I recently defended my PhD in Bioinformatics and Integrative Genomics at Harvard Medical School, advised by Professor Nils Gehlenborg. I graduated from the University of Maryland, College Park in 2019, where I studied Computer Science. My research focuses on interactive visualization of single-cell atlas data.
featured projects
Since 2019, I have worked with the Gehlenborg Lab on Vitessce, an interactive visualization tool for spatial single-cell multi-omics experiments. Vitessce can be used as a React component, Jupyter widget, or R htmlwidget, and has been integrated into the HuBMAP data portal as well as several other projects.
In 2022, I contributed to the development of Polyphony, an interactive transfer learning framework for single-cell data analysis.
Prior to starting graduate studies, I worked with the Gehlenborg Lab on Cistrome Explorer, a wrapper component for HiGlass with features for viewing CistromeDB data and querying CistromeDB Toolkit. This work was presented as a poster at BioVis@ISMB 2020, NCI ITCR 2020, and Genome Informatics 2020.
During the COVID-19 pandemic, I contributed to data visualization & analysis and web development with the Consortium for Clinical Characterization of COVID-19 by EHR (4CE).
During the summer of 2020, I participated in the BEAT-PD DREAM Challenge on winning team dbmi. My contributions included exploratory data analysis and a snakemake pipeline for our team's feature extraction and training code.
As an undergraduate research assistant in the Leiserson Research Group at the University of Maryland, I led the development of ExploSig, a web-based tool to enable exploration and interactive visualization of mutation signatures in human cancer and their etiology. ExploSig was presented as a late-breaking poster at RECOMB 2019 and won best poster at BioVis@ISMB 2019. A screenshot is featured in a video about the research group. More details can be found in my final paper for the course CMSC499A.
This work also included writing a pipeline for processing somatic mutation data and clinical data from TCGA, ICGC, PCAWG, and cBioPortal. This data processing is acknowledged in Robinson et al. Bioinformatics 2019 and Sason et al. RECOMB 2019.
open source
I maintain the following open-source tools and utilities.
news
Defense of PhD
Our report on The State of Single-Cell Atlas Data Visualization in the Biological Literature has been uploaded to OSF Preprints. It is accompanied by an interactive survey browser.
Co-led the visualization interoperability track at the 2024 SpatialData Workshop in Basel, Switzerland (described in a BioHackrXiv preprint).
🎉 Our paper describing Use-Coordination was presented at IEEE VIS 2024 and is available via IEEE Xplore!
✅ Third meeting with dissertation advisory committee.
🎉 Our paper describing Vitessce has been published in Nature Methods!
Presented at the 2024 Kidney Precision Medicine Project fall meeting in Bethesda, MD.
Presented a poster at the 2024 HMS Department of Biomedical Informatics Science Day.
Attended the 2024 Amgen Biotech Day in Cambridge, MA.
Presented at a workshop for trainees during the 2024 Summer Institute in Biomedical Informatics.
Second meeting with dissertation advisory committee.
Use-Coordination preprint uploaded to OSF Preprints.
Co-organized the Scverse hackathon in Boston and co-led a project to improve visualization of SpatialData in Vitessce.
Contributed to preprint describing our approach to visualize 3D spatial data in a mixed reality environment with linked views on a 2D display.
Presented a poster at the NIH-CZI Junior Investigators Atlas Builders meeting in Bethesda, MD.
Co-led a roundtable discussion at the 2023 ASCB Cell Bio conference titled Data Visualization in the Age of Cell Atlases: How will spatial technologies influence visualization in cell biology? in Boston, MA.
Served as a teaching fellow for BMI 709 Creating Biomedical Dashboards with R Shiny.
Presented at the 2023 IEEE VIS conference during the Application Spotlight titled Visualization for spatial single-cell atlases in Melbourne, Australia.
Attended the 2023 Kidney Precision Medicine Project fall meeting in Bethesda, MD.
Attended the Spatial Biology Summit hosted by Alpenglow Biosciences in Cambridge, MA.
Poster accepted for presentation at the 2023 ASN Kidney Week meeting in Philadelphia, PA.
Presented a poster at the 2023 HMS Department of Biomedical Informatics Science Day.
Presented research-in-progress at the HMS Department of Biomedical Informatics trainee talk series.
Attended the SenNet Consortium Meeting on Single Cell Spatial Transcriptomics/Proteomics in Washington, DC.
🎉 OME-Zarr ecosystem manuscript published in Histochemistry and Cell Biology.
Presented at the Inter-Lab Meeting on Visualization and Image Data Management.
Attended NSF workshop on Interactive Visualization and Analysis of High-Dimensional Scientific Data.
Contributed to preprint about the kidney chromatin landscape by developing a visualization tool to explore the data.
Presented a lightning talk at the 2023 HMS BIG PhD program retreat.
🎉 BEAT-PD manuscript published in PLOS Digital Health.
Initial dissertation advisory committee meeting.
Presented at the 2023 Kidney Precision Medicine Project spring meeting in Washington, DC.
Contributed to preprint about OME-Zarr ecosystem.
🎉 Cistrome Explorer published in Bioinformatics.
Polyphony was presented at IEEE VIS 2022 in Oklahoma City, OK by Furui Cheng.
🎉 Polyphony published in IEEE TVCG.
Presented Polyphony at the ISMB BioVis COSI, winning the best long abstract award.
Presented Vitessce at the ISMB Technology Track in Madison, WI.
🎉 Viv published in Nature Methods.
Presented Vitessce at Keystone Symposium on Single Cell Biology in Florence, Italy.
Served as a teaching fellow for BST 281 Genomic Data Manipulation.
Completed preliminary qualifying exam (PQE).
Vitessce preprint uploaded to OSF Preprints.
🎒 First day of PhD program.