Enhancer viruses for combinatorial cell-subclass-specific labeling

Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

(2020) Rebecca D. Hodge et al.   Nature Communications

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

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

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

(2019) Jocelyn Y. Kishi et al.   NATURE METHODS

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

(2019) Josephine Jüttner et al.   NATURE NEUROSCIENCE

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

(2019) Sinisa Hrvatin et al.   eLife

Hierarchical organization of cortical and thalamic connectivity

(2019) Julie A. Harris et al.   NATURE

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

(2018) Tanya L. Daigle et al.   CELL

Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression

(2018) Stefan Blankvoort et al.   CURRENT BIOLOGY

Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences

(2018) Arielle Baker et al.   JOURNAL OF NEUROSCIENCE

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

(2018) Sebastian Preissl 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

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

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

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

(2017) Ken Y Chan et al.   NATURE NEUROSCIENCE

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

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

Cis-regulatory landscapes of four cell types of the retina

(2017) Dominik Hartl et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Lucas T Gray et al.   eLife

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

Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering

(2016) Madina Karimova et al.   Scientific Reports

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

(2015) Jacob H. Levine 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

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Transgenic Mice for Intersectional Targeting of Neural Sensors and Effectors with High Specificity and Performance

(2015) Linda Madisen et al.   NEURON

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

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

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

Rationally Designed MicroRNA-Based Genetic Classifiers Target Specific Neurons in the Brain

(2015) Marianna K. Sayeg et al.   ACS Synthetic Biology

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Correlated Gene Expression and Target Specificity Demonstrate Excitatory Projection Neuron Diversity

(2013) Staci A. Sorensen et al.   CEREBRAL CORTEX

DICE, an efficient system for iterative genomic editing in human pluripotent stem cells

(2013) Fangfang Zhu et al.   NUCLEIC ACIDS RESEARCH

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold 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

A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex

(2011) Hiroki Taniguchi et al.   NEURON

Mapping of fluorescent protein-expressing neurons and axon pathways in adult and developing Thy1-eYFP-H transgenic mice

(2010) Cesar Porrero et al.   BRAIN RESEARCH

Projection-Specific Neuromodulation of Medial Prefrontal Cortex Neurons

(2010) N. C. Dembrow et al.   JOURNAL OF NEUROSCIENCE

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

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Tools for neuroanatomy and neurogenetics in Drosophila

(2008) B. D. Pfeiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Inducible and Reversible Mouse Genetic Rescue System

(2008) Hongkui Zeng et al.   PLoS Genetics