Transcriptome and epigenome landscape of human cortical development modeled in organoids

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

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

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

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

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

(2018) Donna M. Werling et al.   NATURE GENETICS

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

(2018) Suhn K. Rhie et al.   Science Advances

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

(2017) Daniel J Weiner et al.   NATURE GENETICS

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

(2017) M Ryan Corces et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families

(2016) Virpi M. Leppa et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure

(2016) Xuyu Qian et al.   CELL

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Genome-wide changes in lncRNA, splicing and regional gene expression patterns in autism

(2016) Neelroop N. Parikshak et al.   NATURE

Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development

(2016) Tomasz J. Nowakowski et al.   NEURON

denovo-db: a compendium of humande novovariants

(2016) Tychele N. Turner et al.   NUCLEIC ACIDS RESEARCH

A systematic variant annotation approach for ranking genes associated with autism spectrum disorders

(2016) Eric Larsen et al.   Molecular Autism

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

(2015) Jessica Mariani et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Excess of rare, inherited truncating mutations in autism

(2015) Niklas Krumm 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

The PsychENCODE project

(2015) Schahram Akbarian et al.   NATURE NEUROSCIENCE

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

(2015) Stephan J. Sanders et al.   NEURON

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

FastRFunctions for Robust Correlations and Hierarchical Clustering

(2015) Peter Langfelder et al.   Journal of Statistical Software

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

The developmental transcriptome of the human brain

(2014) Andrew T.N. Tebbenkamp et al.   CURRENT OPINION IN NEUROLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Most genetic risk for autism resides with common variation

(2014) Trent Gaugler et al.   NATURE GENETICS

Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network

(2013) Suleyman Gulsuner et al.   CELL

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

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

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

The Patterns of Histone Modifications in the Vicinity of Transcription Factor Binding Sites in Human Lymphoblastoid Cell Lines

(2013) Yumin Nie et al.   PLoS One

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Individual common variants exert weak effects on the risk for autism spectrum disorders

(2012) Richard Anney et al.   HUMAN MOLECULAR GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Common genetic variants, acting additively, are a major source of risk for autism

(2012) Lambertus Klei et al.   Molecular Autism

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

(2011) Carlo Colantuoni et al.   NATURE

A more efficient method to generate integration-free human iPS cells

(2011) Keisuke Okita et al.   NATURE METHODS

Efficient generation of transgene-free human induced pluripotent stem cells (iPSCs) by temperature-sensitive Sendai virus vectors

(2011) H. Ban et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Efficient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome

(2009) Noemi FUSAKI et al.   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY