TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection

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

(2016) Jasreet Hundal et al.   Genome Medicine

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Cancer Neoantigens and Applications for Immunotherapy

(2015) A. Desrichard et al.   CLINICAL CANCER RESEARCH

Landscape of Tumor Antigens in T Cell Immunotherapy

(2015) S. Ilyas et al.   JOURNAL OF IMMUNOLOGY

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Generation of MANAbodies specific to HLA-restricted epitopes encoded by somatically mutated genes

(2015) Andrew D. Skora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

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

(2015) B. M. Carreno et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) M. Rajasagi et al.   BLOOD

HLA Diversity in the 1000 Genomes Dataset

(2014) Pierre-Antoine Gourraud et al.   PLoS One

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

(2013) Paul F Robbins et al.   NATURE MEDICINE

Treating B-cell cancer with T cells expressing anti-CD19 chimeric antigen receptors

(2013) James N. Kochenderfer et al.   Nature Reviews Clinical Oncology

The Future Is Now: Chimeric Antigen Receptors as New Targeted Therapies for Childhood Cancer

(2012) D. W. Lee et al.   CLINICAL CANCER RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Mutant proteins as cancer-specific biomarkers

(2011) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li 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

Mutation-Specific Antibodies for the Detection of EGFR Mutations in Non-Small-Cell Lung Cancer

(2009) J. Yu et al.   CLINICAL CANCER RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS