I design and test new CRISPR-associated proteins with protein language models, then take the candidates to the bench.
Generated Cas12a candidate, residues 1–240 · colored by side-chain class
Hi! I am a chemical engineering and computer science graduate, and current research technician in a molecular diagnostics lab at Tulane University School of Medicine. There I lead two computational protein design projects...
I have extensive experience in both computational and experimental biology work, and my goal is to leverage the advantages of both to answer my research questions.
Using reinforcement learning to fine-tune a protein language model on the Cas12a family to generate novel nucleases with improved thermostability, specificity, and activity to optimize one-pot CRISPR detection assays.
ProGen2 · AMBER · sequence level filtering · OpenRLHF
Expanding the scope of known computational binder design pipelines to small tryptic and disulfide-rich peptides with improved specificity for detection and neutralization purposes.
RFdiffusion · AlphaFold2 Sequence Hallucination · ProteinMPNN · Rosetta ddG
Bulk RNA-seq analysis supporting the lab's infection biology work, including alignment, quality control, and differential expression pipeline.
STAR · FastQC/MultiQC · featureCounts · DESeq2
Identified key downregulated pathways implicated in ZFTA-RELA ependymoma tumorigenesis, corroborated by their presence in in-vitro and in-vivo models.
bulk RNA-seq analysis · ChIP-seq analysis · R
Built and trained a U-Net convolutional neural network to automate unbiased MRI tumor segmentation for fast tumor volume quantification.
PyTorch · CNN · Slicer · Python
Constructed growth curves for multiple patient-derived xenograft ependymoma models to measure the effects of IGF2 treatment.
Cell culture · Western blot · ELISA · PCR · RNA extraction