Jean-Philippe Fortin

Time to retire this account! you can find me on Bluesky: bsky.app/profile/jp-for…

Wish you could develop Bioconductor-like workflows in Python? You can! Don't miss out on @jayaram's BiocPy workshop tomorrow at #bioc2024 cfp.bioconductor.org/2024/talk/SECD… BiocPy: github.com/BiocPy

Powerful use of the RNA-targeting Csm complex! We've now extended the crisprVerse to make CRISPR-Csm gRNA design easy: github.com/crisprVerse/Tu…

Published (and open access)! Super excited to share the final version of our manuscript describing an enhanced mutagenic base editing platform for use in functional genomic screening. See original tweetorial for more details. cell.com/cell-reports/f…

Thrilled to share our pre-print describing a new enAsCas12a transgenic mouse model + genetic screening platform. Made in close collaboration with teams led by @marcoherold_j @onjcri_ceo (@WEHI_research/@onjcri) & @jaypykw (@Genentech)! 1/9 biorxiv.org/content/10.110…

Now online! New-preprint from the always-brilliant Kristel Dorighi with essential contributions from many others at @genentech; enhanced Cas9 base editing (BE) for drug resistance variant discovery. biorxiv.org/content/10.110…

At the core, the pipeline is using the excellent packages from the #crisprVerse suite for #R #bioconductor, developed by the team around @JayPykw . Many thanks for this great foundational work 👏

Our Data Science and Statistical Computing group in the Genentech Computational Hub is seeking a highly motivated Principal Scientist to lead the development of methods and computational tools for genomics workflows. #hiring #genentech #bioinformatics careers.gene.com/us/en/job/GENE…

Do you ever look at something amazing someone in your lab has done and say "Wow; this is awesome!"? Well, here's a very short story starring @DongzeHe! As part of simpleaf (github.com/COMBINE-lab/si…), we rely on another package we wrote called pyroe (github.com/COMBINE-lab/py…). 1/15

a year ago we (+@realAaronLun) announced Kana (kanaverse.org/kana/), to perform #singlecell analysis in the browser powered by #webassembly. This week we released version 3 to support multi-modal data analysis, gene set enrichment and exploration of pre-analyzed results (1/n)

Precise transcript targeting by CRISPR-Csm complexes go.nature.com/3XTaIJQ

Excited to announce the release of #ggplate on CRAN! ggplate is an R package that enables easy visualization of culture and microplate data. Find out how to use it here: jpquast.github.io/ggplate/ 1/5 #rstats #DataScience #datavisualization #Biology #microbiology #AcademicChatter

New preprint! What is all that non-coding DNA doing? To understand if and how non-coding sequences regulate gene expression, we need scalable and reliable perturbation methods Delighted to present the @ENCODE_NIH Multi-center integrated analysis of non-coding CRISPR screens!

I am hiring a 2023 summer intern at Genentech on microscopy-based image processing and statistical analysis. If you happen to be or know anyone who is interested and has relevant experience, please reach out or spread the word! roche.wd3.myworkdayjobs.com/ROG-A2O-GENE/j…

#Illumina's MethylationEPIC v2.0 BeadChip is now available! 935K methylation sites for the same price as EPICv1.0. Learn more here: sapac.illumina.com/content/dam/il…

Thrilled to share our lab’s first paper in which we establish genome-wide CRISPR screening within a single mouse! We are so excited about the power of this platform to enable high-throughput genetic dissection of diverse phenomena within a living mammal. cell.com/cell-genomics/…

Today we report in @NatureBiotech the conversion of adenine base editors (ABE) into next-generation cytosine base editors (TadCBEs) with high on-target activity and reduced off-target activity using phage-assisted continuous evolution (PACE). 1/14 drive.google.com/file/d/1XY3QG-…

.@JayPykw @genentech crisprVerse enables efficient gRNA design and annotation for methods including CRISPRko, CRISPRa, CRISPRi, CRISPRbe and CRISPRkd, enabled for RNA- and DNA-targeting nucleases, including Cas9, Cas12 and Cas13 go.nature.com/3DBIsmD

@aaron_mckenna Thank you!

Oh God, FlashFry went into negative :-) Congrats on a great paper, and looking forward to trying it out!

crisprVerse is an open-source ecosystem, and builds on top of the rich and versatile @Bioconductor project. Check out our GitHub page: github.com/crisprVerse

Our crisprVerse paper is out in @NatureComms. We developed a one-stop shop CRISPR gRNA design tool that works with any nuclease and genome, and includes functionalities for CRISPRko, CRISPRa, CRISPRi, base editing, and RNA-editing. nature.com/articles/s4146…