Timothy E. Reddy

The paper identifies multi-enhancer regulatory hubs critical for Th17 cell identity by analyzing chromatin accessibility and enhancer function in mouse CD4+ T cell subsets.

The paper presents ENCODE, a comprehensive reference map of the genomic basis of gene regulation, including regulatory elements, transcripts, and their interactions in human and mouse genomes.

The paper introduces a structured pooling method for population-scale STARR-seq experiments, improving detection of rare regulatory variants by increasing signal-to-noise ratio and providing Bayesian effect size estimates.

The paper develops a Bayesian method to infer inheritance patterns of allelic imbalance across trios, improving ASE estimation and linking it to chromatin state and causal variants.

The paper introduces BlueSTARR, a predictive modeling framework trained on whole-genome STARR-seq data to assess variant effects on regulatory functions, revealing purifying selection against loss-of-function and gain-of-function variants.

This study identifies hundreds of new cis-regulatory element-gene connections in the MHC locus using CRISPR screens and single-cell transcriptomics, revealing cell type-specific regulatory mechanisms.

The paper functionally measures allele-specific regulatory element activity across five human genomes to fine map causal variants in eQTLs and chromatin QTLs.

The paper identifies a non-coding variant causing GSD IX γ2, validates its splicing effects, and demonstrates reversal using antisense oligonucleotides.

The paper identifies SMARCA2 as a critical cofactor for a subset of glucocorticoid response genes in A549 cells through a CRISPR screen and functional analysis.

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

The paper evaluates the gene regulatory effects of ten synthetic glucocorticoid receptor ligands using mRNA-seq and STARR-seq, finding their responses correlate with dexamethasone and are not selective to subsets of the molecular GC response.

BEASTIE improves allele-specific expression estimation by addressing phasing uncertainty and genotyping errors, enhancing accuracy in detecting rare variants.

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

This paper introduces a consensus variant-to-function score to prioritize disease-causing variants, showing improved performance in heritability enrichment and fine-mapping.

This paper introduces a CRISPRi system using dHyperLbCas12a for highly multiplexed epigenome editing and demonstrates its application in proliferation and CRE analysis screens.

The paper identifies gene regulatory mechanisms in PCOS-associated loci, showing DENND1A-dependent testosterone elevation through experimental and genetic analyses.

The paper uses CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function, finding BATF3 as a key gene that enhances memory T cell features and improves CAR T cell therapy outcomes.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

The paper introduces TOP, a Bayesian framework that quantifies TF occupancy across many conditions using a single DNase-seq experiment, showing changes in 1500 TF motifs across cell types, hormone exposure, and genetic backgrounds.

The paper screens non-coding regulatory elements in human cells to identify those affecting cell fitness and establishes connections between regulatory elements and target genes.

This paper describes the generation of two transgenic mouse lines for in vivo epigenome editing using CRISPR-based systems to activate or repress gene expression.

The paper introduces BETS, a statistical framework for inferring gene regulatory networks from transcriptional time series data, and validates it using glucocorticoid response data and external sources.

The paper integrates GWAS data with functional genomic annotations of decidual stromal cells to identify loci and target genes associated with gestational duration and preterm birth.

The paper identifies technical biases in STARR-seq data, develops a statistical model to correct them, and improves detection of regulatory elements with better precision and recall.

This paper introduces a nonparametric model, DPGP, to cluster gene expression time series data and demonstrates its effectiveness using simulated and real datasets.

The paper develops mSTARR-seq to quantify DNA methylation effects on regulatory elements, identifies MD regulatory elements, and predicts methylation-gene expression correlations.

The paper evaluates chromatin accessibility in prefrontal cortex samples from schizophrenia cases and controls, finding high heritability enrichment in open chromatin regions but no differential accessibility between groups.

The paper uses Mendelian randomization to study lincRNA regulation of mRNA expression across four tissues, finding linc-eQTLs similar to protein-coding eQTLs and identifying lincRNAs associated with adipose-related traits.