Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

(2020) Yingyue Zhou et al.   NATURE MEDICINE

A Chromatin Accessibility Atlas of the Developing Human Telencephalon

(2020) Eirene Markenscoff-Papadimitriou et al.   CELL

Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans

(2020) Douglas Vormstein-Schneider et al.   NATURE NEUROSCIENCE

Functional Access to Neuron Subclasses in Rodent and Primate Forebrain

(2019) Preeti Mehta et al.   Cell Reports

AAVcis-regulatory sequences are correlated with ocular toxicity

(2019) Wenjun Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interrogating the Genetic Determinants of Tourette’s Syndrome and Other Tic Disorders Through Genome-Wide Association Studies

(2019) Dongmei Yu et al.   AMERICAN JOURNAL OF PSYCHIATRY

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans

(2019) Josephine Jüttner et al.   NATURE NEUROSCIENCE

Long-Lasting Rescue of Network and Cognitive Dysfunction in a Genetic Schizophrenia Model

(2019) Arghya Mukherjee et al.   CELL

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease

(2019) Niklas Schwarz et al.   eLife

A scalable platform for the development of cell-type-specific viral drivers

(2019) Sinisa Hrvatin et al.   eLife

Non-immunogenic utrophin gene therapy for the treatment of muscular dystrophy animal models

(2019) Yafeng Song et al.   NATURE MEDICINE

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

(2019) Alexi Nott et al.   SCIENCE

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

An atlas of chromatin accessibility in the adult human brain

(2018) John F. Fullard et al.   GENOME RESEARCH

Optimized Adeno-Associated Virus-Mediated Human Factor VIII Gene Therapy in Cynomolgus Macaques

(2018) Jenny Greig et al.   HUMAN GENE THERAPY

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Genetic identification of brain cell types underlying schizophrenia

(2018) Nathan G. Skene et al.   NATURE GENETICS

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

(2018) James J. Lee et al.   NATURE GENETICS

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome

(2018) Kiran Girdhar et al.   NATURE NEUROSCIENCE

A robust ex vivo experimental platform for molecular-genetic dissection of adult human neocortical cell types and circuits

(2018) Jonathan T. Ting et al.   Scientific Reports

GWAS on family history of Alzheimer’s disease

(2018) Riccardo E. Marioni et al.   Translational Psychiatry

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder

(2018) Ditte Demontis et al.   NATURE GENETICS

h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex

(2018) Brian E. Kalmbach et al.   NEURON

Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability

(2017) L E Duncan et al.   MOLECULAR PSYCHIATRY

Revealing the complex genetic architecture of obsessive–compulsive disorder using meta-analysis

(2017) Paul D Arnold et al.   MOLECULAR PSYCHIATRY

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks

(2017) Florence Demenais et al.   NATURE GENETICS

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

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

(2017) Alicia N Schep et al.   NATURE METHODS

Generation of pure GABAergic neurons by transcription factor programming

(2017) Nan Yang et al.   NATURE METHODS

Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems

(2017) Ken Y Chan et al.   NATURE NEUROSCIENCE

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

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

(2017) Lucas T Gray et al.   eLife

Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

(2017)   Molecular Autism

The industrial melanism mutation in British peppered moths is a transposable element

(2016) Arjen E. van’t Hof et al.   NATURE

Genome-wide association study identifies 74 loci associated with educational attainment

(2016) Aysu Okbay et al.   NATURE

Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain

(2016) Benjamin E Deverman et al.   NATURE BIOTECHNOLOGY

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

A viral strategy for targeting and manipulating interneurons across vertebrate species

(2016) Jordane Dimidschstein et al.   NATURE NEUROSCIENCE

Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate

(2016) Shanni N. Silberberg et al.   NEURON

A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons

(2016) D. Gowanlock R. Tervo et al.   NEURON

Genome-Wide Association Study of Loneliness Demonstrates a Role for Common Variation

(2016) Jianjun Gao et al.   NEUROPSYCHOPHARMACOLOGY

Optogenetic control of human neurons in organotypic brain cultures

(2016) My Andersson et al.   Scientific Reports

Single-Cell Transcriptome Analyses Reveal Signals to Activate Dormant Neural Stem Cells

(2015) Yuping Luo et al.   CELL

Massively parallel cis -regulatory analysis in the mammalian central nervous system

(2015) Susan Q. Shen et al.   GENOME RESEARCH

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

A Cellular Resolution Map of Barrel Cortex Activity during Tactile Behavior

(2015) Simon P. Peron et al.   NEURON

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Widespread neuron-specific transgene expression in brain and spinal cord following synapsin promoter-driven AAV9 neonatal intracerebroventricular injection

(2014) Jesse R. McLean et al.   NEUROSCIENCE LETTERS

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Inhibitory Interneuron Deficit Links Altered Network Activity and Cognitive Dysfunction in Alzheimer Model

(2012) Laure Verret et al.   CELL

A mega-analysis of genome-wide association studies for major depressive disorder

(2012)   MOLECULAR PSYCHIATRY

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

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Specific deletion of NaV1.1 sodium channels in inhibitory interneurons causes seizures and premature death in a mouse model of Dravet syndrome

(2012) C. S. Cheah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association study identifies five new schizophrenia loci

(2011)   NATURE GENETICS

Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4

(2011)   NATURE GENETICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY