Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

Sex differences in the human brain transcriptome of cases with schizophrenia

(2021) Gabriel E. Hoffman et al.   BIOLOGICAL PSYCHIATRY

Distinct nuclear compartment-associated genome architecture in the developing mammalian brain

(2021) Sajad Hamid Ahanger et al.   NATURE NEUROSCIENCE

Associations Between Schizophrenia Polygenic Liability, Symptom Dimensions, and Cognitive Ability in Schizophrenia

(2021) Sophie E. Legge et al.   JAMA Psychiatry

decorate: differential epigenetic correlation test

(2020) Gabriel E Hoffman et al.   BIOINFORMATICS

Epigenetic mechanisms in schizophrenia and other psychotic disorders: a systematic review of empirical human findings

(2020) Lukasz Smigielski et al.   MOLECULAR PSYCHIATRY

On the existence and functionality of topologically associating domains

(2020) Jonathan A. Beagan et al.   NATURE GENETICS

Chromatin three-dimensional interactions mediate genetic effects on gene expression

(2019) O. Delaneau et al.   SCIENCE

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Markers of glutamate and GABA neurotransmission in the prefrontal cortex of schizophrenia subjects: Disease effects differ across anatomical levels of resolution

(2019) Samuel J. Dienel et al.   SCHIZOPHRENIA RESEARCH

Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks

(2019) Seyed Ali Madani Tonekaboni et al.   GENOME RESEARCH

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder

(2019) Gabriel E. Hoffman et al.   Scientific Data

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics

(2019) Christophe Ambroise et al.   Algorithms for Molecular Biology

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

(2018) Nathan H. Lazar et al.   GENOME RESEARCH

An atlas of chromatin accessibility in the adult human brain

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

Differential activity of transcribed enhancers in the prefrontal cortex of 537 cases with schizophrenia and controls

(2018) Mads E. Hauberg et al.   MOLECULAR PSYCHIATRY

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

(2018) Kiran Girdhar et al.   NATURE NEUROSCIENCE

Computational 3D genome modeling using Chrom3D

(2018) Jonas Paulsen et al.   Nature Protocols

HDAC2-dependent Antipsychotic-like Effects of Chronic Treatment with the HDAC Inhibitor SAHA in Mice

(2018) Mario de la Fuente Revenga et al.   NEUROSCIENCE

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers

(2018) Aziz Khan et al.   Epigenetics

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

(2018) Julien Bryois et al.   Nature Communications

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

(2018) Alexey Kozlenkov et al.   Science Advances

Leveraging Polygenic Functional Enrichment to Improve GWAS Power

(2018) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

dtangle: accurate and robust cell type deconvolution

(2018) Gregory J Hunt et al.   BIOINFORMATICS

PET neuroimaging reveals histone deacetylase dysregulation in schizophrenia

(2018) Tonya M. Gilbert et al.   JOURNAL OF CLINICAL INVESTIGATION

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

HDAC1 links early life stress to schizophrenia-like phenotypes

(2017) Sanaz Bahari-Javan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression of HDAC2 but Not HDAC1 Transcript Is Reduced in Dorsolateral Prefrontal Cortex of Patients with Schizophrenia

(2016) Frederick A. Schroeder et al.   ACS Chemical Neuroscience

Gene expression elucidates functional impact of polygenic risk for schizophrenia

(2016) Menachem Fromer et al.   NATURE NEUROSCIENCE

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

(2015)   NATURE NEUROSCIENCE

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex

(2015) Andrew E Jaffe et al.   NATURE NEUROSCIENCE

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci

(2015) Eilis Hannon et al.   NATURE NEUROSCIENCE

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

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

Substantial DNA methylation differences between two major neuronal subtypes in human brain

(2015) Alexey Kozlenkov et al.   NUCLEIC ACIDS RESEARCH

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

Conducting Meta-Analyses inRwith themetaforPackage

(2015) Wolfgang Viechtbauer   Journal of Statistical Software

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

Loss-of-Function Variants in Schizophrenia Risk and SETD1A as a Candidate Susceptibility Gene

(2014) Atsushi Takata et al.   NEURON

A Role for Noncoding Variation in Schizophrenia

(2014) Panos Roussos et al.   Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

Prefrontal Cortical Dysfunction After Overexpression of Histone Deacetylase 1

(2013) Mira Jakovcevski et al.   BIOLOGICAL PSYCHIATRY

Uniform, optimal signal processing of mapped deep-sequencing data

(2013) Vibhor Kumar et al.   NATURE BIOTECHNOLOGY

Coordinated Cell Type–Specific Epigenetic Remodeling in Prefrontal Cortex Begins before Birth and Continues into Early Adulthood

(2013) Hennady P. Shulha et al.   PLoS Genetics

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Maternal immune activation alters behavior in adult offspring, with subtle changes in the cortical transcriptome and epigenome

(2012) Caroline M. Connor et al.   SCHIZOPHRENIA RESEARCH

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex

(2010) I. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

Isolation of neuronal chromatin from brain tissue

(2008) Yan Jiang et al.   BMC NEUROSCIENCE