pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

EpiToolKit—a web-based workbench for vaccine design

(2015) Benjamin Schubert et al.   BIOINFORMATICS

An overview of bioinformatics tools for epitope prediction: Implications on vaccine development

(2015) Ruth E. Soria-Guerra et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Prediction of CD8+ Epitopes in Leishmania braziliensis Proteins Using EPIBOT: In Silico Search and In Vivo Validation

(2015) Angelo Duarte et al.   PLoS One

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Genome Modeling System: A Knowledge Management Platform for Genomics

(2015) Malachi Griffith et al.   PLoS Computational Biology

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

(2014) M. Rajasagi et al.   BLOOD

Somatically mutated tumor antigens in the quest for a more efficacious patient-oriented immunotherapy of cancer

(2014) Zlatko Trajanoski et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

(2014) Fei Duan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

(2014) Carsten Linnemann et al.   NATURE MEDICINE

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

(2013) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Exploiting the Mutanome for Tumor Vaccination

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

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The IMGT/HLA database

(2012) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Targeted Assembly of Short Sequence Reads

(2011) René L. Warren et al.   PLoS One

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prediction of epitopes using neural network based methods

(2010) Claus Lundegaard et al.   JOURNAL OF IMMUNOLOGICAL METHODS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods

(2008) Hao Zhang et al.   BIOINFORMATICS

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan

(2008) Morten Nielsen et al.   PLoS Computational Biology