3D promoter architecture re-organization during iPSC-derived neuronal cell differentiation implicates target genes for neurodevelopmental disorders

A practical view of fine-mapping and gene prioritization in the post-genome-wide association era

(2020) R. V. Broekema et al.   Open Biology

Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells

(2020) Chun Su et al.   Nature Communications

Genome-wide association study identifies 30 loci associated with bipolar disorder

(2019) Eli A. Stahl et al.   NATURE GENETICS

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data

(2019) Jonathan Cairns et al.   BIOINFORMATICS

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

(2019) Michael Song et al.   NATURE GENETICS

ETV5 is Essential for Neuronal Differentiation of Human Neural Progenitor Cells by Repressing NEUROG2 Expression

(2019) Yang Liu et al.   Stem Cell Reviews and Reports

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

(2019) Elizabeth K. Ruzzo et al.   CELL

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Neural deletion of Sh2b1 results in brain growth retardation and reactive aggression

(2018) Lin Jiang et al.   FASEB JOURNAL

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence

(2018) Jeanne E. Savage et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

A promoter interaction map for cardiovascular disease genetics

(2018) Lindsey E Montefiori et al.   eLife

KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons

(2018) Zimei Wang et al.   Scientific Reports

Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder

(2018) Ditte Demontis et al.   NATURE GENETICS

BiFET: sequencing Bias-free transcription factor Footprint Enrichment Test

(2018) Ahrim Youn et al.   NUCLEIC ACIDS RESEARCH

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

(2018) Prashanth Rajarajan et al.   SCIENCE

The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders

(2018) Chao Chen et al.   Science Translational Medicine

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci

(2017) John F Fullard et al.   HUMAN MOLECULAR GENETICS

The Heritability of Autism Spectrum Disorder

(2017) Sven Sandin et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Revealing the complex genetic architecture of obsessive–compulsive disorder using meta-analysis

(2017) Paul D Arnold et al.   MOLECULAR PSYCHIATRY

Aberrant iPSC-derived human astrocytes in Alzheimer's disease

(2017) V C Jones et al.   Cell Death & Disease

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

(2017) Paula Freire-Pritchett et al.   eLife

Genome-Wide Association Studies of a Broad Spectrum of Antisocial Behavior

(2017) Jorim J. Tielbeek et al.   JAMA Psychiatry

Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

(2017)   Molecular Autism

FOXP1 Promotes Embryonic Neural Stem Cell Differentiation by Repressing Jagged1 Expression

(2017) Luca Braccioli et al.   Stem Cell Reports

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Generation of human control iPS cell line CHOPWT10 from healthy adult peripheral blood mononuclear cells

(2016) Jean Ann Maguire et al.   Stem Cell Research

Obsessive–compulsive symptoms in a large population-based twin-family sample are predicted by clinically based polygenic scores and by genome-wide SNPs

(2016) A den Braber et al.   Translational Psychiatry

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Discontinuity in the genetic and environmental causes of the intellectual disability spectrum

(2015) Abraham Reichenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Regulation of cerebral cortical neurogenesis by the Pax6 transcription factor

(2015) Martine N. Manuel et al.   Frontiers in Cellular Neuroscience

Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type

(2015) Angela Yen et al.   Nature Communications

Biological interpretation of genome-wide association studies using predicted gene functions

(2015) Tune H. Pers et al.   Nature Communications

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

Heritability of Autism Spectrum Disorder in a UK Population-Based Twin Sample

(2015) Emma Colvert et al.   JAMA Psychiatry

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

(2014) S. Anders et al.   BIOINFORMATICS

New classification for neurodevelopmental disorders in DSM-5

(2014) James C. Harris   CURRENT OPINION IN PSYCHIATRY

Dissecting neural differentiation regulatory networks through epigenetic footprinting

(2014) Michael J. Ziller et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Tcf3 Represses Wnt–β-Catenin Signaling and Maintains Neural Stem Cell Population during Neocortical Development

(2014) Atsushi Kuwahara et al.   PLoS One

Gene Silencing and Polycomb Group Proteins: An Overview of their Structure, Mechanisms and Phylogenetics

(2013) Shahram Golbabapour et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2009) M. D. Robinson et al.   BIOINFORMATICS

AP2γ regulates basal progenitor fate in a region- and layer-specific manner in the developing cortex

(2009) Luisa Pinto et al.   NATURE NEUROSCIENCE

Pax6 promotes neurogenesis in human neural stem cells

(2008) Therése Kallur et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Satb2 Is a Postmitotic Determinant for Upper-Layer Neuron Specification in the Neocortex

(2008) Olga Britanova et al.   NEURON

Concise Review: Pax6 Transcription Factor Contributes to both Embryonic and Adult Neurogenesis as a Multifunctional Regulator

(2008) Noriko Osumi et al.   STEM CELLS