Evolving neoantigen profiles in colorectal cancers with DNA repair defects

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

(2019) Robert M. Samstein et al.   NATURE GENETICS

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

(2019) Yansheng Liu et al.   NATURE BIOTECHNOLOGY

A genomic analysis workflow for colorectal cancer precision oncology

(2019) Giorgio Corti et al.   Clinical Colorectal Cancer

Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples

(2018) Marcos Díaz-Gay et al.   BMC BIOINFORMATICS

Radiologic and Genomic Evolution of Individual Metastases during HER2 Blockade in Colorectal Cancer

(2018) Giulia Siravegna et al.   CANCER CELL

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different

(2018) Chung-Han Lee et al.   TRENDS IN IMMUNOLOGY

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

(2018) Razvan Cristescu et al.   SCIENCE

The Clinical Impact of the Genomic Landscape of Mismatch Repair–Deficient Cancers

(2018) Giovanni Germano et al.   Cancer Discovery

Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N -glycosylases

(2017) Serge Boiteux et al.   FREE RADICAL BIOLOGY AND MEDICINE

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

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

Nivolumab in patients with metastatic DNA mismatch repair-deficient or microsatellite instability-high colorectal cancer (CheckMate 142): an open-label, multicentre, phase 2 study

(2017) Michael J Overman et al.   LANCET ONCOLOGY

Inactivation of DNA repair triggers neoantigen generation and impairs tumour growth

(2017) Giovanni Germano et al.   NATURE

Patient-derived xenografts undergo mouse-specific tumor evolution

(2017) Uri Ben-David et al.   NATURE GENETICS

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

A Specific Mutational Signature Associated with DNA 8-Oxoguanine Persistence in MUTYH-defective Colorectal Cancer

(2017) Alessandra Viel et al.   EBioMedicine

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Predictive biomarkers for checkpoint inhibitor-based immunotherapy

(2016) Geoffrey T Gibney et al.   LANCET ONCOLOGY

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Mutational signatures associated with tobacco smoking in human cancer

(2016) L. B. Alexandrov et al.   SCIENCE

Registered report: Systematic identification of genomic markers of drug sensitivity in cancer cells

(2016) John P Vanden Heuvel et al.   eLife

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

Exonuclease 1-dependent and independent mismatch repair

(2015) Eva M. Goellner et al.   DNA REPAIR

The genomic landscape of response to EGFR blockade in colorectal cancer

(2015) Andrea Bertotti et al.   NATURE

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers

(2015) Adam Shlien et al.   NATURE GENETICS

Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients

(2015) Giulia Siravegna et al.   NATURE MEDICINE

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Innate and adaptive immune cells in the tumor microenvironment

(2013) Thomas F Gajewski et al.   NATURE IMMUNOLOGY

Xenome--a tool for classifying reads from xenograft samples

(2012) T. Conway et al.   BIOINFORMATICS

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency

(2012) Sun Tian et al.   JOURNAL OF PATHOLOGY

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Genetic and Expression Analysis of MET, MACC1, and HGF in Metastatic Colorectal Cancer: Response to Met Inhibition in Patient Xenografts and Pathologic Correlations

(2011) F. Galimi et al.   CLINICAL CANCER RESEARCH

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

(2010) Heng Li et al.   BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inherited predisposition to colorectal adenomas caused by multiple rare alleles of MUTYH but not OGG1, NUDT1, NTH1 or NEIL 1, 2 or 3

(2008) A R Dallosso et al.   GUT