The neoepitope landscape in pediatric cancers

Evaluation of computational programs to predict HLA genotypes from genomic sequencing data

(2016) Denis C. Bauer et al.   BRIEFINGS IN BIOINFORMATICS

JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells

(2016) Yuxin Li et al.   JOURNAL OF PROTEOME RESEARCH

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance

(2016) Maria Secrier et al.   NATURE GENETICS

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

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

Tumor neoantigens: building a framework for personalized cancer immunotherapy

(2015) Matthew M. Gubin et al.   JOURNAL OF CLINICAL INVESTIGATION

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias

(2015) Anna K Andersson et al.   NATURE GENETICS

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Mutational profiling of colorectal cancers with microsatellite instability

(2015) Elaine I. Lin et al.   Oncotarget

Identification of T-cell Receptors Targeting KRAS-Mutated Human Tumors

(2015) Q. J. Wang et al.   Cancer Immunology Research

Neoepitopes of Cancers: Looking Back, Looking Ahead

(2015) P. K. Srivastava   Cancer Immunology Research

Targetable Kinase-Activating Lesions in Ph-like Acute Lymphoblastic Leukemia

(2015) Kathryn G. Roberts et al.   NEW ENGLAND JOURNAL OF MEDICINE

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

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

(2014) M. Rajasagi et al.   BLOOD

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

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

PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors

(2014) Alena Gros et al.   JOURNAL OF CLINICAL INVESTIGATION

JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

(2014) Xusheng Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

A vaccine targeting mutant IDH1 induces antitumour immunity

(2014) Theresa Schumacher et al.   NATURE

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma

(2014) Gang Wu et al.   NATURE GENETICS

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

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

Exploiting the Mutanome for Tumor Vaccination

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

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

(2012) Hirokazu Matsushita et al.   NATURE

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

(2012) Jinghui Zhang et al.   NATURE

Expression of tumour-specific antigens underlies cancer immunoediting

(2012) Michel DuPage et al.   NATURE

The Pediatric Cancer Genome Project

(2012) James R Downing et al.   NATURE GENETICS

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

(2011) Edita Karosiene et al.   IMMUNOGENETICS

Prediction of epitopes using neural network based methods

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

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

The Immune Epitope Database 2.0

(2009) Randi Vita et al.   NUCLEIC ACIDS RESEARCH