Hi, my name is Sam. I am a PhD Candidate at UC Irvine in the Swarup Lab, where I work on studying neurodegeneration using high-dimensional genomics approaches like single-cell RNA-seq and spatial transcriptomics.
I am broadly interested in leveraging big data and bioinformatics to better understand the molecular and genetic underpinnings of human central nervous system diseases/disorders. Through my research, my PhD training in Mathematical Computational Systems Biology (MCSB), and my undergraduate in Bioengineering & Bioinformatics, I have spent nearly a decade developing data science skills (especially statistics and machine learning) to interrogate complex biological systems.
I enjoy drinking coffee, playing with my cats, and listening to music. I also like playing video games, hiking, going to the beach, and going to concerts. Sometimes I tweet about science.
|Sep 23, 2022||hdWGCNA, an R package that I developed for performing co-expression network analysis in single-cell and spatial transcriptomics data, is now on bioRxiv! hdWGCNA uses Seurat objects and essentially begins where the Seurat tutorial ends. Check out the hdWGCNA manuscript on bioRxiv and the hdWGCNA R package on GitHub.|
|Aug 27, 2022||I was recently awarded a Predoctoral Individual National Research Service Award (F31) from the National Institute on Aging for my research proposal titled “Single-cell epigenomic roadmap of Alzheimer’s disease”. This preliminary results for this project can be found in my Nature Genetics paper. I am immensely thankful for the support system in my lab and at UC Irvine that helped me to achieve this fellowship.|
|Oct 31, 2021||In our new article in Neurobiology of Disease, we reviewed what is currently known about the role of genetics in AD and related tauopathies. We dive into how systems genomics approaches such as co-expression network analysis are being used to understand genetic risk signals in these complex polygenic diseases. Check out the full study here!|
|Jul 8, 2021||Our study of AD using chromatin accessibility (snATAC-seq) and transcriptomics (snRNA-seq) at cellular resultion was just published today in Nature Genetics. We found genes, pathways, networks, cis- and trans- regulatory elements dysregulated in AD in specific cell types, and we defined the cis-regulatory architecture at selected GWAS loci such as BIN1 and APOE. Read the full manuscript here.|
- bioRxivHigh dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systemsbioRxiv 2022
- Nat GenetSingle-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s diseaseNature Genetics 2021
- Hum Mol GenetIntegrative genomics approach identifies conserved transcriptomic networks in Alzheimer’s diseaseHuman Molecular Genetics 2020