Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia

Bayesian multiple logistic regression for case-control GWAS

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Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

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

(2019) Michael Song et al.   NATURE GENETICS

Genetic mapping of cell type specificity for complex traits

(2019) Kyoko Watanabe et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

More than just Stem Cells: Functional Roles of the Transcription Factor Sox2 in Differentiated Glia and Neurons

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Neurobiological functions of transcriptional enhancers

(2019) Alex S. Nord et al.   NATURE NEUROSCIENCE

Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease

(2018) Paul W. Hook et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

(2018) Douglas M. Ruderfer et al.   CELL

An atlas of chromatin accessibility in the adult human brain

(2018) John F. Fullard et al.   GENOME RESEARCH

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

(2018) Farhad Hormozdiari 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

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

(2018) Hilary K. Finucane 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

Analysis of shared heritability in common disorders of the brain

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Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot

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Global dynamics of stage-specific transcription factor binding during thymocyte development

(2018) Tomonori Hosoya et al.   Scientific Reports

Enrichment of schizophrenia heritability in both neuronal and glia cell regulatory elements

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GWAS on family history of Alzheimer’s disease

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Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia

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A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Long noncoding RNA Sox2ot and transcription factor YY1 co-regulate the differentiation of cortical neural progenitors by repressing Sox2

(2018) Jennifer L. Knauss et al.   Cell Death & Disease

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons

(2018) Sarah A. McClymont et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces 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

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

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Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

(2017) Lucas T Gray et al.   eLife

Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors

(2017) Andrew E. O. Hughes et al.   Scientific Reports

Improved methods for multi-trait fine mapping of pleiotropic risk loci

(2016) Gleb Kichaev et al.   BIOINFORMATICS

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar et al.   NATURE

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Microglia development follows a stepwise program to regulate brain homeostasis

(2016) O. Matcovitch-Natan et al.   SCIENCE

Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies

(2015) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites: Fig. 1.

(2015) Simon G. Coetzee et al.   BIOINFORMATICS

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

(2015) Olgert Denas et al.   BMC GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

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Long non-coding RNA SOX2OT: expression signature, splicing patterns, and emerging roles in pluripotency and tumorigenesis

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How to make a hippocampal dentate gyrus granule neuron

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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

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

(2014) Gleb Kichaev et al.   PLoS Genetics

Sox2, a key factor in the regulation of pluripotency and neural differentiation

(2014) Shuchen Zhang   World Journal of Stem Cells

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

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A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

A Polymorphism in IRF4 Affects Human Pigmentation through a Tyrosinase-Dependent MITF/TFAP2A Pathway

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(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

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

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

An integrated encyclopedia of DNA elements in the human genome

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Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

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Complex architecture and regulated expression of the Sox2ot locus during vertebrate development

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Impaired generation of mature neurons by neural stem cells from hypomorphic Sox2 mutants

(2008) M. Cavallaro et al.   DEVELOPMENT

Identification of loci associated with schizophrenia by genome-wide association and follow-up

(2008) Michael C O'Donovan et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY