Current QB3 Fellows 2025

QB3-UCSC Graduate Fellowship for Innovators

Gali Bai

My research focuses on developing innovative methods to map chromatin accessibility using nanopore long-read sequencing with the ultimate goal of better understanding how epigenetic changes impact RNA processing. In Brooks lab, we designed an end-to-end platform combining Add-seq, a novel method for chromatin accessibility profiling, and NEMO, a deep learning model for accurate detection of DNA modifications from nanopore signals. Unlike traditional approaches requiring nuclei extraction, Add-seq uses a cell-permeable small molecule, angelicin, to crosslink nucleotides in accessible chromatin regions, achieving DNA labeling just from intact cells. The continued development of this approach will allow for single-molecule chromatin accessibility profiling in low-input samples like liquid biopsy and single cells and has great potential in translational research.

Radcliff Huffman

I’m utilizing methods in synthetic chemistry and marine algal enzymology to make new chemical tools to study glutamate receptors within the mammalian brain. The specific family of neuronal receptors I’m targeting are implicated in a wide range of biomedical phenomena from addiction, pain, and neurodegeneration to learning, memory, and synaptic plasticity. However, neuroscientists have very few efficacious tools to interrogate the properties and functions of these receptors. Through the use of biosynthetic enzymes from marine algae I’ve established access to the kainoid class of natural products which are potent neurotoxins as agonists of these glutamate receptors. Additionally I’ve been able to use this framework to create novel kainoids with new functionalities that expand the utility of these neurotoxins to be better tools for neuroscientists studying ionotropic glutamate receptors. 

Viktor Yurevych

I investigate the intricate molecular processes underlying human brain development, particularly focusing on the role of extracellular RNA (exRNA) in early corticogenesis. I utilize human cortical organoids, 3D cell models that mimic the developing brain, to study how exRNA, secreted from cells within vesicles, can act as a signal, conveying information about cellular stress, state, and identity. My work aims to develop non-invasive “liquid biopsy” techniques using exRNA to monitor the health and differentiation of brain organoids, ultimately leading to a deeper understanding of intercellular communication in the developing brain and the identification of biomarkers for neurological disorders. My research explores how exRNA is transferred between cells and the implications for gene expression, offering a new perspective on the mechanisms that govern early human brain development.

Alumni QB3 Fellows 2024

QB3-UCSC Graduate Fellowship for Interdisciplinary Excellence

Jackson Calhoun

I have been a rotation student on the CB3 track for my fellowship year. I have been fortunate to work with the McKinnie and Lokey labs thus far. In the McKinnie Lab I probed the substrate preference and activity of a PLP-dependent enzyme. My work led to the discovery and understanding of interesting background epimerization that the enzyme performs, and also which amino acids it prefers to utilize for its unique beta-substitution. I learned new techniques in NMR-based assays and began work with LC-MS techniques, which both helped validate my results. In the Lokey Lab I have been developing a cyclic peptide library to be tested against RNA structures. I am learning Solid-Phase Synthesis (SPS) of peptides and peptoid structures. I hope to soon test the nearly 200,000 compound library against telomerase RNA (and mutated variants) along with other therapeutically relevant RNAs. In doing so I will be learning how to adapt an affinity column to our RNA-cyclic peptide(peptoid) system, and validate these results through a fluorescence based assay.

Taylor Won

I am doing rotations in the Fall and Winter quarters. In my first rotation, I worked in Dr. Benedict Paten’s lab to assess the performance of a genome assembly polish tool for the pangenome project. I’m doing my second rotation in Dr. Russell Corbett-Detig’s lab on developing a pipeline to generate a phylogeny tree for Candida auris, a fungal species with growing public health concerns. My research interests primarily lie in infectious disease and public health. As I continue my rotation and graduate studies, I want to build expertise in computational skills and become proficient in the field. As a scientist, I aspire to apply my biology and computer science knowledge to aid people with medical needs.

Alumni QB3 Fellows