Az Zhang

The subject of this project delves into the nuanced regulatory functions of Long Undecoded Transcript Isoforms (LUTIs) within the realm of gene expression. This line of inquiry is driven by a pivotal question: Given LUTIs, once simply considered alternatively spliced coding transcripts, are found not translated into proteins, how do they impact gene expression across the genome? This inquiry is crucial, as it challenges existing models of genetic regulation. To address this question, the project integrates in silico analysis with experimental validation to systematically identify LUTIs and delineate their mechanisms […]

Luyang Zhang

Plants defend themselves against disease using germline-encoded innate immune receptors. Even so, pathogens are particularly challenging in that they often reproduce more rapidly than plants and tend to accumulate mutations that drive their evolution and diversification at an elevated pace. This accelerated evolutionary process necessitates the development of equally dynamic plant mechanisms of pathogen recognition. Deaminases are enzymes that remove amine groups from their nucleotide substrates. Existing literature indicates that certain classes of deaminases are capable of creating cytosine to uracil point mutations in DNA that contribute to bacterial and […]

Alana Yang

The development of programmable nuclease CRISPR-Cas9 has given scientists the opportunity to correct disease-causing genes in patients with unprecedented precision. Building upon these advancements, my collaborators and I are developing a non-viral CRISPR-Cas therapeutic platform for rare inherited immune diseases. Our current focus is the specific application of this platform approach to treating Artemis-deficient severe combined immunodeficiency (ART-SCID), which is the most difficult form of SCID to treat. Furthermore, the current method of diagnosis for ART-SCID is a radiosensitivity assay that takes 6-8 weeks–far too long for patients whose life […]

Christopher Yoo

Atypical somatosensation is associated with a variety of neurodevelopmental disorders, but the mechanisms responsible for experience-dependent somatosensory cortex (S1) development are largely unknown at the cellular level. While single-cell transcriptomes exist for adult S1, none have been completed across early developmental timepoints. Understanding the contribution of sensory experience to cell type development and plasticity is essential for developing treatments for neurodevelopmental disorders, like autism, that are characterized by impairment of experience-dependent plasticity. My project will test the hypothesis that sensory experience is crucial for normal S1 development. I will use […]

Jonanne Talebloo

In today’s digital age, there is increasing worry about how children and adolescents are affected by their screen habits. Excessive screen time among them has been tied to various health issues like mental health concerns, physical ailments, obesity, sedentary lifestyles, and sleep disturbances. As parents play key roles during childhood and adolescence, parenting approaches, and home atmospheres have been recognized as influencers that may contribute to children’s screen use patterns. In general, more attentive parental supervision has been linked to reduced total screen usage among children and adolescents. Our purpose […]

Anthony Neil Tan

Maker programs for middle school and high school students have become commonplace as the demand for STEM professionals has exponentially increased in the 21st century. Many of these academic enrichment programs are administered by non-profit initiatives and they serve as a stepping stone for pre-engineering students on a trajectory towards higher education. However, metrics for assessing the impact of out-of-school programs have been poorly defined and data points that track student learning have been sparse. One area of interest is quantifying students’ mastery of skills gained through these programs and […]

Michael Tanios

My research investigates the neural mechanisms by which chronic high-fat diet (HFD) consumption alters hedonic feeding behavior, contributing to obesity. Obesity has rapidly become a global crisis, and with health concerns linked to chronic diseases, there is an urgent need for intervention strategies. Despite its prevalence, the neurological mechanisms that connect pleasure-driven eating to obesity remain largely unexplored. Understanding how the brain’s reward pathways adjust to chronic exposure to high-calorie foods is vital for closing the gap in our knowledge of how dietary habits influence brain function and contribute to […]

Danh Tran

Microbiome editing is a new and growing area in machine learning, focused on understanding and controlling how groups of bacteria behave and interact, something that has been hard to study previously. This research could lead to breakthroughs in personalized medicine and the environment. The Rubin Lab is integrating machine learning into microbiome editing to improve how we understand and change these bacterial communities. We are creating advanced models of bacterial DNA and mobile genetic elements, which will help predict bacterial behavior and make the editing process more efficient. By using […]

Brandon Tu

Prostate cancer is among the most prevalent forms of cancer in the United States. Recent research studies in both mouse and human prostate tumors have uncovered a heightened dependency on small molecules known as polyamines. Polyamines are crucial signaling molecules for cellular growth and survival, supporting enhanced protein expression, nucleic acid synthesis, and chromatin remodeling. Understanding the factors which regulate polyamine production can provide insights into tumorigenesis and suggest targets for therapeutic benefit. The polyamine producing enzyme adenosyl-methionine decarboxylase 1 (AMD1) is highly upregulated in prostate cancer models. The cellular […]

Aakarsh Vermani

The rate at which DNA mutations occur is highly variable at different positions of the human genome. An accurate characterization of localized mutation rates could enable us to infer evolutionary histories, identify disease-associated genes, and even predict viral evolution, helping prevent pandemics like COVID-19. The heterogeneity of rates across the genome and the myriad of factors affecting them complicate this task, but the recent success of biological language models on related tasks like variant effect prediction signifies they could be a valuable tool for predicting mutation rates. Our preliminary results […]