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Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Schizophrenia as a Complex Trait
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BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
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10 Years of GWAS Discovery: Biology, Function, and Translation
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Discovering genome regulation with 3C and 3C-related technologies
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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
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Super-Enhancers in the Control of Cell Identity and Disease
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An Expanded View of Complex Traits: From Polygenic to Omnigenic
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Common Disease Is More Complex Than Implied by the Core Gene Omnigenic Model
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Defining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders
inferredcites →https://doi.org/10.1016/j.cell.2019.12.036openalex-snapshot
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
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A Role for Noncoding Variation in Schizophrenia
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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
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Understanding the genetic liability to schizophrenia through the neuroepigenome
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Breaking TADs: How Alterations of Chromatin Domains Result in Disease
inferredcites →https://doi.org/10.1038/mp.2014.40openalex-snapshot
Copy number variation in schizophrenia in Sweden
inferredcites →https://doi.org/10.1038/nature07239openalex-snapshot
Rare chromosomal deletions and duplications increase risk of schizophrenia
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Integrating common and rare genetic variation in diverse human populations
inferredcites →https://doi.org/10.1038/nature11049openalex-snapshot
Spatial partitioning of the regulatory landscape of the X-inactivation centre
inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot
Topological domains in mammalian genomes identified by analysis of chromatin interactions
inferredcites →https://doi.org/10.1038/nature12644openalex-snapshot
A high-resolution map of the three-dimensional chromatin interactome in human cells
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Obesity-associated variants within FTO form long-range functional connections with IRX3
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Condensin-driven remodelling of X chromosome topology during dosage compensation
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A global reference for human genetic variation
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An integrated map of structural variation in 2,504 human genomes
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Schizophrenia risk from complex variation of complement component 4
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The genetic architecture of type 2 diabetes
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Chromosome conformation elucidates regulatory relationships in developing human brain
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Genetic effects on gene expression across human tissues
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GREAT improves functional interpretation of cis-regulatory regions
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Biological interpretation of genome-wide association studies using predicted gene functions
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Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs
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Genome-wide association analysis identifies 13 new risk loci for schizophrenia
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LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
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Meta-analysis of the heritability of human traits based on fifty years of twin studies
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Partitioning heritability by functional annotation using genome-wide association summary statistics
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An atlas of genetic correlations across human diseases and traits
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Truncating mutations in RBM12 are associated with psychosis
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The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer
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Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
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ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
inferredcites →https://doi.org/10.1038/nmeth.4197openalex-snapshot
Salmon provides fast and bias-aware quantification of transcript expression
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Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders
inferredcites →https://doi.org/10.1038/nn.4399openalex-snapshot
Gene expression elucidates functional impact of polygenic risk for schizophrenia
inferredcites →https://doi.org/10.1038/nn.4402openalex-snapshot
Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia
inferredcites →https://doi.org/10.1038/nrg.2016.112openalex-snapshot
Organization and function of the 3D genome
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Erratum: Organization and function of the 3D genome
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Deciphering non-coding variation with 3D epigenomics
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The statistical properties of gene-set analysis
inferredcites →https://doi.org/10.1038/nrg2611openalex-snapshot
Genetics in geographically structured populations: defining, estimating and interpreting FST
inferredcites →https://doi.org/10.1038/nrm.2016.104openalex-snapshot
Genome-wide mapping and analysis of chromosome architecture
inferredcites →https://doi.org/10.1038/nrm.2016.126openalex-snapshot
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
inferredcites →https://doi.org/10.1038/nrm.2016.138openalex-snapshot
Regulation of disease-associated gene expression in the 3D genome
inferredcites →https://doi.org/10.1038/nrm.2016.151openalex-snapshot
Mapping the 3D genome: Aiming for consilience
inferredcites →https://doi.org/10.1038/nrn.2016.124openalex-snapshot
Spatial genome organization and cognition
inferredcites →https://doi.org/10.1038/s41467-018-05379-yopenalex-snapshot
Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia
inferredcites →https://doi.org/10.1038/s41588-018-0059-2openalex-snapshot
Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection
inferredcites →https://doi.org/10.1038/s41588-018-0081-4openalex-snapshot
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
inferredcites →https://doi.org/10.1038/s41588-018-0129-5openalex-snapshot
Genetic identification of brain cell types underlying schizophrenia
inferredcites →https://doi.org/10.1038/s41588-018-0152-6openalex-snapshot
Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence
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A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex
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Common Genetic Variation and Human Traits
inferredcites →https://doi.org/10.1086/427926openalex-snapshot
Ethnicity and Human Genetic Linkage Maps
inferredcites →https://doi.org/10.1086/514346openalex-snapshot
Mendelian Inheritance in Man and Its Online Version, OMIM
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts570openalex-snapshot
HiCNorm: removing biases in Hi-C data via Poisson regression
inferredcites →https://doi.org/10.1093/bioinformatics/btv650openalex-snapshot
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data
inferredcites →https://doi.org/10.1093/bioinformatics/btw240openalex-snapshot
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data
inferredcites →https://doi.org/10.1093/genetics/166.2.835openalex-snapshot
Molecular and Comparative Genetics of Mental Retardation
inferredcites →https://doi.org/10.1093/hmg/ddi232openalex-snapshot
Factors influencing recombination frequency and distribution in a human meiotic crossover hotspot
inferredcites →https://doi.org/10.1093/molbev/msx154openalex-snapshot
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome
inferredcites →https://doi.org/10.1093/nar/gkt1188openalex-snapshot
1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans
inferredcites →https://doi.org/10.1101/245688openalex-snapshot
Easy Hi-C: A simple efficient protocol for 3D genome mapping in small cell populations
inferredcites →https://doi.org/10.1101/272245openalex-snapshot
Most regulatory interactions are not in linkage disequilibrium
inferredcites →https://doi.org/10.1101/gr.160374.113openalex-snapshot
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
inferredcites →https://doi.org/10.1101/gr.232488.117openalex-snapshot
An atlas of chromatin accessibility in the adult human brain
inferredcites →https://doi.org/10.1101/gr.238022.118openalex-snapshot
Most chromatin interactions are not in linkage disequilibrium
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ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
inferredcites →https://doi.org/10.1126/science.1117196openalex-snapshot
A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome
inferredcites →https://doi.org/10.1126/science.1152850openalex-snapshot
Gene Regulation in the Third Dimension
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
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A Draft Sequence of the Neandertal Genome
inferredcites →https://doi.org/10.1126/science.aag0776openalex-snapshot
Detection of human adaptation during the past 2000 years
inferredcites →https://doi.org/10.1126/science.aap8757openalex-snapshot
Analysis of shared heritability in common disorders of the brain
inferredcites →https://doi.org/10.1126/science.aat7615openalex-snapshot
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
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Comprehensive functional genomic resource and integrative model for the human brain
inferredcites →https://doi.org/10.1128/mcb.01384-09openalex-snapshot
Upregulation of c- MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells
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The Three-Dimensional Organization of Mammalian Genomes
inferredcites →https://doi.org/10.1146/annurev-genet-111212-133526openalex-snapshot
Detecting Natural Selection in Genomic Data
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IQ and Schizophrenia in a Swedish National Sample: Their Causal Relationship and the Interaction of IQ With Genetic Risk
inferredcites →https://doi.org/10.1176/appi.ajp.2017.17030283openalex-snapshot
Psychiatric Genomics: An Update and an Agenda
inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot
WGCNA: an R package for weighted correlation network analysis
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Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-018-1567-1openalex-snapshot
Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders
inferredcites →https://doi.org/10.1186/s13073-017-0497-yopenalex-snapshot
Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders
inferredcites →https://doi.org/10.1192/bjp.bp.106.025585openalex-snapshot
Schizophrenia: a common disease caused by multiple rare alleles
inferredcites →https://doi.org/10.1192/bjp.bp.107.044461openalex-snapshot
Intellectual disability co-occurring with schizophrenia and other psychiatric illness: population-based study
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Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
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Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
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A Map of Recent Positive Selection in the Human Genome
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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
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A Population Genetic Signal of Polygenic Adaptation
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Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders
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Cutadapt removes adapter sequences from high-throughput sequencing reads
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Sex‐stratified genome‐wide meta‐analysis identifies novel loci for cognitive decline in older adults
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Genomewide Association Studies of LRRK2 Modifiers of Parkinson's Disease
inferred← citeshttps://doi.org/10.1016/b978-0-12-819602-1.00002-4openalex-snapshot
Schizophrenia genomics
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HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test
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Emerging Methods and Resources for Biological Interrogation of Neuropsychiatric Polygenic Signal
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Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome
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FIREcaller: Detecting frequently interacting regions from Hi-C data
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Characterizing the polygenic overlaps of bipolar disorder subtypes with schizophrenia and major depressive disorder
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Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome
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3D genome organization in the central nervous system, implications for neuropsychological disorders
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SATB2 organizes the 3D genome architecture of cognition in cortical neurons
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Uncovering the Genetic Architecture of Major Depression
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A systems biology-based identification and in vivo functional screening of Alzheimer’s disease risk genes reveal modulators of memory function
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Unrevealing the shared genetic mechanisms underlying C-reactive protein and schizophrenia
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Comprehensive analysis of shared genetic loci between hippocampal volume and schizophrenia
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Multivariate GWAS of psychiatric disorders and their cardinal symptoms reveal two dimensions of cross-cutting genetic liabilities
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MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples
inferred← citeshttps://doi.org/10.1038/s41380-022-01857-4openalex-snapshot
Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia
inferred← citeshttps://doi.org/10.1038/s41398-020-0765-2openalex-snapshot
Genetic overlap between psychotic experiences in the community across age and with psychiatric disorders
inferred← citeshttps://doi.org/10.1038/s41398-021-01436-1openalex-snapshot
Genetic underpinnings of affective temperaments: a pilot GWAS investigation identifies a new genome-wide significant SNP for anxious temperament in ADGRB3 gene
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Non-coding variability at the APOE locus contributes to the Alzheimer’s risk
inferred← citeshttps://doi.org/10.1038/s41467-020-15707-wopenalex-snapshot
Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
inferred← citeshttps://doi.org/10.1038/s41467-020-20851-4openalex-snapshot
Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries
inferred← citeshttps://doi.org/10.1038/s41467-023-38480-yopenalex-snapshot
The contributions of mitochondrial and nuclear mitochondrial genetic variation to neuroticism
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Genetic architecture distinguishes tinnitus from hearing loss
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Multi-omic spatial effects on high-resolution AI-derived retinal thickness
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Sex-stratified genome-wide association meta-analysis of major depressive disorder
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Association between genes regulating neural pathways for quantitative traits of speech and language disorders
inferred← citeshttps://doi.org/10.1038/s41562-021-01069-wopenalex-snapshot
The genetic architecture of structural left–right asymmetry of the human brain
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Genome-wide meta-analysis of quantitatively measured generalized anxiety symptoms in individuals of European ancestry
inferred← citeshttps://doi.org/10.1038/s41588-019-0439-2openalex-snapshot
Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa
inferred← citeshttps://doi.org/10.1038/s41588-022-01039-6openalex-snapshot
Common variants contribute to intrinsic human brain functional networks
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Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder
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Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK
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The overlapping genetic architecture of psychiatric disorders and cortical brain structure
inferred← citeshttps://doi.org/10.1073/pnas.2200638119openalex-snapshot
Using neuroimaging genomics to investigate the evolution of human brain structure
inferred← citeshttps://doi.org/10.1073/pnas.2214834120openalex-snapshot
Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness
inferred← citeshttps://doi.org/10.1093/bfgp/elab024openalex-snapshot
Review of multi-omics data resources and integrative analysis for human brain disorders
inferred← citeshttps://doi.org/10.1093/bib/bbae096openalex-snapshot
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
inferred← citeshttps://doi.org/10.1093/cercor/bhae078openalex-snapshot
Neuroimaging genomics as a window into the evolution of human sulcal organization
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Nucleotide excision repair hotspots and coldspots of UV-induced DNA damage in the human genome
inferred← citeshttps://doi.org/10.1101/2020.04.22.054825openalex-snapshot
Combining multivariate genomic approaches to elucidate the comorbidity between ASD and ADHD
inferred← citeshttps://doi.org/10.1101/2020.07.27.222364openalex-snapshot
Statistical model integrating interactions into genotype-phenotype association mapping: an application to reveal 3D-genetic basis underlying Autism
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Common variants contribute to intrinsic human brain functional networks
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Genome-wide association study identifies new locus associated with OCD
inferred← citeshttps://doi.org/10.1101/2022.11.11.516161openalex-snapshot
Cell adhesion molecules play subclass-specific roles in electrophysiological response and Schizophrenia risk
inferred← citeshttps://doi.org/10.1101/2022.12.20.521277openalex-snapshot
DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network
inferred← citeshttps://doi.org/10.1101/2023.06.02.23290906openalex-snapshot
Combined GWAS and single cell transcriptomics uncover the underlying genes and cell types in disorders of gut-brain interaction
inferred← citeshttps://doi.org/10.1101/2024.07.24.24310923openalex-snapshot
Uncovering the multivariate genetic architecture of frailty with genomic structural equation modelling
inferred← citeshttps://doi.org/10.1101/603134openalex-snapshot
Multivariate GWAS of psychiatric disorders and their cardinal symptoms reveal two dimensions of cross-cutting genetic liabilities
inferred← citeshttps://doi.org/10.1101/619288openalex-snapshot
FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data
inferred← citeshttps://doi.org/10.1101/842872openalex-snapshot
Transcriptome-wide association analysis of 211 neuroimaging traits identifies new genes for brain structures and yields insights into the gene-level pleiotropy with other complex traits
inferred← citeshttps://doi.org/10.1111/jcpp.13479openalex-snapshot
Combining multivariate genomic approaches to elucidate the comorbidity between autism spectrum disorder and attention deficit hyperactivity disorder
inferred← citeshttps://doi.org/10.1126/sciadv.add2870openalex-snapshot
Genetic architecture of the white matter connectome of the human brain
inferred← citeshttps://doi.org/10.1126/science.aay6690openalex-snapshot
The genetic architecture of the human cerebral cortex
inferred← citeshttps://doi.org/10.1172/jci.insight.170068openalex-snapshot
Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH
inferred← citeshttps://doi.org/10.1177/2470547020924844openalex-snapshot
Heterogeneity and Polygenicity in Psychiatric Disorders: A Genome-Wide Perspective
inferred← citeshttps://doi.org/10.1186/s11689-022-09429-xopenalex-snapshot
Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm
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A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons
inferred← citeshttps://doi.org/10.1186/s13073-023-01158-7openalex-snapshot
Ultra-low-coverage genome-wide association study—insights into gestational age using 17,844 embryo samples with preimplantation genetic testing
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THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data
inferred← citeshttps://doi.org/10.18699/bgrs/sb-2022-056openalex-snapshot
Maps of chromatin conformation in the cerebral cortex
inferred← citeshttps://doi.org/10.18699/sbb-2022-056openalex-snapshot
Maps of chromatin conformation in the cerebral cortex
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2399024/v1openalex-snapshot
DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network
inferred← citeshttps://doi.org/10.3390/genes13010106openalex-snapshot
Adolescent Verbal Memory as a Psychosis Endophenotype: A Genome-Wide Association Study in an Ancestrally Diverse Sample
inferred← citeshttps://doi.org/10.3390/genes13040586openalex-snapshot
Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization
inferred← citeshttps://doi.org/10.3390/ijms22147612openalex-snapshot
Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits
inferred← citeshttps://doi.org/10.3390/ijms24021428openalex-snapshot
Molecular Landscape of Tourette’s Disorder
inferred← citeshttps://doi.org/10.3390/ijms26083578openalex-snapshot
GWAS by Subtraction to Disentangle RBD Genetic Background from α-Synucleinopathies
inferred← citeshttps://doi.org/10.3390/ijms26146940openalex-snapshot
APOE Genotype-Stratified Meta-Analysis of Cognitive Decline Reveals Novel Loci for Language and Global Cognitive Function in Older Adults
inferred← citeshttps://doi.org/10.34133/cbsystems.0451openalex-snapshot
Hemispheric Asymmetry in the Genetic Overlap between Schizophrenia and White Matter Microstructure
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