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

Loss of function of the retinoid-related nuclear receptor (RORB) gene and epilepsy

(2016) Gabrielle Rudolf et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

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

(2016) M Ryan Corces et al.   NATURE GENETICS

Genomic footprinting

(2016) Jeff Vierstra et al.   NATURE METHODS

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Foxp2 controls synaptic wiring of corticostriatal circuits and vocal communication by opposing Mef2c

(2016) Yi-Chuan Chen et al.   NATURE NEUROSCIENCE

Cux1 Enables Interhemispheric Connections of Layer II/III Neurons by Regulating Kv1-Dependent Firing

(2016) Fernanda M. Rodríguez-Tornos et al.   NEURON

Mutually repressive interaction between Brn1/2 and Rorb contributes to the establishment of neocortical layer 2/3 and layer 4

(2016) Koji Oishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex

(2016) L. Telley et al.   SCIENCE

Knockout of Foxp2 disrupts vocal development in mice

(2016) Gregg A. Castellucci et al.   Scientific Reports

Epigenomic landscapes of retinal rods and cones

(2016) Alisa Mo et al.   eLife

A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types

(2016) Yasuyuki Shima et al.   eLife

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

The ciliogenic transcription factor Rfx3 is required for the formation of the thalamocortical tract by regulating the patterning of prethalamus and ventral telencephalon

(2015) Dario Magnani et al.   HUMAN MOLECULAR GENETICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

(2015) Christopher L Frank et al.   NATURE NEUROSCIENCE

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

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

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

(2015) Yu Gyoung Tak et al.   Epigenetics & Chromatin

Genetic association study of circadian genes with seasonal pattern in bipolar disorders

(2015) Pierre Alexis Geoffroy et al.   Scientific Reports

Conversion of MyoD to a Neurogenic Factor: Binding Site Specificity Determines Lineage

(2015) Abraham P. Fong et al.   Cell Reports

A chromosomal rearrangement in a child with severe speech and language disorder separates FOXP2 from a functional enhancer

(2015) Martin Becker et al.   Molecular Cytogenetics

Brain-specific transcriptional regulator T-brain-1 controls brain wiring and neuronal activity in autism spectrum disorders

(2015) Tzyy-Nan Huang et al.   Frontiers in Neuroscience

Investigation of Associations between NR1D1, RORA and RORB Genes and Bipolar Disorder

(2015) Yin-Chieh Lai et al.   PLoS One

Foxp2 regulates neuronal differentiation and neuronal subtype specification

(2014) Yi-Chi Chiu et al.   Developmental Neurobiology

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Mutual antagonism between Sox10 and NFIA regulates diversification of glial lineages and glioma subtypes

(2014) Stacey M Glasgow et al.   NATURE NEUROSCIENCE

Translaminar Inhibitory Cells Recruited by Layer 6 Corticothalamic Neurons Suppress Visual Cortex

(2014) Dante S. Bortone et al.   NEURON

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

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

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

Correlated Gene Expression and Target Specificity Demonstrate Excitatory Projection Neuron Diversity

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

RORB gene and 9q21.13 microdeletion: Report on a patient with epilepsy and mild intellectual disability

(2013) Maria Giuseppina Baglietto et al.   European Journal of Medical Genetics

Expression analysis of the speech-related genes FoxP1 and FoxP2 and their relation to singing behavior in two songbird species

(2013) Q. Chen et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

FoxP2 Regulates Neurogenesis during Embryonic Cortical Development

(2013) D. Tsui et al.   JOURNAL OF NEUROSCIENCE

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

In vivo reprogramming of circuit connectivity in postmitotic neocortical neurons

(2013) Andres De la Rossa et al.   NATURE NEUROSCIENCE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Diminished FoxP2 Levels Affect Dopaminergic Modulation of Corticostriatal Signaling Important to Song Variability

(2013) Malavika Murugan et al.   NEURON

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene

(2012) Tomislav Maricic et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

The Ciliogenic Transcription Factor RFX3 Regulates Early Midline Distribution of Guidepost Neurons Required for Corpus Callosum Development

(2012) Carine Benadiba et al.   PLoS Genetics

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

Tbr1 and Fezf2 Regulate Alternate Corticofugal Neuronal Identities during Neocortical Development

(2011) W. L. McKenna et al.   JOURNAL OF NEUROSCIENCE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract

(2011) W. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Foxp2 Regulates Gene Networks Implicated in Neurite Outgrowth in the Developing Brain

(2011) Sonja C. Vernes et al.   PLoS Genetics

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Foxp1/2/4-NuRD Interactions Regulate Gene Expression and Epithelial Injury Response in the Lung via Regulation of Interleukin-6

(2010) Ann L. Chokas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cux1 and Cux2 Regulate Dendritic Branching, Spine Morphology, and Synapses of the Upper Layer Neurons of the Cortex

(2010) Beatriz Cubelos et al.   NEURON

The Transcription Factor Cux1 Regulates Dendritic Morphology of Cortical Pyramidal Neurons

(2010) Ning Li et al.   PLoS One

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson 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

Ultrasonic vocalization impairment of Foxp2 (R552H) knockin mice related to speech-language disorder and abnormality of Purkinje cells

(2008) E. Fujita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA