Chromatin accessibility dynamics in a model of human forebrain development

Chromatin accessibility and the regulatory epigenome

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

Malformations of Cerebral Cortex Development: Molecules and Mechanisms

(2019) Gordana Juric-Sekhar et al.   Annual Review of Pathology-Mechanisms of Disease

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

Organoid single-cell genomic atlas uncovers human-specific features of brain development

(2019) Sabina Kanton et al.   NATURE

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

(2018) Antonio F. Pardiñas et al.   NATURE GENETICS

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

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Generation and assembly of human brain region–specific three-dimensional cultures

(2018) Steven A. Sloan et al.   Nature Protocols

Reliability of human cortical organoid generation

(2018) Se-Jin Yoon et al.   NATURE METHODS

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces 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

Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

(2017) Anastasia Levchenko et al.   Genome Biology and Evolution

Assembly of functionally integrated human forebrain spheroids

(2017) Fikri Birey et al.   NATURE

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

Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells

(2017) Steven A. Sloan et al.   NEURON

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

(2016) Evgeny Z. Kvon et al.   CELL

TBR1 regulates autism risk genes in the developing neocortex

(2016) James H. Notwell et al.   GENOME RESEARCH

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

(2016) John C. Silbereis et al.   NEURON

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Molecular Identity of Human Outer Radial Glia during Cortical Development

(2015) Alex A. Pollen et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

An atlas of genetic correlations across human diseases and traits

(2015) Brendan Bulik-Sullivan et al.   NATURE GENETICS

Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture

(2015) Anca M Paşca et al.   NATURE METHODS

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex

(2015) Andrew E Jaffe et al.   NATURE NEUROSCIENCE

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

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

(2015) Irene Gallego Romero et al.   eLife

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Interneuron cell types are fit to function

(2014) Adam Kepecs et al.   NATURE

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism

(2013) A. Jeremy Willsey et al.   CELL

Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism

(2013) Neelroop N. Parikshak et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

Many human accelerated regions are developmental enhancers

(2013) J. A. Capra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

(2012) Hongkui Zeng et al.   CELL

Multiple Autism-Linked Genes Mediate Synapse Elimination via Proteasomal Degradation of a Synaptic Scaffold PSD-95

(2012) Nien-Pei Tsai et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

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

Functional and Molecular Characterization of the Role of CTCF in Human Embryonic Stem Cell Biology

(2012) Sri Kripa Balakrishnan et al.   PLoS One

Molecular Control of Neurogenesis: A View from the Mammalian Cerebral Cortex

(2012) B. Martynoga et al.   Cold Spring Harbor Perspectives in Biology

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

(2011) D. Kostka et al.   MOLECULAR BIOLOGY AND EVOLUTION

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome

(2011) Sergiu P Paşca et al.   NATURE MEDICINE

Annual Research Review: Development of the cerebral cortex: implications for neurodevelopmental disorders

(2010) John L.R. Rubenstein   JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Uniquely Hominid Features of Adult Human Astrocytes

(2009) N. A. Oberheim et al.   JOURNAL OF NEUROSCIENCE

Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo

(2008) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lhx2 Selector Activity Specifies Cortical Identity and Suppresses Hippocampal Organizer Fate

(2008) V. S. Mangale et al.   SCIENCE