jfortin1,Jean-Philippe Fortin,JayPykw,github

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

As maintainer

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