Therapy-induced APOBEC3A drives evolution of persistent cancer cells

The current toolbox for APOBEC drug discovery

(2022) Michael J. Grillo et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Mechanisms of APOBEC3 mutagenesis in human cancer cells

(2022) Mia Petljak et al.   NATURE

Molecular Biomarkers of Disease Outcomes and Mechanisms of Acquired Resistance to First-Line Osimertinib in Advanced EGFR-Mutant Lung Cancers

(2022) Noura J. Choudhury et al.   Journal of Thoracic Oncology

Genotoxic stress and viral infection induce transient expression of APOBEC3A and pro-inflammatory genes through two distinct pathways

(2021) Sunwoo Oh et al.   Nature Communications

Pan-cancer analysis of whole genomes

(2020)   NATURE

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

(2020) David Mas-Ponte et al.   NATURE GENETICS

Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots

(2020) Pégah Jalili et al.   Nature Communications

Small cell transformation of ROS1 fusion-positive lung cancer resistant to ROS1 inhibition

(2020) Jessica J. Lin et al.   npj Precision Oncology

APOBEC3A catalyzes mutation and drives carcinogenesis in vivo

(2020) Emily K. Law et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

(2020) Matthew H. Bailey et al.   Nature Communications

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

(2019) Mia Petljak et al.   CELL

Concurrent RB1 and TP53 Alterations Define a Subset of EGFR-Mutant Lung Cancers at risk for Histologic Transformation and Inferior Clinical Outcomes

(2019) Michael Offin et al.   Journal of Thoracic Oncology

Targeting FGFR overcomes EMT-mediated resistance in EGFR mutant non-small cell lung cancer

(2019) Sana Raoof et al.   ONCOGENE

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

(2019) Rémi Buisson et al.   SCIENCE

APOBEC3A is a prominent cytidine deaminase in breast cancer

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

SHP2 inhibition restores sensitivity in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

(2018) Leila Dardaei et al.   NATURE MEDICINE

Osimertinib in Untreated EGFR-Mutated Advanced Non–Small-Cell Lung Cancer

(2018) Jean-Charles Soria et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sequential ALK Inhibitors Can Select for Lorlatinib-Resistant Compound ALK Mutations in ALK-Positive Lung Cancer

(2018) Satoshi Yoda et al.   Cancer Discovery

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

(2018) Kyle Ellrott et al.   Cell Systems

Clonal History and Genetic Predictors of Transformation Into Small-Cell Carcinomas From Lung Adenocarcinomas

(2017) June-Koo Lee et al.   JOURNAL OF CLINICAL ONCOLOGY

Family-Wide Comparative Analysis of Cytidine and Methylcytidine Deamination by Eleven Human APOBEC Proteins

(2017) Fumiaki Ito et al.   JOURNAL OF MOLECULAR BIOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Stem-loop structure preference for site-specific RNA editing by APOBEC3A and APOBEC3G

(2017) Shraddha Sharma et al.   PeerJ

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition

(2016) Aaron N Hata et al.   NATURE MEDICINE

Resensitization to Crizotinib by the Lorlatinib ALK Resistance Mutation L1198F

(2016) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Transient overexpression of exogenous APOBEC3A causes C-to-U RNA editing of thousands of genes

(2016) Shraddha Sharma et al.   RNA Biology

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Molecular Mechanisms of Resistance to First- and Second-Generation ALK Inhibitors in ALK-Rearranged Lung Cancer

(2016) J. F. Gainor et al.   Cancer Discovery

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

(2015) Kin Chan et al.   NATURE GENETICS

APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages

(2015) Shraddha Sharma et al.   Nature Communications

RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer

(2015) Matthew J. Niederst et al.   Nature Communications

NF-κB-Activating Complex Engaged in Response to EGFR Oncogene Inhibition Drives Tumor Cell Survival and Residual Disease in Lung Cancer

(2015) Collin M. Blakely et al.   Cell Reports

Chromosomal Instability Selects Gene Copy-Number Variants Encoding Core Regulators of Proliferation in ER+Breast Cancer

(2014) David Endesfelder et al.   CANCER RESEARCH

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Patient-derived models of acquired resistance can identify effective drug combinations for cancer

(2014) Adam S. Crystal et al.   SCIENCE

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

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

OpenComet: An automated tool for comet assay image analysis

(2014) Benjamin M. Gyori et al.   Redox Biology

Replication stress links structural and numerical cancer chromosomal instability

(2013) Rebecca A. Burrell et al.   NATURE

APOBEC3B is an enzymatic source of mutation in breast cancer

(2013) Michael B. Burns et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

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

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

(2012) Y. Drier et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FAS and NF-κB signalling modulate dependence of lung cancers on mutant EGFR

(2011) Trever G. Bivona et al.   NATURE

Genotypic and Histological Evolution of Lung Cancers Acquiring Resistance to EGFR Inhibitors

(2011) L. V. Sequist et al.   Science Translational Medicine

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

(2010) Heng Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY