Diane E. Dickel

This study uses deep mutational scanning to analyze TYK2 variants and their impact on function and drug response, identifying novel therapeutic targets and degradation strategies.

The paper identifies hidden enhancers in mouse embryos that are not detected by conventional chromatin profiling methods, highlighting a significant gap in enhancer discovery.

The paper identifies a conserved cis-acting element, REX, that enables extreme long-range enhancer-promoter interactions in mammals by increasing the genomic interaction range of enhancers.

The paper maps the mutagenic sensitivity of human enhancers in vivo by systematically mutating enhancer sequences and using predictive modeling to identify critical nucleotides.

This study applies high-resolution deep mutational scanning to the melanocortin-4 receptor to identify functionally significant variants and guide drug development.

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.

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

The paper identifies combinatorial TF-cRE interactions in mouse basal ganglia development, revealing modules that drive GABAergic neurogenesis and suppress other fates.

The paper examines 3D enhancer-promoter interactions during mammalian development, finding that most enhancers bypass neighboring genes and show tissue-specific conformations with increased interactions upon activation.

The paper reconstructs a gene regulatory network directed by PBX1/2 and HAND2 in mouse limb development, showing their genetic interaction and tissue-specific function.

The paper identifies 14,000 human craniofacial enhancers across developmental stages and shows 56% are conserved in mice, providing cell type- and stage-specific activity profiles.

The paper identifies widespread epigenomic changes in idiopathic dilated cardiomyopathy, showing a shift toward fetal-like enhancer states and providing a data resource for further study.

The paper uses single-cell RNA sequencing to systematically phenotype mouse genetic models, identifying molecular and cellular changes across multiple mutants and wildtypes.

The paper identifies a transcription factor network and enhancers involved in cortical regional patterning using mouse embryonic data.

Whole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3.

This study shows that deleting TAD boundaries in mice often causes molecular or developmental phenotypes, highlighting their importance for genome function.

This study shows that deleting a non-canonical regulatory region of Scn1a in mice leads to reduced Scn1a expression and epileptic symptoms.

This study identifies a gene desert critical for Shox2 regulation and embryonic survival through enhancer networks in mouse development.

The paper quantifies the mouse embryo transcriptome from E10.5 to birth using whole-tissue and single-cell RNA-seq, identifying key gene expression patterns and cell types.

The paper maps DNA methylation changes across 12 mouse tissues at 8 developmental stages, identifying methylation variant regions and tissue-specific enhancers linked to human genetic diseases.

This paper develops a cross-organism framework for enhancer prediction using Drosophila STARR-seq data and supervised machine learning, validated in mouse and human with 153 enhancers.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

The paper identifies Parkinson's risk variants in a SNCA enhancer by analyzing open chromatin in mouse dopamine neurons and validates their function in zebrafish and mice.

The paper uses single nucleus ATAC-seq to analyze chromatin accessibility in mouse forebrain development, identifying cell-type-specific regulatory sequences and transcriptional regulators.