Research Themes
Visual Analytics Systems for Multi-Modal and Spatial Single-Cell Data
Since 2019, I have led the development of the Vitessce framework, which enables visualization of data from widely used single-cell data formats directly in a web browser.
Details
Vitessce supports multiple interactive plot types, ranging from dimensionality reduction scatterplots to scalable heatmaps to domain-specific dot plots to statistical charts such as histograms and violin plots. Leveraging my experience in working with genome-mapped and bioimaging data, Vitessce also enables analysts to integratively view these data types alongside single-cell data in a single interactive tool, reducing friction and enabling relation of findings across data modalities. Vitessce has been integrated into specialized applications, such as Polyphony for human-in-the-loop cell type annotation, as well as large atlas mapping consortia data portals and commercial software solutions. Analysts can use Vitessce directly in scripts and notebooks via packages in Python and R.Comparative Analysis of Data from Multiple Single-Cell Experiments
In multiple projects, I have used Vitessce to build interactive visualization systems tailored to comparison of multiple single-cell datasets (i.e., between conditions, such as health vs. disease or between disease subtypes).
Details
A key goal of the single-cell field is to leverage metadata (e.g., clinical variables of tissue donors) to make comparisons between conditions that can inform the development of diagnostics, prognostics, and therapeutics.In the Polyphony project, I contributed to the development of an interactive system for reference-based cell type annotation. Reference-based cell type annotation reduces the effort required to annotate cells by projecting a new "query" dataset onto an existing, well-annotated "reference" dataset and transferring cell type labels from reference to query. Polyphony is a human-in-the-loop system that enables expert users to steer a machine learning model to make improved cell type annotation predictions.
In the Compasce (COMPAre Single Cell Experiments) project, I developed an interactive system to explore and confirm the results of comparative analysis of single-cell data, focusing on comparisons between case and control conditions (e.g., samples from donors with Acute Kidney Injury versus reference/non-disease samples). The design of this system has been informed by interviews that I conducted with individuals from its intended user audience, comprising biologists, pathologists, and clinicians within the Kidney Precision Medicine Project (KPMP). Compasce contains both confirmatory (e.g., How does abundance of a biomarker of interest differ between groups?) and exploratory (e.g., What are the most significant differences between groups?) interfaces and visualizations.
Reproducibility in Research Software Development and Scientific Data Processing
I am passionate about reproducibility in my scientific and software development work
Details
I use and advocate for workflow management tools such as Snakemake to develop efficient data processing pipelines that can be executed with a single command. In my visualization tool development, I have integrated techniques such as provenance tracking (e.g., undo/redo for action recovery). My tools load data from community standard data formats (e.g., AnnData, SpatialData, OME-TIFF, OME-Zarr). When possible, I use client-side web architectures that avoid complex server-side infrastructure requirements.Domain-Specific Literature Surveys to inform Visualization Research
I am interested in meta-science and leveraging the wealth of information that is contained in the scientific literature to inform future visualization research.
Details
I conducted a survey of over 1,800 figures appearing within 45 publications describing single-cell data to provide an overview of the landscape of static single-cell data visualizations. I annotated the figures with 85 categories related to plot types, data types, figure purpose, and other visualization characteristics. This survey has enabled quantification of visualization usage patterns within the single-cell literature and provides background on the single-cell field for researchers from other domains.Latest News
Our work on EasyVitessce was presented at the Scverse Conference 2025 and in a VUES seminar.
Preprint on the HuBMAP Data Portal uploaded to arXiv.
Preprint on visualization of micro-compartmental segmentations and pathomic features uploaded to arXiv.
EasyVitessce preprint uploaded to arXiv.
Presented a mini-talk describing recent updates to Vitessce during the data visualization session of the Spatial biology conference organized by EMBL and the European Society for Spatial Biology (ESSB).
Presented a poster at the 2025 HMS Department of Biomedical Informatics Science Day.
🎉 Our report on The State of Single-Cell Atlas Data Visualization in the Biological Literature has been published at IEEE Computer Graphics and Applications. It is accompanied by extensive supplementary materials and an interactive survey browser.
Presented at The University of Sydney Precision Data Science Centre's Statistical Bioinformatics Seminar series.
✅ Defense of PhD
Our report on The State of Single-Cell Atlas Data Visualization in the Biological Literature has been uploaded to OSF Preprints.
Co-led the visualization interoperability track at the 2024 SpatialData Workshop in Basel, Switzerland (described in a BioHackrXiv preprint).
Served as a teaching fellow for BMI 709 Creating Biomedical Dashboards with R Shiny.
🎉 Our paper describing Use-Coordination was presented at IEEE VIS 2024 and is published in 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.