Mutational processes of tobacco smoking and APOBEC activity generate protein-truncating mutations in cancer genomes

APOBEC mutagenesis is a common process in normal human small intestine

(2023) Yichen Wang et al.   NATURE GENETICS

Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer

(2023) Xiaoling Li et al.   CANCER CELL

Therapy-induced APOBEC3A drives evolution of persistent cancer cells

(2023) Hideko Isozaki et al.   NATURE

Mechanisms of APOBEC3 mutagenesis in human cancer cells

(2022) Mia Petljak et al.   NATURE

Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin

(2022) Oliver Ocsenas et al.   PLoS Computational Biology

Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A

(2022) Juan C. Serrano et al.   ACS Chemical Biology

Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness

(2021) Haritha Mathsyaraja et al.   eLife

Monoallelic deleterious MUTYH germline variants as a driver for tumorigenesis

(2021) Rodrigo Araujo Sequeira Barreiro et al.   JOURNAL OF PATHOLOGY

ROS in cancer therapy: the bright side of the moon

(2020) Bruno Perillo et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Pan-cancer analysis of whole genomes

(2020)   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Integrative pathway enrichment analysis of multivariate omics data

(2020) Marta Paczkowska et al.   Nature Communications

Fat1 deletion promotes hybrid EMT state, tumour stemness and metastasis

(2020) Ievgenia Pastushenko et al.   NATURE

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

A Compendium of Mutational Signatures of Environmental Agents

(2019) Jill E. Kucab et al.   CELL

trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data

(2019) Jianhong Ou et al.   NATURE METHODS

Scales and mechanisms of somatic mutation rate variation across the human genome

(2019) Fran Supek et al.   DNA REPAIR

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features

(2019) Rémi Buisson et al.   SCIENCE

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

The mutational footprints of cancer therapies

(2019) Oriol Pich et al.   NATURE GENETICS

APOBEC3A is a prominent cytidine deaminase in breast cancer

(2019) Luis M. Cortez et al.   PLoS Genetics

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

The effects of mutational processes and selection on driver mutations across cancer types

(2018) Daniel Temko et al.   Nature Communications

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

(2018) Kyle Ellrott et al.   Cell Systems

Mutational processes shape the landscape of TP53 mutations in human cancer

(2018) Andrew O. Giacomelli et al.   NATURE GENETICS

Loss of the FAT1 Tumor Suppressor Promotes Resistance to CDK4/6 Inhibitors via the Hippo Pathway

(2018) Zhiqiang Li et al.   CANCER CELL

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations

(2018) Rebecca C. Poulos et al.   PLoS Genetics

The receptor tyrosine kinase EphA2 promotes glutamine metabolism in tumors by activating the transcriptional coactivators YAP and TAZ

(2017) Deanna N. Edwards et al.   Science Signaling

The receptor tyrosine kinase EphA2 promotes glutamine metabolism in tumors by activating the transcriptional coactivators YAP and TAZ

(2017) Deanna N. Edwards et al.   Science Signaling

Tissue-specific mutation accumulation in human adult stem cells during life

(2016) Francis Blokzijl et al.   NATURE

Mutational signatures associated with tobacco smoking in human cancer

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

Mutational signatures of ionizing radiation in second malignancies

(2016) Sam Behjati et al.   Nature Communications

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

APOBECs and virus restriction

(2015) Reuben S. Harris et al.   VIROLOGY

Different prognostic impact of STK11 mutations in non-squamous non-small-cell lung cancer

(2015) Nicolas Pécuchet et al.   Oncotarget

Reactive oxygen species, nutrition, hypoxia and diseases: Problems solved?

(2015) Agnes Görlach et al.   Redox Biology

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool

(2013) S. L. Poon et al.   Science Translational Medicine

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Somatic hypermutation of human mitochondrial and nuclear DNA by APOBEC3 cytidine deaminases, a pathway for DNA catabolism

(2011) R. Suspene et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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