A5049861618- Pancreatic function and diabetes
- Diabetes and associated disorders
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Diabetes Management and Research
- CRISPR and Genetic Engineering
- HIV Research and Treatment
- Epigenetics and DNA Methylation
- Machine Learning in Bioinformatics
- Respiratory viral infections research
- RNA modifications and cancer
- Digestive system and related health
- Natural Language Processing Techniques
- T-cell and B-cell Immunology
- Endoplasmic Reticulum Stress and Disease
- Extracellular vesicles in disease
- Bioinformatics and Genomic Networks
- Diet and metabolism studies
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Neonatal Respiratory Health Research
- Biomedical Text Mining and Ontologies
- Advanced biosensing and bioanalysis techniques
- Nutrition, Genetics, and Disease
- SARS-CoV-2 and COVID-19 Research
University of California, San Diego
2020-2023
University of Nevada, Las Vegas
2016-2022
UC San Diego Health System
2022
Respiratory failure associated with COVID-19 has placed focus on the lungs. Here, we present single-nucleus accessible chromatin profiles of 90,980 nuclei and matched transcriptomes 46,500 in non-diseased lungs from donors ~30 weeks gestation,~3 years years. We mapped candidate
Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) genotyping in peripheral blood mononuclear cells from 13 individuals. Clustering chromatin accessibility profiles 96,002 total nuclei identified 17 immune types sub-types. We mapped QTLs (caQTLs) each sub-type using individuals European...
We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta cell survival in response proinflammatory cytokines. mapped 38,931 cytokine-responsive candidate cis-regulatory elements (cCREs) cells using ATAC-seq snATAC-seq linked them target genes co-accessibility HiChIP. Using a genome-wide CRISPR screen EndoC-βH1 cells, we identified 867 affecting cytokine-induced survival, promoting up-regulated cytokines were enriched...
SUMMARY Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) human lung, generated in parallel with snRNA-seq (46,500 nuclei), from healthy donors ~30 weeks, ~3 years age. Focusing on genes implicated SARS-CoV-2 cell entry, observed an increase proportion alveolar epithelial cells expressing ACE2 TMPRSS2 adult compared to young lungs. Consistent expression...
High-throughput assay systems have had a large impact on understanding the mechanisms of basic cell functions. However, high-throughput assays that directly assess molecular functions are limited. Herein, we describe “GigaAssay”, modular one-pot system for measuring thousands genetic variants at once. In this system, each was infected with one virus from library encoding Tat mutant proteins, viral particle random unique identifier (UMI). We demonstrate proof concept by transcription GFP...
All translated proteins end with a carboxylic acid commonly called the C-terminus. Many short functional sequences (minimotifs) are located on or immediately proximal to However, information about function of protein C-termini has not been consolidated into single source. Here, we built new "C-terminome" database and web system focused human proteins. Approximately 3,600 in proteome have minimotif an established molecular function. To help evaluate remaining proteome, inferred minimotifs...
Dietary guidelines recommended by key health agencies are generally designed for a global population. However, ethnicity affects human disease and environment-gene interactions, including nutrient intake. Historically, isolated populations with different genetic backgrounds have adapted to distinct environments varying food sources. Ethnicity is relevant the interaction of intake genes susceptibility; yet major do not recommend nutrients codified population genotypes their frequencies. In...
Abstract Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) genotyping in peripheral blood mononuclear cells from 10 individuals. Clustering chromatin accessibility profiles 66,843 total nuclei identified 14 immune types sub-types. We mapped QTLs (caQTLs) each sub-type which 6,248 caQTLs,...
ABSTRACT Beta cells intrinsically contribute to the pathogenesis of type 1 diabetes (T1D), but genes and molecular processes that mediate beta cell survival in T1D remain largely unknown. We combined high throughput functional genomics human genetics identify risk loci regulating affecting response proinflammatory cytokines IL-1β, IFNγ, TNFα. mapped 38,931 cytokine-responsive candidate cis -regulatory elements (cCREs) active using ATAC-seq single nuclear (snATAC-seq), linked cCREs putative...
The C-termini of proteins often possess minimotifs (also known as short linear motifs). Minimotifs are 2–15 amino acids long contiguous peptide sequences with a function in at least one protein. regulate cellular functions by binding to other molecules cell, trafficking different compartments, and through post-translational modifications. analysis ~550,000 from the Minimotif Miner 3.0 database revealed 3,593 on human proteins. These encoded 13% genes. We asked if remaining 87% genes also...
Abstract High-throughput assay systems have had a disproportionally large impact on uncovering how cells function, as well misregulation can lead to disease. However, no high-throughput been developed systematically address mutations molecular functions or cell processes in human cells. This is arguably one of the most critical assays because pathology and treatment are largely based upon functions. To this challenge, herein we engineered, developed, tested first modular function system....