pTuneos: prioritizing tumor neoantigens from next-generation sequencing data

Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers

(2019) Maria R. Parkhurst et al.   Cancer Discovery

Toward in silico Identification of Tumor Neoantigens in Immunotherapy

(2019) Chi Zhou et al.   TRENDS IN MOLECULAR MEDICINE

A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer

(2018) Xinxin Peng et al.   CANCER CELL

Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer

(2018) Nikolaos Zacharakis et al.   NATURE MEDICINE

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

(2018) Qingsong Gao et al.   Cell Reports

Cancer-Specific Splicing Changes and the Potential for Splicing-Derived Neoantigens

(2018) Luisa Escobar Hoyos et al.   CANCER CELL

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

Lung Adenocarcinoma and Squamous Cell Carcinoma Gene Expression Subtypes Demonstrate Significant Differences in Tumor Immune Landscape

(2017) Hawazin Faruki et al.   Journal of Thoracic Oncology

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer

(2017) Vinod P. Balachandran et al.   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

Neoantigen prediction and the need for validation

(2017) Antonella Vitiello et al.   NATURE BIOTECHNOLOGY

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

(2017) Anne-Mette Bjerregaard et al.   Frontiers in Immunology

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

(2017) Zhan Zhou et al.   Royal Society Open Science

Mutanome directed cancer immunotherapy

(2016) Mathias Vormehr et al.   CURRENT OPINION IN IMMUNOLOGY

Rekindling cancer vaccines

(2016) Malorye Allison Branca   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

(2016) Alena Gros et al.   NATURE MEDICINE

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

(2016) Jasreet Hundal et al.   Genome Medicine

Biomarkers in Cancer Immunotherapy

(2015) Ton N. Schumacher et al.   CANCER CELL

The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers

(2015) Leng Han et al.   CANCER CELL

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

Immunogenic peptide discovery in cancer genomes

(2015) Alexandra Snyder et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

Combination cancer immunotherapy and new immunomodulatory targets

(2015) Kathleen M. Mahoney et al.   NATURE REVIEWS DRUG DISCOVERY

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+T cell epitopes

(2015) Diego Chowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Neoantigens in cancer immunotherapy

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

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran 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

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

(2015) N. A. Rizvi et al.   SCIENCE

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

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

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

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

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

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

NetCTLpan: pan-specific MHC class I pathway epitope predictions

(2010) Thomas Stranzl et al.   IMMUNOGENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

T-cell receptor binding affinities and kinetics: impact on T-cell activity and specificity

(2008) Jennifer D. Stone et al.   IMMUNOLOGY