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

Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences

(2019) Richard Karlsson Linnér et al.   NATURE GENETICS

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons

(2019) Simon T. Schafer et al.   NATURE NEUROSCIENCE

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

(2019) Marta Joana Costa Jordão et al.   SCIENCE

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Genome-wide analysis of insomnia in 1,331,010 individuals identifies new risk loci and functional pathways

(2019) Philip R. Jansen et al.   NATURE GENETICS

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

(2019) Ivan Juric et al.   PLoS Computational Biology

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

BIN1 favors the spreading of Tau via extracellular vesicles

(2019) Andrea Crotti et al.   Scientific Reports

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

(2018) Verena M. Link et al.   CELL

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

(2018) Douglas M. Ruderfer et al.   CELL

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

Meta-analysis of genome-wide association studies for neuroticism in 449,484 individuals identifies novel genetic loci and pathways

(2018) Mats Nagel 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

Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

(2018) Gail Davies et al.   Nature Communications

Genetic risk for Alzheimer’s disease is concentrated in specific macrophage and microglial transcriptional networks

(2018) Katherine E. Tansey et al.   Genome Medicine

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Development and validation of a simplified method to generate human microglia from pluripotent stem cells

(2018) Amanda McQuade et al.   Molecular Neurodegeneration

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

(2018) Ditte Demontis et al.   NATURE GENETICS

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

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

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

(2017) Kuan-lin Huang et al.   NATURE NEUROSCIENCE

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells

(2017) Renata Santos et al.   Stem Cell Reports

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications

(2016) Ya Cui et al.   BIOINFORMATICS

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis

(2016) Wouter van Rheenen et al.   NATURE GENETICS

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

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

(2016) Ye Zhang et al.   NEURON

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

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

(2016) B. B. Lake et al.   SCIENCE

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

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

Generation of multiciliated cells in functional airway epithelia from human induced pluripotent stem cells

(2014) A. L. Firth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

(2013) Ashley H Beecham et al.   NATURE GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

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

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY