Jared Simpson

Our paper on mutational processes in prostate cancer is out now in Nature! By analysing nearly 1,000 primary prostate cancer genomes from the Pan Prostate Cancer Group (PPCG), we identified the major mutational processes shaping prostate cancer genomes. www.nature.com/articles/s41... [1/5]

Can we predict which T cells recognize which peptides? A lot of the signal is hiding in AlphaFold3's (AF3's) hallucinations. enFoldX: instead of one predicted structure, we use the whole noisy ensemble to predict TCR:pMHC binding. www.biorxiv.org/content/10.6... 💻 🧬 github.com/jonlevi/enFoldX

📣Delighted to share two new studies from our team using germline genome sequencing 🧬 to understand #cancer #predisposition! Interested? 🧵👇 for details 1/15

1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...

Interested in DNA damage and the mechanisms of mutagenesis? We are hiring post-doctoral scientists as part of the amazing CAUSE Cancer Grand Challenge team. Biochemistry, genomics and computational biology... tinyurl.com/yc5xs3wa tinyurl.com/4unu5uu9 CAUSE www.cancergrandchallenges.org/cause

🧬 We're hiring scientists! I'm building a new team at the Generative Biology Institute, Ellison Institute of Technology Oxford, next to colleagues in AI, Robotics, and Plant Biology.

hello @bsky.app! let's get 🍊 juices flowing with the latest from the lab → how we used whole genome passenger somatic mutation patterns 🧬 to trace the origins of never-smoker lung adenocarcinoma (LUAD) to cells of the proximal lung 🫁 @NatureGenet www.nature.com/articles/s41... 1/🧵

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto. www.nature.com/naturecareer... Please repost!

We are recruiting a Principal Investigator in Computational Biology at @oicr.on.ca: oicr.bamboohr.com/careers/378. This position is in downtown Toronto, adjacent to the University of Toronto where your university appointment would be. Please contact me if you have any questions!

We are happy to share our enhancer scramble story, a strategy to create hundreds of stochastic deletions, inversions, and duplications within mammalian gene regulatory regions and associate these new architectures with gene expression levels 🧵 www.biorxiv.org/content/10.1...

Excited to share our preprint describing a new naked mole rat reference genome! www.biorxiv.org/content/10.1... 1/9

For a few years I've been thinking about calling somatic mutations without matched normals using long read haplotypes. I've posted a preprint with my experiments to explore when this works (and when it doesn't) and developing a prototype mutation caller ("smrest"): www.biorxiv.org/content/10.1...