Gene regulation by gonadal hormone receptors underlies brain sex differences

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Neural circuits of social behaviors: innate yet flexible

(2021) Dongyu Wei et al.   NEURON

Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization

(2021) Margarita V. Brovkina et al.   PLoS Genetics

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

(2021) Zizhen Yao et al.   CELL

ERα is an RNA-binding protein sustaining tumor cell survival and drug resistance

(2021) Yichen Xu et al.   CELL

Molecular logic of cellular diversification in the mouse cerebral cortex

(2021) Daniela J. Di Bella et al.   NATURE

Oestrogen engages brain MC4R signalling to drive physical activity in female mice

(2021) William C. Krause et al.   NATURE

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

(2020) F. Kyle Satterstrom et al.   CELL

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Coordination of social behaviors by the bed nucleus of the stria terminalis

(2020) Meghan E. Flanigan et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

A circuit logic for sexually shared and dimorphic aggressive behaviors in Drosophila

(2020) Hui Chiu et al.   CELL

Distinct hypothalamic control of same- and opposite-sex mounting behaviour in mice

(2020) Tomomi Karigo et al.   NATURE

Signatures of sex: Sex differences in gene expression in the vertebrate brain

(2019) Bruno Gegenhuber et al.   Wiley Interdisciplinary Reviews-Developmental Biology

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

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

Interneuron Types as Attractors and Controllers

(2019) Gord Fishell et al.   Annual Review of Neuroscience

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 genomic landscape of estrogen receptor α binding sites in mouse mammary gland

(2019) Murugesan Palaniappan et al.   PLoS One

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

A central extended amygdala circuit that modulates anxiety

(2018) Sandra Ahrens et al.   JOURNAL OF NEUROSCIENCE

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Sex differences in neural mechanisms mediating reward and addiction

(2018) Jill B. Becker et al.   NEUROPSYCHOPHARMACOLOGY

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

(2018) Megan Crow et al.   Nature Communications

Medial preoptic area in mice is capable of mediating sexually dimorphic behaviors regardless of gender

(2018) Yi-Chao Wei et al.   Nature Communications

Neural coding of sex-specific social information in the mouse brain

(2018) Ying Li et al.   CURRENT OPINION IN NEUROBIOLOGY

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Genome-Wide Mapping of In Vivo ERα–Binding Sites in Male Mouse Efferent Ductules

(2017) Guangxin Yao et al.   ENDOCRINOLOGY

Estrogen receptor alpha is required in GABAergic, but not glutamatergic, neurons to masculinize behavior

(2017) Melody V. Wu et al.   HORMONES AND BEHAVIOR

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

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Esr1+ cells in the ventromedial hypothalamus control female aggression

(2017) Koichi Hashikawa et al.   NATURE NEUROSCIENCE

Why estrogens matter for behavior and brain health

(2017) Liisa A.M. Galea et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

The Neural Circuitry that Functions as a Switch for Courtship versus Aggression in Drosophila Males

(2016) Masayuki Koganezawa et al.   CURRENT BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Hypothalamic control of the male neonatal testosterone surge

(2016) Jenny Clarkson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites to Alter the Breast Cancer Cell Transcriptome

(2015) Hector L. Franco et al.   MOLECULAR CELL

Neurogliaform cells in cortical circuits

(2015) Linda Overstreet-Wadiche et al.   NATURE REVIEWS NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Multimodal Chemosensory Circuits Controlling Male Courtship in Drosophila

(2015) E. Josephine Clowney et al.   NEURON

Excitation and inhibition onto central courtship neurons biases Drosophila mate choice

(2015) Benjamin R Kallman et al.   eLife

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

(2014) Guangchuang Yu et al.   BIOINFORMATICS

Transient Estrogen Receptor Binding and p300 Redistribution Support a Squelching Mechanism for Estradiol-Repressed Genes

(2014) Michael J. Guertin et al.   MOLECULAR ENDOCRINOLOGY

Research Resource: Aorta- and Liver-Specific ERα-Binding Patterns and Gene Regulation by Estrogen

(2014) Francesca K. Gordon et al.   MOLECULAR ENDOCRINOLOGY

Scalable control of mounting and attack by Esr1+ neurons in the ventromedial hypothalamus

(2014) Hyosang Lee et al.   NATURE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The Role of Estrogens in Control of Energy Balance and Glucose Homeostasis

(2013) Franck Mauvais-Jarvis et al.   ENDOCRINE REVIEWS

Estrogen receptor β expression in the mouse forebrain: Age and sex differences

(2013) Damian G. Zuloaga et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

(2013) Jason Gertz et al.   MOLECULAR CELL

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Research Resource: Whole-Genome Estrogen Receptor α Binding in Mouse Uterine Tissue Revealed by ChIP-Seq

(2012) Sylvia C. Hewitt et al.   MOLECULAR ENDOCRINOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Effects of Aromatase or Estrogen Receptor Gene Deletion on Masculinization of the Principal Nucleus of the Bed Nucleus of the Stria Terminalis of Mice

(2011) Shinji Tsukahara et al.   NEUROENDOCRINOLOGY

Leptin Action on GABAergic Neurons Prevents Obesity and Reduces Inhibitory Tone to POMC Neurons

(2011) Linh Vong et al.   NEURON

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

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

Estrogen Masculinizes Neural Pathways and Sex-Specific Behaviors

(2009) Melody V. Wu et al.   CELL

The Epigenetics of Sex Differences in the Brain

(2009) M. M. McCarthy et al.   JOURNAL OF NEUROSCIENCE

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

MEME SUITE: tools for motif discovery and searching

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

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estradiol and the Developing Brain

(2008) MARGARET M. McCARTHY   PHYSIOLOGICAL REVIEWS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY