Trainees
Abby Bergman
Department of Genetics
Baker Lab
Research: The placenta is critical for gestation, tasked with an intricate balancing act of supporting fetal development and growth while also protecting maternal resources from over parasitism of the fetus. An interesting evolutionary result of this balancing act has been the placental-specific activation and co-option of endogenous retroelements. Additionally, there has been observation of viral-like particles at the placental interface in many species, suggesting an activation of a particle-competent retroelement. Through genomic analysis, we have identified a subfamily of endogenized retroviruses as a strong candidate. I am working to reveal the functional role of this subfamily in placental formation and maternal-fetal communication.
Meenakshi (Meena) Chakraborty
Department of Genetics
Rotating
Research: As a first year student, I am currently rotating through labs. First, I rotated with Professor Aaron Gitler, studying the regulation of proteins linked to the neurodegenerative disease ALS. Next, I rotated with Professor Ami Bhatt, primarily investigating the connection between the gut and the brain. Finally, I am rotating with Professor Mike Snyder, assisting with a project to determine the biological signatures of depression and mental wellness.
Connor Duffy
Department of Genetics
Konermann Lab
Research: I am studying the genetics of late-onset Alzheimer’s disease (AD) risk using high-throughput CRISPR perturbation experiments in human stem cell-derived neurons and glia. My work aims to develop a general experimental framework for modeling complex disease risk, elucidate core genes and molecular pathways driving AD pathogenesis, and inform therapeutic strategies for mitigating risk in individuals of high polygenic risk burden.
Joy Doong
Department of Developmental Biology
Snyder Lab
Research: My current research focuses on the health effects of a fermentable dietary fiber, arabinoxylan, which is associated with large changes in multi-omic profiles in human subjects. It is unclear, however, to what degree such effects are facilitated by the gut microbiome. To better understand the microbial contribution to the multi-omic and health effects of dietary fiber, I am studying the effects of arabinoxylan supplementation on the immunome and metabolome in germ free mice with humanized microbiota. Differences in the multiomics profiles of these mice will elucidate which observed effects may be attributed to the presence of specific microbes or microbial pathways - an important step in revealing the potential role of arabinoxylan in precision health.
Syed Usman Enam
Department of Genetics
Rotating
Research: Straight Lab: Developing a technique to map DNA-RNA contacts near proteins of interest.
Sarnow Lab: Investigating the role of the spliceosome complex in the generation of HCV-derived circRNAs.
Fire Lab: TBD
Pagé Goddard
Department of Genetics
Montgomery Lab
Research: Pagé’s research is centered on improving genetic diagnostics for individuals with rare, undiagnosed disease, and for communities that have been historically excluded from and exploited by genetic research. Her work includes the redesign a clinical RNA-seq pipeline as part of the Undiagnosed Disease Network, and the ongoing, collaborative development of an African functional genomics resource (AFGR; preliminary data available at https://github.com/smontgomlab/AFGR). She presented her work integrating AFGR expression data with Ugandan GWAS to improve causal variant identification in a platform talk at ASHG 2020, and received the inaugural Health Disparity Research Award for her poster at the 2021 Stanford Pathology Research Retreat highlighting the novel transcriptional diversity of the HLA region in the AFGR RNA-seq data.
Michael Hayers
Department of Genetics
Fordyce Lab
Research: Transcription factors (TFs) dynamically regulate expression of target genes in response to stimuli. Transcriptional networks mediating these responses are often rewired during evolution by TF gene duplication events in which each paralog evolves to diversify their functions. Understanding paralog specificity poses a challenge, as they remain structurally similar with highly conserved DNA binding domains, often have identical binding motifs, and yet regulate distinct target genes. My research in Polly Fordyce’s lab aims to understand mechanisms by which paralogous TFs find and bind their target sites by combining high-throughput in vivo and in vitro measurements of TF binding to understand binding sequence determinants of paralog specificity, as well as the protein sequences underlying them, with the ultimate goal of understanding determinants of TF binding more broadly.
Brian Ho
Department of Microbiology and Immunology
Kirkegaard Lab
Research: My project uses mouse models to study the effect of a lncRNA, NeST, on the immune system's response to inflammatory insults. NeST is expressed exclusively in lymphocytes and at very low levels. Yet, its effect on the immune response to viral infection is profound, its absence significantly increasing viral spread and pathogenesis in a mouse model of poliovirus infection. I am interested in determining which lymphocytes are causal for the different phenotypes we observe in the poliovirus, and other mouse models. We have obtained T cell-specific NeST knockout mouse lines and I will deplete NK cells via antibody infusion. Characterizing the effects of individual lymphocyte populations will enable us to ask more mechanistic questions about NeST's role in the genetic regulation of immune system function.
Tanner Jensen
Department of Genetics
Rotating
Research: I am interested in how structural variation play a role in Mendelian and complex disease. I study sequencing technologies and algorithms to determine the best ways to call structural variants. and then using information on how they vary in global populations and the genomic context where they appear, classify their likelihood to be pathogenic. I am also interested in studying how structural variants can effect expression and other functional genomics traits. By integrating functional genomics assays like transcriptomics or epigenomics combined with the large structural changes we observe through long-read sequencing, we can prioritize variants and identify the "rules" to determine how structural rearrangements will impact cell biology and ultimately human health.
Alex Kern
Department of Genetics
Fraser Lab
Research: I study genetic adaptations that affect multiple genes using both computational and experimental approaches. So far I have examined selection on an essential metabolic pathway in yeast, and experimentally measured the effects of single nucleotide variants on fitness in yeast in different environments. I plan to examine determinants of gene expression differences between chimps and humans next.
Vincent Liu
Department of Genetics
Engreitz Lab
Research: TBD
Rosa Ma
Department of Genetics
Gitler Lab
Research: My research focuses on understanding the role of TDP-43 cryptic splicing in the pathogenesis and prognosis of ALS. TDP-43 is an RNA binding protein that normally localizes to the nucleus. It binds to thousands of pre-mRNA/mRNA targets in the nucleus and acts as a repressor of cryptic exon inclusion during RNA splicing. Cryptic exons are intronic sequences that are normally excluded from mature mRNA. A hallmark pathological feature of ALS is the depletion of TDP-43 from the nucleus, which leads to cryptic exon inclusion into mRNAs. The process affects myriad genes by introducing fame shifts and premature termination or even reduced RNA stability. My project aims to identify dysregulated genes that are important in driving the disease by combining cell and molecular biology and bioinformatics data analysis.
Robin Meyers
Department of Genetics
Khavari Lab
Research: In the lab of Dr. Paul Khavari, I am studying the roles of ATP-dependent chromatin remodeling complexes in cellular differentiation. These multimeric, combinatorially-assembled complexes are deeply conserved and genetically non-redundant, though all act by destabilizing nucleosomes. Using multiplexed CRISPR perturbations and single-cell transcriptomic and epigenomic readouts in 2D and 3D models of differentiation in the human epidermis, I am systematically mapping the roles of over 100 chromatin remodeler subunits. This research aims to elucidate global rules that dictate chromatin remodeling activity across the genome, and thereby the function of these complexes in regulating gene expression. I also perform research establishing the function of non-coding regulatory genetic variants associated with risk of many types of skin disease.
Michael Montgomery
Department of Genetics
Rotating
Research: I have completed rotations in the labs of Dr. Jesse Engreitz (Fall 2020) and Dr. Maria Barna (Winter 2020). In the Engreitz lab I established a method for precision gene editing and used this method to investigate the sequence logic of enhancers. In the Barna lab I used a proximity labeling technique that I helped optimize to study ribosome heterogeneity across sub-cellular space. I also investigated methylation patterns of 45S rDNA copies across the human genome using a computational pipeline that I established and nanopore long read DNA sequencing data.
Roshni Patel
Department of Genetics
Pritchard Lab
Research: I develop and apply statistical methods to understand how the genetic architecture of traits differs across global populations. Over the last two decades, genome-wide association studies have helped identify the genetic basis of complex traits such as height and heart disease. However, these studies have largely been conducted in individuals of European ancestry. In order to ensure that genetic research equitably benefits all populations, it is essential to characterize trait architectures in non-European populations.
Alanna Pyke
Department of Genetics
Rotating
Research: My scientific interests surround genetic evolution. I've rotated with Dr. Mike Snyder, Dr. Moi Exposito-Alonso, and I'm currently rotating with Dr. Gavin Sherlock. In the Snyder lab, I participated in a collaborative research project with a Tribal nation in South Dakota, to investigate the higher rate of incidence of autoimmune disease within their population. In the Exposito-Alonso lab, I worked on a computational project to compare different methods of DNA collection from Arabidopsis, and learned about caring for Arabidopsis plants in the lab. In the Sherlock lab, I am studying wild S. cerevisiae strains from a large variety of backgrounds, and will investigate differences between their genomes.
Rachel Ungar
Department of Genetics
Montgomery Lab
Research: Rare variants (which have a minor allele frequency of less than 1%) collectively are the most abundant type of variant, yet we cannot systematically study every single variant. Therefore, understanding the patterns of how rare variants influence gene expression can helpful to better understand the biological and clinical impact of a previously unseen variant. I am interested in classifying the effects of rare variants on transcriptomic data. I am working to identify the functional effect of rare variants on the X chromosome and autosomes across tissues, and determining how this might vary by sex. I am also part of the Undiagnosed Disease Network, in which I work with clinicians, genetic counselors, and researchers to help identify disease-causing genes in undiagnosed patients. To do so, I integrate multi-omic data to identify transcriptomic outliers with a nearby rare variant that might contribute to disease.
Raeline Valbuena
Department of Genetics
Rotating
Research: The ability to acquire anti-drug resistance is highly beneficial to a virus but presents a difficult problem for drug development. Designing anti-viral therapeutics against dominant drug targets can help suppress the emergence of resistant strains. Previous work in the Kirkegaard lab has found that the multimerizing M1 matrix protein of Influenza A (IAV) is a potential dominant drug target. During my rotation, I am developing a high-throughput assay and analysis pipeline to find novel inhibitors of IAV by assessing the effect of custom compounds on M1 stability. Ultimately, the goal is to use a combination of genetic and chemical approaches to develop effective anti-viral therapies.
Ronghao Zhou
Department of Genetics
Rotating
Research: I am interested in studying the genetic and epigenetic changes during aging through CRISPR perturbation screen.