Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain

Neuronal Kmt2a/Mll1 Histone Methyltransferase Is Essential for Prefrontal Synaptic Plasticity and Working Memory

(2015) M. Jakovcevski et al.   JOURNAL OF NEUROSCIENCE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

(2015)   NATURE NEUROSCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Prdm9 Polymorphism Unveils Mouse Evolutionary Tracks

(2014) H. Kono et al.   DNA RESEARCH

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

Genetic Evidence for the Adhesion Protein IgSF9/Dasm1 to Regulate Inhibitory Synapse Development Independent of its Intracellular Domain

(2014) A. Mishra et al.   JOURNAL OF NEUROSCIENCE

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Predicting the human epigenome from DNA motifs

(2014) John W Whitaker et al.   NATURE METHODS

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss-of-Function Variants in Schizophrenia Risk and SETD1A as a Candidate Susceptibility Gene

(2014) Atsushi Takata et al.   NEURON

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Human-specific CpG ‘beacons’ identify human-specific prefrontal cortex H3K4me3 chromatin peaks

(2014) Christopher G Bell et al.   Epigenomics

Primate evolution of the recombination regulator PRDM9

(2014) Jerrod J. Schwartz et al.   Nature Communications

Elfn1 recruits presynaptic mGluR7 in trans and its loss results in seizures

(2014) Naoko H. Tomioka et al.   Nature Communications

Dynamic expression of MEIS1 homeoprotein in E14.5 forebrain and differentiated forebrain-derived neural stem cells

(2013) Benjamin A. Barber et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression

(2013) Jerry Guintivano et al.   Epigenetics

Insulin suppresses distal-less homeobox 5 expression through the up-regulation of microRNA-124 in 3T3-L1 cells

(2013) Abdul S. Qadir et al.   EXPERIMENTAL CELL RESEARCH

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinated Cell Type–Specific Epigenetic Remodeling in Prefrontal Cortex Begins before Birth and Continues into Early Adulthood

(2013) Hennady P. Shulha et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

(2012) Michael E. Talkowski et al.   CELL

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Intra-axonal Translation of SMAD1/5/8 Mediates Retrograde Regulation of Trigeminal Ganglia Subtype Specification

(2012) Sheng-Jian Ji et al.   NEURON

Elfn1 Regulates Target-Specific Release Probability at CA1-Interneuron Synapses

(2012) E. L. Sylwestrak et al.   SCIENCE

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

(2012) Hennady P. Shulha et al.   PLOS BIOLOGY

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

(2012) Jun Zhu et al.   PLOS BIOLOGY

Epigenetic Signatures of Autism

(2011) Hennady P. Shulha   ARCHIVES OF GENERAL PSYCHIATRY

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Genome-wide Maps of Histone Modifications Unwind In Vivo Chromatin States of the Hair Follicle Lineage

(2011) Wen-Hui Lien et al.   Cell Stem Cell

Path lengths in protein-protein interaction networks and biological complexity

(2011) Ke Xu et al.   PROTEOMICS

Rare mutations in N-methyl-D-aspartate glutamate receptors in autism spectrum disorders and schizophrenia

(2011) J Tarabeux et al.   Translational Psychiatry

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Dlx5 and Dlx6 Regulate the Development of Parvalbumin-Expressing Cortical Interneurons

(2010) Y. Wang 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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex

(2010) I. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination

(2010) S. Myers et al.   SCIENCE

hPDI: a database of experimental human protein-DNA interactions

(2009) Z. Xie et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cingulate White Matter Neurons in Schizophrenia and Bipolar Disorder

(2009) Caroline M. Connor et al.   BIOLOGICAL PSYCHIATRY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

TGF -Smad2 Signaling Regulates the Cdh1-APC/SnoN Pathway of Axonal Morphogenesis

(2008) J. Stegmuller et al.   JOURNAL OF NEUROSCIENCE

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY