Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons

Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation

(2020) Erik C. B. Johnson et al.   NATURE MEDICINE

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution

(2020) Christian D. Huber et al.   PLoS Genetics

Identification of Conserved Proteomic Networks in Neurodegenerative Dementia

(2020) Vivek Swarup et al.   Cell Reports

Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons

(2019) Simon T. Schafer et al.   NATURE NEUROSCIENCE

Whole genome experimental maps of DNA G-quadruplexes in multiple species

(2019) Giovanni Marsico et al.   NUCLEIC ACIDS RESEARCH

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Early neuronal accumulation of DNA double strand breaks in Alzheimer’s disease

(2019) Niraj M. Shanbhag et al.   Acta Neuropathologica Communications

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

DNA methylation-based biomarkers and the epigenetic clock theory of ageing

(2018) Steve Horvath et al.   NATURE REVIEWS GENETICS

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

(2018) Akihide Takeuchi et al.   Cell Reports

Integrative detection and analysis of structural variation in cancer genomes

(2018) Jesse R. Dixon et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

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

(2017) Michael A. Lodato et al.   SCIENCE

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

(2017) Priit Pruunsild et al.   Cell Reports

DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age

(2017) Alexey Kozlenkov et al.   Genes

Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells

(2016) Pei-Chi Wei et al.   CELL

Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice

(2016) W. P. Vermeij et al.   NATURE

G-quadruplex structures mark human regulatory chromatin

(2016) Robert Hänsel-Hertsch et al.   NATURE GENETICS

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

(2016) Hisham Mohammed et al.   Nature Protocols

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter

(2015) Lin He et al.   ANALYTICAL CHEMISTRY

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

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

(2015) Ram Madabhushi et al.   CELL

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

(2015) T. Xu et al.   Journal of Proteomics

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Genomic integrity and the ageing brain

(2015) Hei-man Chow et al.   NATURE REVIEWS NEUROSCIENCE

Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair

(2015) Dylan A. Reid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Controlled induction of DNA double-strand breaks in the mouse liver induces features of tissue ageing

(2015) Ryan R. White et al.   Nature Communications

DNA Damage, DNA Repair, Aging, and Neurodegeneration

(2015) Scott Maynard et al.   Cold Spring Harbor Perspectives in Medicine

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Human iPSC Neurons Display Activity-Dependent Neurotransmitter Secretion: Aberrant Catecholamine Levels in Schizophrenia Neurons

(2014) Vivian Hook et al.   Stem Cell Reports

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Maintaining genome stability in the nervous system

(2013) Peter J McKinnon   NATURE NEUROSCIENCE

Physiologic brain activity causes DNA double-strand breaks in neurons, with exacerbation by amyloid-β

(2013) Elsa Suberbielle et al.   NATURE NEUROSCIENCE

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY