Braeden K. Ego
A5062525503- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Bacterial Genetics and Biotechnology
- Neurogenetic and Muscular Disorders Research
- Calcium signaling and nucleotide metabolism
- Immune Cell Function and Interaction
- Cellular transport and secretion
- IL-33, ST2, and ILC Pathways
- Eosinophilic Esophagitis
- Immunodeficiency and Autoimmune Disorders
- Phagocytosis and Immune Regulation
- Genomics and Rare Diseases
- Insect Resistance and Genetics
- Endoplasmic Reticulum Stress and Disease
- Neuroinflammation and Neurodegeneration Mechanisms
Stanford University
2018-2023
Boston University
2023
Harvard University
2023
Abstract Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects these experiments have not been systematically evaluated. Here, we investigate Cas9, dCas9, and CRISPRi/a activity essential elements. The sgRNAs with largest genome-scale CTCF loop anchors K562 cells were single guide RNAs (sgRNAs) that disrupted gene expression near on-target anchor. Rather, had high that, while only weakly...
Abstract Introduction The Undiagnosed Diseases Network (UDN), a clinical research study funded by the National Institutes of Health, aims to provide answers for patients with undiagnosed conditions and generate knowledge about underlying disease mechanisms. UDN evaluations involve collaboration between clinicians researchers go beyond what is possible in settings. While medical outcomes have been explored, this first formal assessment patient caregiver experience. Methods We invited...
Abstract Background Over the past decade, human Interleukin 33 (hIL-33) has emerged as a key contributor to pathogenesis of numerous inflammatory diseases. Despite existence several commercial hIL-33 assays spanning multiple platform technologies, their ability provide accurate concentration measurements and differentiate between active (reduced) inactive (oxidized) in various matrices remains uncertain. This is especially true for lower sample volumes, with low concentrations, elevated...
Abstract Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects these experiments not been systematically evaluated. Here, we conducted genome-scale screen essential CTCF loop anchors K562 leukemia cell line. Surprisingly, primary drivers of signal this were single guide RNAs (sgRNAs) with low specificity scores. After removing guides, found that there no critical growth. We...
Summary Thousands of proteins localize to the nucleus; however, it remains unclear which contain transcriptional effectors. Here, we develop HT-recruit - a pooled assay where protein libraries are recruited reporter, and their effects measured by sequencing. Using this approach, measure gene silencing activation for thousands domains. We find relationship between repressor function evolutionary age KRAB domains, discover Homeodomain strength is collinear with Hox genetic organization,...