Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders

Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

(2021) Gloriia Novikova et al.   Nature Communications

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

(2020) F. Kyle Satterstrom et al.   CELL

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

(2020) Arya Kaul et al.   Nature Protocols

Chromatin accessibility dynamics in a model of human forebrain development

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A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons

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Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration

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A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles

(2020) Nancy Y. A. Sey et al.   NATURE NEUROSCIENCE

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

(2020) Matthew Halvorsen et al.   Nature Communications

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

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

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Genome-wide association study identifies 30 loci associated with bipolar disorder

(2019) Eli A. Stahl et al.   NATURE GENETICS

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

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The Major Risk Factors for Alzheimer’s Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques

(2019) Carlo Sala Frigerio et al.   Cell Reports

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation

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Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

(2019) Elizabeth K. Ruzzo et al.   CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

A compendium of promoter-centered long-range chromatin interactions in the human genome

(2019) Inkyung Jung et al.   NATURE GENETICS

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

(2019) Alexandra Grubman et al.   NATURE NEUROSCIENCE

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

(2019) Alexi Nott et al.   SCIENCE

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

(2019) Phil H. Lee et al.   CELL

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

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

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

Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome

(2018) Kiran Girdhar et al.   NATURE NEUROSCIENCE

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

(2018) Alexey Kozlenkov et al.   Science Advances

A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex

(2018) Sarah J. Marzi et al.   NATURE NEUROSCIENCE

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

(2018) Michael J. Gandal et al.   SCIENCE

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

(2018) Prashanth Rajarajan et al.   SCIENCE

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci

(2017) John F Fullard et al.   HUMAN MOLECULAR GENETICS

Transcriptome alterations of prefrontal cortical parvalbumin neurons in schizophrenia

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(2017) Shane A. Liddelow et al.   NATURE

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

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer’s Disease

(2017) Nicholas T. Seyfried et al.   Cell Systems

Chromosome conformation elucidates regulatory relationships in developing human brain

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NeuN+ neuronal nuclei in non-human primate prefrontal cortex and subcortical white matter after clozapine exposure

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

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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment

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(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

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

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Genetic variation within transcriptional regulatory elements and its implications for human disease

(2014) Alvaro Rada-Iglesias   BIOLOGICAL CHEMISTRY

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

(2013) Neelroop N. Parikshak et al.   CELL

Increased expression of BIN1 mediates Alzheimer genetic risk by modulating tau pathology

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Polygenic dissection of diagnosis and clinical dimensions of bipolar disorder and schizophrenia

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

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functional gene group analysis identifies synaptic gene groups as risk factor for schizophrenia

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REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

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Astrocytes are important mediators of Aβ-induced neurotoxicity and tau phosphorylation in primary culture

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The role of microglia in amyloid clearance from the AD brain

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Molecular Determinants of Dysregulated GABAergic Gene Expression in the Prefrontal Cortex of Subjects with Schizophrenia

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AMPH-1/Amphiphysin/Bin1 functions with RME-1/Ehd1 in endocytic recycling

(2009) Saumya Pant et al.   NATURE CELL BIOLOGY

The IRF Family Transcription Factors in Immunity and Oncogenesis

(2008) Tomohiko Tamura et al.   Annual Review of Immunology

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(2008) Yong Zhang et al.   GENOME BIOLOGY

Neuronal Nuclei Isolation from Human Postmortem Brain Tissue

(2008) Anouch Matevossian et al.   Jove-Journal of Visualized Experiments