Senior Bioinformatics Data Scientist, ClearNote Health
I am a senior bioinformatics data scientist at ClearNote Health, specializing in the computational research of cfDNA fragmentomics for cancer detection.
I received my Ph.D. in Bioengineering from Stanford University, co-advised by Dr. Stephen Quake and Dr. John Boothroyd. My dissertation focused on developing and applying single-cell transcriptomic methods to study host-pathogen interactions. I characterized the intracellular life cycle of Toxoplasma gondii and discovered novel antigenic variation mechanisms (published in eLife), led computational analysis of macrophage responses to persistent Salmonella Typhimurium infection (published in Science Advances), and profiled DNA polymerase fidelity across broad evolutionary origins (published in Journal of Biological Chemistry). For more details on my research, please see my research projects.
If you are interested in connecting, please feel free to reach out to my email.
Can stable epigenomic marks in tumors be read from a blood draw? We profiled 5hmC across tumor tissues and cell-free DNA in five cancer types to ask whether hydroxymethylation signatures can detect cancer and pinpoint its tissue of origin.
Communications Biology, 2025.
When a photosymbiotic animal is wounded, does its algal partner respond too? We use single-cell transcriptomics to explore how a regenerative acoel and its intracellular algae coordinate molecular responses to injury across species boundaries.
Nature Communications, 2024.
Macrophages can both fight and harbor Salmonella, so what tips the balance? We use single-cell transcriptomics to dissect macrophage diversity within granulomas during persistent infection and identify a subpopulation that resists becoming a bacterial reservoir.
Science Advances, 2023.
Temperature is a fundamental parameter of every polymerase reaction, yet how it affects error rates across thermally adapted enzymes is underexplored. We profile fidelity at single-molecule resolution for polymerases from psychrophilic to thermophilic origins, and find one that works below the freezing point of water.
Journal of Biological Chemistry, 2021.
What decides whether a parasite germline stem cell self-renews or differentiates into gametes? We apply single-cell RNA sequencing to Schistosoma mansoni during gonad development to uncover the regulatory circuit at this crossroad and trace how it has been repurposed across flatworm evolution.
Nature Communications, 2021.
Toxoplasma injects effector proteins into host cells even when invasion fails. We exploit these "uninfected-injected" cells and single-cell transcriptomics to tease apart the individual contributions of ROP and GRA effectors to host gene expression in the earliest hours of infection.
mBio, 2020.
How does Toxoplasma gondii navigate its complex asexual life cycle, and why do individual parasites display such varied surface antigen profiles? We built a single-parasite transcriptional atlas across multiple strains and developmental stages to map hidden states, identify regulators of antigenic switching, and compare programs with the malaria parasite.
eLife, 2020.
When biologically meaningful differences between cells are subtle, how do you separate signal from noise? SAM uses iterative soft feature selection to automatically rescale feature for superior manifold learning, validated by discovering novel stem cell populations in Schistosoma mansoni and benchmarked across 56 datasets.
eLife, 2019.
Zinc supplements can treat infantile diarrhea, but how? We show that micromolar zinc triggers envelope stress in enteropathogenic E. coli, activating the alternate sigma factor RpoE, which in turn suppresses virulence gene expression through multiple mechanisms.
Applied and Environmental Microbiology, 2015.
Lysosomes execute autophagy, but does the autophagic process itself regulate lysosomal function? We dissect a dual activation mechanism involving mTORC1 suppression and autophagosome-lysosome fusion that upregulates lysosomal activity during autophagy.
Cell Research, 2013.