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Leveraging functional annotation to identify genes associated with complex diseases

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression
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Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test
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Colocalization of GWAS and eQTL Signals Detects Target Genes
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Functional Architectures of Local and Distal Regulation of Gene Expression in Multiple Human Tissues
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Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS
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TIGAR: An Improved Bayesian Tool for Transcriptomic Data Imputation Enhances Gene Mapping of Complex Traits
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The Role of Chromatin during Transcription
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Trans Effects on Gene Expression Can Drive Omnigenic Inheritance
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A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers
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Genetic interactions associated with 12-month atrophy in hippocampus and entorhinal cortex in Alzheimer's Disease Neuroimaging Initiative
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Histone modifications in transcriptional regulation
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Roadmap for regulation
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Histone modifications at human enhancers reflect global cell-type-specific gene expression
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An integrated encyclopedia of DNA elements in the human genome
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Mapping cis- and trans-regulatory effects across multiple tissues in twins
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Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease
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A gene-based association method for mapping traits using reference transcriptome data
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Partitioning heritability by functional annotation using genome-wide association summary statistics
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Integrative approaches for large-scale transcriptome-wide association studies
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Case–control association mapping by proxy using family history of disease
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Estimating the selective effects of heterozygous protein-truncating variants from human exome data
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CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants
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ChromHMM: automating chromatin-state discovery and characterization
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Liver X receptors in lipid metabolism: opportunities for drug discovery
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A brief history of human disease genetics
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A statistical framework for cross-tissue transcriptome-wide association analysis
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Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome
inferredcites →https://doi.org/10.1073/pnas.1503027112openalex-snapshot
Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression
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Activation of Asparaginyl Endopeptidase Leads to Tau Hyperphosphorylation in Alzheimer Disease
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Variational Bayes for High-Dimensional Linear Regression With Sparse Priors
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A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project
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CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies
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GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
inferredcites →https://doi.org/10.1093/hmg/ddp413openalex-snapshot
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB
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Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells
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INFERNO: inferring the molecular mechanisms of noncoding genetic variants
inferredcites →https://doi.org/10.1101/108316openalex-snapshot
Modeling prediction error improves power of transcriptome-wide association studies
inferredcites →https://doi.org/10.1101/334979openalex-snapshot
TMEM135 is an LXR-inducible regulator of peroxisomal metabolism
inferredcites →https://doi.org/10.1101/gr.155192.113openalex-snapshot
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
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Regularization and Variable Selection Via the Elastic Net
inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
inferredcites →https://doi.org/10.1186/1471-2105-14-128openalex-snapshot
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
inferredcites →https://doi.org/10.1186/gb-2011-12-2-r15openalex-snapshot
A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets
inferredcites →https://doi.org/10.1186/gb-2012-13-9-r53openalex-snapshot
Modeling gene expression using chromatin features in various cellular contexts
inferredcites →https://doi.org/10.1186/s13059-016-1142-6openalex-snapshot
Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
inferredcites →https://doi.org/10.1214/12-ba703openalex-snapshot
Scalable Variational Inference for Bayesian Variable Selection in Regression, and Its Accuracy in Genetic Association Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1000294openalex-snapshot
Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans
inferredcites →https://doi.org/10.1371/journal.pgen.1003264openalex-snapshot
Polygenic Modeling with Bayesian Sparse Linear Mixed Models
inferredcites →https://doi.org/10.1371/journal.pgen.1003709openalex-snapshot
Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1006646openalex-snapshot
Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization
inferredcites →https://doi.org/10.1371/journal.pgen.1006933openalex-snapshot
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease
inferredcites →https://doi.org/10.1534/genetics.117.300270openalex-snapshot
A Powerful Framework for Integrating eQTL and GWAS Summary Data
inferredcites →https://doi.org/10.2174/156720508783884675openalex-snapshot
Functional Role of Lipoprotein Receptors in Alzheimers Disease
inferredcites →https://doi.org/10.3233/jad-2008-14210openalex-snapshot
Evaluation of Coenzyme Q as an Antioxidant Strategy for Alzheimer's Disease
inferredcites →https://doi.org/10.3389/fnins.2015.00405openalex-snapshot
Defects in the COG complex and COG-related trafficking regulators affect neuronal Golgi function
inferredcites →https://doi.org/10.34944/dspace/4648openalex-snapshot
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics
inferredcites →https://doi.org/10.48550/arxiv.1709.06597openalex-snapshot
varbvs: Fast Variable Selection for Large-scale Regression

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1371/journal.pgen.1010825openalex-snapshot
A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases
inferred← citeshttps://doi.org/10.21203/rs.3.rs-275314/v1openalex-snapshot
A Statistical Framework to Identify Cell Types Whose Genetically Regulated Proportions are Associated with Complex Diseases
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