Nonsense-mediated mRNA decay (NMD) is a translation-coupled quality control pathway that degrades mRNAs that harbor a premature termination codon (PTC) and 5-30% of normal cellular mRNAs. The NMD field sits […]
The COVID-19 pandemic generated genomic data at unprecedented scale, with tens of millions of SARS-CoV-2 genomes deposited in public repositories and thousands of new sequences added each day. This dissertation develops methods for analyzing genomic datasets at this scale, unified by the idea that encoding genomes according to their evolutionary relationships can make otherwise intractable […]
Host-microbe systems are core to some of biology’s most consequential interactions, from the pathogens that drive infectious disease to symbionts affecting agricultural pest control and vector-borne disease transmission. Yet unlike the model organisms that have driven most of modern molecular biology, the microbes at the center of these interactions are rarely genetically tractable: many cannot […]
Genomes are often viewed as cooperative systems in which genes work together to support organismal function. Yet genetic elements can also act in ways that favor their own transmission or persistence, creating conflict within the genome. In this talk, I examine the evolutionary and functional consequences of such genomic conflict across three systems. First, I […]
Alternative splicing, the process generating different RNA isoforms from a single gene, is considered one of the main factors driving increased organism complexity in eukaryotes. Variations in isoform and gene […]
This event celebrates and highlights the work of UCSC graduate students in all academic divisions. Enrolled graduate students will present either a poster, talk, or mixed media presentation. Judges will select and award a top prize for each academic division. This event is free and open to the public. Location : Science Hill Research talks […]
Intracellular symbionts are microorganisms, such as bacteria, that live within host cells. These associations are widespread throughout the invertebrate tree of life, and can perform a diversity of key metabolic, immune-response, or other functions that the host is dependent on for survival or reproduction. Intracellular symbioses allow both the host and the symbiont to occupy […]
Please join us for our BME 280B seminar series Thursday (5/28/26) in person at Biomed 200. The event will run from 11:40 AM to 1:15 PM and feature our 4th […]
Presenter: Dylan Shropshire, Assistant Professor in the Department of Biological Sciences, Lehigh University Description: Maternally transmitted Wolbachia bacteria inhabit roughly half of all arthropod species, making them likely the most common animal-associated microbe on Earth. Wolbachia alter host reproduction, persist across deep evolutionary timescales, and move into new host species in ways that we are only beginning to resolve. Wolbachia’s […]
Sequencing technologies have revolutionized our understanding of biology, yet many existing methods require fragmentation of DNA or RNA, fundamentally limiting our ability to study these molecules in their native, intact forms. Long-read sequencing overcomes this constraint by enabling the sequencing of long, single-molecule native DNA and RNA, providing simultaneous access to both sequence and base […]
Presenter: Dr. Magdalena Zernicka-Goetz, Bren Professor of Biology and Biological Engineering, California Institute of Technology Description: N/A Bio: Magdalena Zernicka-Goetz is a Bren Professor of Biology and Biological Engineering at the California Institute of Technology. Over the past 25 years, the Zernicka-Goetz Lab has pioneered key discoveries in early mammalian development, including the first studies […]
Please join us for our BME 280B seminar series Thursday (5/7/26) in person at Biomed 200. The event will run from 11:40 AM to 1:15 PM and feature our 4th year grad talks. 11:40AM – 11:50AM: Jodie Jacobs Topic/Title: Impact of Wolbachia infection on host gene expression in pseudotime 11:53AM – 12:03PM: Ariana Cisneros Topic/Title: Engineering tunable […]
Presenter: Dr. Newman, Associate Professor in the Department of Biomedical Data Science, Stanford University Description: Determining the factors that shape cell potency—the ability of a cell to differentiate into other cell types—is essential for understanding tissue biology in health and disease, including cancer. In previous work, we found that single-cell transcriptional diversity decreases across […]
Presenter: Dr. Suchetana (Tuli) Mukhopadhyay, Professor, Indiana University Description: N/A Bio: Suchetana “Tuli” Mukhopadhyay, Ph.D., is a professor in the Department of Biology at Indiana University, Bloomington. She received her B.A. in chemistry from DePauw University and her Ph.D. in chemistry from the University of Illinois at Chicago. Following her doctoral studies, Mukhopadhyay conducted postdoctoral […]
Translation is a central and highly regulated step of gene expression, yet there are few quantitative, high-throughput tools to study translation. Existing methods such as sucrose gradients provide only bulk ribosome counts, while Ribo-Seq offers positional information in the genome but destroys long-range structure and transcript expression information. Because of these limitations, many fundamental questions […]
Local ancestry methods classify the segments of DNA inherited from a specific ancestry (e.g., African, East Asian, European), improving analyses of admixed populations. Aim 1 applies ancestry-specific analysis to more […]
Transfer RNA (tRNA) modifications are essential for structural integrity, decoding fidelity, and stress adaptation, yet their dynamics across phylogenetically distinct archaeal species and their functional roles during stress remain incompletely understood. This dissertation aims to address some of these gaps through a multi-scale investigation that spans the evolutionary dynamics, stress-responsive functions, and direct detection of […]
The explosive growth of genomic data, driven by advances in sequencing and inference technologies, presents both an opportunity and a challenge for evolutionary biology and public health. Existing visualization and analysis tools often fall short in handling the scale, complexity, and uncertainty of modern genomic datasets—especially in the areas of pathogen surveillance and ancestral recombination […]