I'm currently a Senior Principal Scientist and Group Leader in the gRED Computational Sciences Hub at Genentech. My group focuses on developing robust and modular software tools for implementing computational methods applied to functional genomics data. Check out our crisprVerse work. Selected works:
- crisprVerse: design of CRISPR guide RNAs across nucleases and technologies, Nature Communications
- Biases in genome-wide pooled CRISPR screening, Genome Biology
- Enhanced scalable mutagenic base editor platform, Cell Reports
- AsCas12a ultra-compact CRISPR screening libraries, bioRxiv
Before Genentech, I got my PhD degree in Biostatistics at Johns Hopkins University under the supervision of Dr. Kasper Hansen, during which I focused on developing statistical methodology for the analysis of methylation array. I then pursued a postdoctoral degree in Neuroinformatics at the University of Pennsylvania with Dr. Taki Shinohara. My work focused on the multi-scanner harmonization and normalization of different neuroimaging modalities (MRI, DTI, etc). Selected works from my PhD and Postdoc:
- Functional normalization for methylation arrays (minfi), Genome Biology
- Hi-C reconstruction from methylation data, Genome Biology
- Processing of Illumina EPIC arrays, Bioinformatics
- shinyMethy: interactive visualization of methylation arrays, F1000Research
- Harmonization of structural MRI, Neuroimage
- Harmonization of DTI, Neuroimage
- Harmonization of cortical thickness measurements, Neuroimage
Bioconductor contributions
| Package | BioC-release | BioC-devel | Description |
|---|---|---|---|
| crisprVerse |  |
 |
Easily install of the crisprVerse ecosystem |
| crisprDesign |  |
 |
Core gRNA design package across nucleases and applications |
| crisprBase |  |
 |
Base functions and classes for CRISPR gRNA design |
| crisprBowtie |  |
 |
Alignment of gRNA spacer sequences using bowtie |
| crisprBwa |  |
 |
Alignment of gRNA spacer sequences using BWA |
| crisprScore |  |
 |
On-target and off-target scoring for CRISPR gRNAs |
| crisprScoreData |  |
 |
Pre-trained models for the crisprScore package |
| crisprViz |  |
 |
Visualization of CRISPR gRNAs using genomic tracks |
| crisprShiny |  |
 |
Shiny interface for CRISPR gRNAs |
| Rbwa |  |
 |
R wrapper for BWA-backtrack and BWA-MEM aligners |
| ARRmNormalization |  |
 |
Normalization for methylation arrays |
| shinyMethyl |  |
 |
Interactive visualization for Illumina methylation arrays |
| Package | BioC-release | BioC-devel | Description |
|---|---|---|---|
| minfi |  |
 |
Analyze Illumina Infinium DNA methylation arrays |
| screenCounter |  |
 |
Counting Reads in High-Throughput Sequencing Screens |