A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes

(2021) Ethan J. Armand et al.   NEURON

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

(2021) Meng Zhang et al.   NATURE

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

(2020) Yupeng He et al.   NATURE

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Common cell type nomenclature for the mammalian brain

(2020) Jeremy A Miller et al.   eLife

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler 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

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics

(2018) Kenneth D. Harris et al.   PLOS BIOLOGY

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

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Robust single-cell DNA methylome profiling with snmC-seq2

(2018) Chongyuan Luo et al.   Nature Communications

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Distinct descending motor cortex pathways and their roles in movement

(2018) Michael N. Economo et al.   NATURE

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Perspectives on defining cell types in the brain

(2018) Eran A Mukamel et al.   CURRENT OPINION IN NEUROBIOLOGY

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Neuronal cell-type classification: challenges, opportunities and the path forward

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

Substance P signalling in primary motor cortex facilitates motor learning in rats

(2017) Benjamin Hertler et al.   PLoS One

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Chongyuan Luo et al.   SCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Anatomical characterization of Cre driver mice for neural circuit mapping and manipulation

(2014) Julie A. Harris et al.   Frontiers in Neural Circuits

A genuine layer 4 in motor cortex with prototypical synaptic circuit connectivity

(2014) Naoki Yamawaki et al.   eLife

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

RORβ Induces Barrel-like Neuronal Clusters in the Developing Neocortex

(2011) Denis Jabaudon et al.   CEREBRAL CORTEX

Lhx2 and Lhx9 Determine Neuronal Differentiation and Compartition in the Caudal Forebrain by Regulating Wnt Signaling

(2011) Daniela Peukert et al.   PLOS BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

(2009) Linda Madisen et al.   NATURE NEUROSCIENCE

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY