A5101626525- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Genomic variations and chromosomal abnormalities
- CRISPR and Genetic Engineering
- Chromosomal and Genetic Variations
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Evacuation and Crowd Dynamics
- Crime Patterns and Interventions
- Crime, Illicit Activities, and Governance
- Nuclear Structure and Function
- T-cell and B-cell Immunology
- Structural Health Monitoring Techniques
- Genomics and Phylogenetic Studies
- Hippo pathway signaling and YAP/TAZ
- Traffic and Road Safety
- Optical measurement and interference techniques
- Ubiquitin and proteasome pathways
- Direction-of-Arrival Estimation Techniques
- Glycosylation and Glycoproteins Research
- Wnt/β-catenin signaling in development and cancer
- Cancer-related molecular mechanisms research
- Immunotherapy and Immune Responses
Cleveland Clinic
2020-2024
Cleveland Clinic Lerner College of Medicine
2024
Case Western Reserve University
2015-2024
California State University, Fullerton
2016
Abstract Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools define loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for (SnapHiC), a method that can identify and accuracy data. Using 742 mouse embryonic stem cells, benchmark SnapHiC against number of developed mapping interactions bulk Hi-C. We further demonstrate its use by analyzing...
Abstract The dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to function. Here, we integrate a wide variety genomic data generated by 4D Nucleome Project provide detailed view 3D in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We extensive benchmarking mapping assays these diverse datasets annotate spatial features across scales. reveal rich complexity chromatin domains their sub-nuclear positions,...
Emerging evidence suggests that cryptic translation beyond the annotated translatome produces proteins with developmental or physiological functions. However, functions of non-canonical open reading frames (ORFs) in cancer remain largely unknown. To fill this gap and systematically identify colorectal (CRC) dependency on ORFs, we apply an integrative multiomic strategy, combining ribosome profiling a CRISPR-Cas9 knockout screen large-scale analysis molecular clinical data. Many such ORFs are...
Current pooled CRISPR screens for cis-regulatory elements (CREs), based on transcriptional output changes, are typically limited to characterizing CREs of only one gene. Here, we describe CRISPRpath, a scalable screening strategy parallelly genes linked the same biological pathway and converging phenotypes. We demonstrate ability CRISPRpath simultaneously identifying functional enhancers six in 6-thioguanine–induced DNA mismatch repair using both interference (CRISPRi) nuclease (CRISPRn)...
Single cell Hi-C (scHi-C) technologies enable the study of chromatin spatial organization directly from complex tissues at single resolution. However, identification loops cells is challenging, largely due to extremely sparse data. Our recently developed SnapHiC pipeline provides first tool map scHi-C data, but it computationally intensive. Here we introduce SnapHiC2, which adapts a sliding window approximation when imputing missing contacts in each and reduces both memory usage...
Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens nanometers and up several kilobases resolution single cells. However, computational methods reliably identify loops from such datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed FISH (SnapFISH), process data loops. SnapFISH can known mouse embryonic stem cells with high sensitivity accuracy. In addition,...
Abstract While a rich set of putative cis -regulatory sequences involved in mouse fetal development have been annotated recently on the basis chromatin accessibility and histone modification patterns, delineating their role developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped contacts between promoters distal across genome seven tissues six developmental stages forebrain. We identified 248,620 long-range interactions centered at 14,138...
Crime prevention is a major goal of law-enforcement agencies. Often, these agencies have limited resources and officers available for patrolling responding to calls. However, police visibility can influence individuals not perform criminal acts. Therefore, it necessary the optimize their strategies deter most crime. Previous studies created agent-based models simulate agents interacting in city, indicating “cops on dots” strategy as viable method mitigate large amounts Unfortunately,...
Abstract Single cell Hi-C (scHi-C) analysis has been increasingly used to map the chromatin architecture in diverse tissue contexts, but computational tools define contacts at high resolution from scHi-C data are still lacking. Here, we describe SnapHiC, a method that can identify loops and accuracy data. We benchmark SnapHiC against HiCCUPS, common tool for mapping bulk data, using 742 mouse embryonic stem cells. further demonstrate its utility by analyzing single-nucleus methyl-3C-seq...
Evacuation is a complex social phenomenon with individuals tending to exit confined space as soon possible. Social factors that influence an individual include collision avoidance and conformity others respect the tendency exit. While has been heavily focused on by agent-based models used frequently simulate evacuation scenarios, these typically assume all agents have equal desire scene in given situation. It more likely that, out of those who are exiting, some patient while seek Here, we...
Single-cell high-throughput chromatin conformation capture technologies (scHi-C) has been used to map spatial organization in complex tissues. However, computational tools detect differential contacts (DCCs) from scHi-C datasets development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a pipeline identify DCCs between two datasets. Compared methods designed for bulk Hi-C data, SnapHiC-D detects with high sensitivity accuracy. We cell-type-specific at 10 Kb...
Nucleotide sequences were determined for α1,3 galactosyltransferases (α1,3 GalTs) from several species (bat, mink, dog, sheep, and dolphin) compared with those previously this enzyme members of the galactosyl/N-acetylgalactosyltransferase Gal(NAc)Ts) family enzymes. Sequence comparison newly characterized GalT nucleotide predicted amino acid other α1,3GalT enzymes demonstrated a remarkable level sequence identity at level. The each as an was confirmed by expressing encoded protein...
High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of spatial organization. Most recently, Hi-C-derived enrichment-based including HiChIP PLAC-seq, offer attractive alternatives due to their high signal-to-noise ratio low cost. While a series computational tools been developed for data, methods tailored PLAC-seq data are still under development. Here we present HPTAD, method identify topologically associating domains (TADs)...
Abstract Single cell Hi-C (scHi-C) has been used to map genome organization in complex tissues. However, computational tools detect dynamic chromatin contacts from scHi-C datasets development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a pipeline identify differential (DCCs) between two datasets. Compared methods designed for bulk data, SnapHiC-D detects DCCs with high sensitivity accuracy. We celltype-specific at 10 kilobase resolution mouse hippocampal...
Abstract While a rich set of putative cis -regulatory sequences involved in mouse fetal development has been annotated recently based on chromatin accessibility and histone modification patterns, delineating their role developmentally regulated gene expression continues to be challenging. To fill this gap, we mapped contacts between promoters distal genome-wide seven tissues, for one them, across six developmental stages. We identified 248,620 long-range interactions centered at 14,138...
Abstract Current pooled CRISPR screens for cis -regulatory elements (CREs) can only accommodate one gene based on its expression level. Here, we describe CRISPRpath, a scalable screening strategy parallelly characterizing CREs of genes linked to the same biological pathway and converging phenotypes. We demonstrate ability CRISPRpath simultaneously identifying functional enhancers six in 6-thioguanine-induced DNA mismatch repair using both interference (CRISPRi) nuclease (CRISPRn) approaches....
Abstract Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens nanometer and kilobase resolution single cells. However, computational methods reliably identify loops from such datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed FISH (SnapFISH), process data loops. SnapFISH can known mouse embryonic stem cells with high sensitivity accuracy. In addition,...