The accessible chromatin landscape of the murine hippocampus at single-cell resolution

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Remote Memory and Cortical Synaptic Plasticity Require Neuronal CCCTC-Binding Factor (CTCF)

(2018) Somi Kim et al.   JOURNAL OF NEUROSCIENCE

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

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

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

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

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

Developmental diversification of cortical inhibitory interneurons

(2018) Christian Mayer et al.   NATURE

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

CTCF Governs the Identity and Migration of MGE-Derived Cortical Interneurons

(2018) Adrienne Elbert et al.   JOURNAL OF NEUROSCIENCE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

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

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

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

(2017) Alicia N Schep et al.   NATURE METHODS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Neuronal activity modifies the chromatin accessibility landscape in the adult brain

(2017) Yijing Su et al.   NATURE NEUROSCIENCE

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc

(2016) Dev Sharan Sams et al.   Cell Reports

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons

(2016) Mark S Cembrowski et al.   eLife

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

USP18 lack in microglia causes destructive interferonopathy of the mouse brain

(2015) T. Goldmann et al.   EMBO JOURNAL

NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

(2015) A. Pataskar et al.   EMBO JOURNAL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Stimulus-specific combinatorial functionality of neuronal c-fos enhancers

(2015) Jae-Yeol Joo et al.   NATURE NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

The hematopoietic regulator, ELF-1, enhances the transcriptional response to Interferon-β of the OAS1 anti-viral gene

(2015) Steven Larsen et al.   Scientific Reports

SOX3 expression in the glial system of the developing and adult mouse cerebellum

(2015) Pike-See Cheah et al.   SpringerPlus

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Preemptive Regulation of Intracellular pH in Hippocampal Neurons by a Dual Mechanism of Depolarization-Induced Alkalinization

(2011) N. Svichar et al.   JOURNAL OF NEUROSCIENCE

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Alterations of Glial Cells in the Mouse Hippocampus During Postnatal Development

(2009) Hiroki Kimoto et al.   CELLULAR AND MOLECULAR NEUROBIOLOGY

Neurogenin2 Directs Granule Neuroblast Production and Amplification while NeuroD1 Specifies Neuronal Fate during Hippocampal Neurogenesis

(2009) Laurent Roybon et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY