

(2013) Cedrik M Britten et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Optimal Decharging and Clustering of Charge Ladders Generated in ESI−MS

(2010) Chris Bielow et al.   JOURNAL OF PROTEOME RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

(2008) C. Lundegaard et al.   BIOINFORMATICS

The MHC class I peptide repertoire is molded by the transcriptome

(2008) Marie-Hélène Fortier et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self

(2008) Fiyaz Mohammed et al.   NATURE IMMUNOLOGY

Clustering Millions of Tandem Mass Spectra

(2007) Ari M. Frank et al.   JOURNAL OF PROTEOME RESEARCH