Projects & Software
A closer look at the work, from a flagship reporter project to the computational tools I've built for large-scale screening and single-cell microscopy. Public code is on GitHub.
A cell-encoded OFF→ON fluorescent reporter that lights up only in live flavivirus infection — turning single-cell infection dynamics into a readable signal.
Tagging RNA viruses with fluorescent proteins is unstable and reduces the viral fitness and yield that high-throughput experiments demand. Existing OFF→ON cell-encoded reporters only work when the viral protease is overexpressed, not in a live virus infection.
We built on an existing translocation-based fluorescent reporter of dengue virus infection to create a new OFF→ON reporter driven by the reconstitution of a fluorescent protein producing a signal that appears only during genuine infection.
V-SWITCH is sensitive, specific, and dynamic. Fluorescence intensity tracks viral RNA replication directly, and its activation dynamics let us resolve the kinetics of infection at single-cell resolution by live-cell imaging.
We're using V-SWITCH to study the heterogeneity of infection outcomes at the single-cell level, and to run CRISPR screens that identify new host factors of flaviviruses and candidate targets for antiviral strategies.
Single-cell image-analysis pipeline for the split-mNG OFF→ON reporter that measures viral protease activity by live fluorescence microscopy. Three stages: nuclear segmentation (Cellpose) and single-cell tracking (Ultrack), mNG/BFP trajectory extraction and normalization, then sigmoid fitting, activation detection, and response-group classification. Built for HPC (SLURM) on multi-dimensional ZARR microscopy data.
Interactive Python web dashboard for exploring genome-scale CRISPRi screen results — hit ranking, gene-level statistics, and comparison across DNA viruses.
Optimized OME-ZARR conversion pipeline for high-content microscopy data, delivering a ~10× throughput improvement for downstream single-cell analysis.
sgRNA sublibrary design compatible with FACS-based, optical pooled screening and Perturb-seq workflows, plus inducible CRISPRi/a systems to model essential-gene perturbations.