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

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS

(2018) Amanda Dobbyn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Polygenic Risk Scores in Clinical Psychology: Bridging Genomic Risk to Individual Differences

(2018) Ryan Bogdan et al.   Annual Review of Clinical Psychology

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

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

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

(2018) Sofia A. Quinodoz et al.   CELL

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

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

(2017) Jiaxu Wang et al.   GENOME RESEARCH

Pervasive coexpression of spatially proximal genes is buffered at the protein level

(2017) Georg Kustatscher et al.   Molecular Systems Biology

The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

(2017) Yan Jiang et al.   NATURE GENETICS

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains

(2017) Gabriel E. Hoffman et al.   Nature Communications

Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes

(2017) Seok-Man Ho et al.   Stem Cell Reports

An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells

(2017) Julia TCW et al.   Stem Cell Reports

Rapid Ngn2-induction of excitatory neurons from hiPSC-derived neural progenitor cells

(2016) Seok-Man Ho et al.   METHODS

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

Gene expression elucidates functional impact of polygenic risk for schizophrenia

(2016) Menachem Fromer et al.   NATURE NEUROSCIENCE

Spatial genome organization and cognition

(2016) Prashanth Rajarajan et al.   NATURE REVIEWS NEUROSCIENCE

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells

(2016) Aaron Topol et al.   Cell Reports

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

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

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

(2015)   NATURE NEUROSCIENCE

Lineage Tracing Using Cux2-Cre and Cux2-CreERT2 Mice

(2015) Cristina Gil-Sanz et al.   NEURON

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

The Ubiquitin Ligase RNF220 Enhances Canonical Wnt Signaling through USP7-Mediated Deubiquitination of  -Catenin

(2014) P. Ma et al.   MOLECULAR AND CELLULAR BIOLOGY

Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia

(2014) K Brennand et al.   MOLECULAR PSYCHIATRY

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Conserved Higher-Order Chromatin Regulates NMDA Receptor Gene Expression and Cognition

(2014) Rahul Bharadwaj et al.   NEURON

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Dendrite Development Regulated by the Schizophrenia-Associated Gene FEZ1 Involves the Ubiquitin Proteasome System

(2014) Yasuhito Watanabe et al.   Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

The Genome in Three Dimensions: A New Frontier in Human Brain Research

(2013) Amanda C. Mitchell et al.   BIOLOGICAL PSYCHIATRY

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

(2013) Suleyman Gulsuner et al.   CELL

Clustered protocadherins

(2013) W. V. Chen et al.   DEVELOPMENT

Conserved Chromosome 2q31 Conformations Are Associated with Transcriptional Regulation of GAD1 GABA Synthesis Enzyme and Altered in Prefrontal Cortex of Subjects with Schizophrenia

(2013) R. Bharadwaj et al.   JOURNAL OF NEUROSCIENCE

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Mutations in ANO3 Cause Dominant Craniocervical Dystonia: Ion Channel Implicated in Pathogenesis

(2012) Gavin Charlesworth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

Biochemical Fractionation and Stable Isotope Dilution Liquid Chromatography-mass Spectrometry for Targeted and Microdomain-specific Protein Quantification in Human Postmortem Brain Tissue

(2012) Matthew L. MacDonald et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Diverse types of genetic variation converge on functional gene networks involved in schizophrenia

(2012) Sarah R Gilman et al.   NATURE NEUROSCIENCE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Molecular codes for neuronal individuality and cell assembly in the brain

(2012) Takeshi Yagi   Frontiers in Molecular Neuroscience

Modelling schizophrenia using human induced pluripotent stem cells

(2011) Kristen J. Brennand et al.   NATURE

A CaMKIIβ signaling pathway at the centrosome regulates dendrite patterning in the brain

(2011) Sidharth V Puram et al.   NATURE NEUROSCIENCE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Post-Synaptic Density of Human Postmortem Brain Tissues: An Experimental Study Paradigm for Neuropsychiatric Illnesses

(2009) Chang-Gyu Hahn et al.   PLoS One

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY