Integrative functional genomic analysis of human brain development and neuropsychiatric risks

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

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

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

(2018) Douglas M. Ruderfer et al.   CELL

Brain transcriptome databases: a user's guide

(2018) Jason M. Keil et al.   JOURNAL OF NEUROSCIENCE

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

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

Genetic identification of brain cell types underlying schizophrenia

(2018) Nathan G. Skene et al.   NATURE GENETICS

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

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

Early emergence of cortical interneuron diversity in the mouse embryo

(2018) Da Mi et al.   SCIENCE

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

(2018) Michael J. Gandal et al.   SCIENCE

Spatiotemporal transcriptomic divergence across human and macaque brain development

(2018) Ying Zhu et al.   SCIENCE

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Association analysis in over 329,000 individuals identifies 116 independent variants influencing neuroticism

(2017) Michelle Luciano et al.   NATURE GENETICS

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex

(2017) Tomasz J. Nowakowski et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

(2017) Eleanor Wheeler et al.   PLOS MEDICINE

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

(2016) Ryan N. Doan et al.   CELL

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons

(2016) Xavier Caubit et al.   NATURE GENETICS

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

(2016) John C. Silbereis et al.   NEURON

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Tcf4 Regulates Synaptic Plasticity, DNA Methylation, and Memory Function

(2016) Andrew J. Kennedy et al.   Cell Reports

MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders

(2016) Adam J Harrington et al.   eLife

Generating Neuronal Diversity in the Mammalian Cerebral Cortex

(2015) Simona Lodato et al.   Annual Review of Cell and Developmental Biology

Genetic Changes Shaping the Human Brain

(2015) Byoung-Il Bae et al.   DEVELOPMENTAL CELL

Methylomic trajectories across human fetal brain development

(2015) Helen Spiers et al.   GENOME RESEARCH

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

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

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

Genomic Perspectives of Transcriptional Regulation in Forebrain Development

(2015) Alex S. Nord et al.   NEURON

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

(2015) Stephan J. Sanders et al.   NEURON

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis 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

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

(2015) M. Florio et al.   SCIENCE

From trans to cis: transcriptional regulatory networks in neocortical development

(2015) Mikihito Shibata et al.   TRENDS IN GENETICS

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

Basolateral amygdala volume and cell numbers in major depressive disorder: a postmortem stereological study

(2014) Marisa J. Rubinow et al.   Brain Structure & Function

Cell Type-Specific Expression Analysis to Identify Putative Cellular Mechanisms for Neurogenetic Disorders

(2014) X. Xu et al.   JOURNAL OF NEUROSCIENCE

Zac1 Regulates Cell Cycle Arrest in Neuronal Progenitors via Tcf4

(2014) U. Schmidt-Edelkraut et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease

(2014) Mike A Nalls et al.   NATURE GENETICS

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Temporal Specification and Bilaterality of Human Neocortical Topographic Gene Expression

(2014) Mihovil Pletikos et al.   NEURON

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Advanced Heat Map and Clustering Analysis Using Heatmap3

(2014) Shilin Zhao et al.   Biomed Research International

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

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Suleyman Gulsuner 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

Activity-dependent neuronal signalling and autism spectrum disorder

(2013) Daniel H. Ebert et al.   NATURE

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Cortical Evolution: Judge the Brain by Its Cover

(2013) Daniel H. Geschwind et al.   NEURON

Progress in the Genetics of Polygenic Brain Disorders: Significant New Challenges for Neurobiology

(2013) Steven A. McCarroll et al.   NEURON

Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites

(2013) Alexey Kozlenkov et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

(2012) B. S. Pedersen et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Haploinsufficiency ofSOX5at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features

(2012) Allen N. Lamb et al.   HUMAN MUTATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Prolonged myelination in human neocortical evolution

(2012) D. J. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

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

(2011) Carlo Colantuoni et al.   NATURE

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mutations in MEF2C from the 5q14.3q15 microdeletion syndrome region are a frequent cause of severe mental retardation and diminish MECP2 and CDKL5 expression

(2010) Markus Zweier et al.   HUMAN MUTATION

Molecular analysis of neocortical layer structure in the ferret

(2010) Joanna J. Rowell et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis

(2009) Matthew B. Johnson et al.   NEURON

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Amygdala volume in major depressive disorder: a meta-analysis of magnetic resonance imaging studies

(2008) J P Hamilton et al.   MOLECULAR PSYCHIATRY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Why do many psychiatric disorders emerge during adolescence?

(2008) Tomáš Paus et al.   NATURE REVIEWS NEUROSCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY