Somatic genomic changes in single Alzheimer’s disease neurons

Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease

(2021) Kun Leng et al.   NATURE NEUROSCIENCE

Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands

(2021) Dong Xing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic mutation landscapes at single-molecule resolution

(2021) Federico Abascal et al.   NATURE

Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data

(2021) Shishi Min et al.   NEUROBIOLOGY OF AGING

Accurate genomic variant detection in single cells with primary template-directed amplification

(2021) Veronica Gonzalez-Pena et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease

(2020) David Gate et al.   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Deletion of Topoisomerase 1 in excitatory neurons causes genomic instability and early onset neurodegeneration

(2020) Giulia Fragola et al.   Nature Communications

HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer’s disease

(2020) Ping-Chieh Pao et al.   Nature Communications

Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain

(2020) August Yue Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long genes are more frequently affected by somatic mutations and show reduced expression in Alzheimer's disease: Implications for disease etiology

(2020) Sourena Soheili‐Nezhad et al.   Alzheimers & Dementia

APP gene copy number changes reflect exogenous contamination

(2020) Junho Kim et al.   NATURE

Severe reactive astrocytes precipitate pathological hallmarks of Alzheimer’s disease via H2O2− production

(2020) Heejung Chun et al.   NATURE NEUROSCIENCE

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

(2019) Craig L. Bohrson et al.   NATURE GENETICS

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

(2019) Mia Petljak et al.   CELL

A Compendium of Mutational Signatures of Environmental Agents

(2019) Jill E. Kucab et al.   CELL

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

(2019) Lei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer

(2019) Myrthe Jager et al.   GENOME RESEARCH

Brain somatic mutations observed in Alzheimer’s disease associated with aging and dysregulation of tau phosphorylation

(2019) Jun Sung Park et al.   Nature Communications

Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

(2019) Cynthia J. Sakofsky et al.   PLOS BIOLOGY

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance

(2019) Lovelace J. Luquette et al.   Nature Communications

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

(2018) Irene Franco et al.   Nature Communications

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

(2018) Francis Blokzijl et al.   Genome Medicine

Somatic APP gene recombination in Alzheimer’s disease and normal neurons

(2018) Ming-Hsiang Lee et al.   NATURE

Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations

(2018) Vladimir B. Seplyarskiy et al.   NATURE GENETICS

A tau homeostasis signature is linked with the cellular and regional vulnerability of excitatory neurons to tau pathology

(2018) Hongjun Fu et al.   NATURE NEUROSCIENCE

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

High prevalence of focal and multi-focal somatic genetic variants in the human brain

(2018) Michael J. Keogh et al.   Nature Communications

Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis

(2018) Fernando G. Osorio et al.   Cell Reports

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

(2017) Xiao Dong et al.   NATURE METHODS

Aging and neurodegeneration are associated with increased mutations in single human neurons

(2017) Michael A. Lodato et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

The amyloid hypothesis of Alzheimer's disease at 25 years

(2016) Dennis J Selkoe et al.   EMBO Molecular Medicine

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

(2016) Francis Blokzijl et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning

(2016) Jennifer L. Hazen et al.   NEURON

Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing

(2016) Margaret L. Hoang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations inEscherichia coli

(2016) Ashok S. Bhagwat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the identification of low allele frequency mosaic mutations in the brains of Alzheimer's disease patients

(2015) Carlo Sala Frigerio et al.   Alzheimers & Dementia

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

Reactive Oxygen Species, Redox Signaling and Neuroinflammation in Alzheimer's Disease: The NF-κB Connection

(2015) Upinder Kaur et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

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

(2015) I. Martincorena et al.   SCIENCE

REST and stress resistance in ageing and Alzheimer’s disease

(2014) Tao Lu et al.   NATURE

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

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

National Institute on Aging–Alzheimer's Association guidelines for the neuropathologic assessment of Alzheimer's disease

(2012) Bradley T. Hyman et al.   Alzheimers & Dementia

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

Microglia and Inflammation in Alzheimers Disease

(2012) Shweta Mandrekar-Colucci et al.   CNS & Neurological Disorders-Drug Targets

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Our fragile intellect. Part I

(2012) Gerald R. Crabtree   TRENDS IN GENETICS

A neuroprotective role for the DNA damage checkpoint in tauopathy

(2011) Vikram Khurana et al.   AGING CELL

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DNA Damage and Repair in Alzheimers Disease

(2009) Fabio Coppede et al.   Current Alzheimer Research

Transcription induces strand-specific mutations at the 5' end of human genes

(2008) P. Polak et al.   GENOME RESEARCH