Jared Simpson

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/🧵

01.12.2025 14:22 — 👍 5    🔁 1    💬 1    📌 0

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

07.09.2025 23:34 — 👍 114    🔁 79    💬 5    📌 5

Image of Toronto

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!

28.08.2025 06:34 — 👍 132    🔁 170    💬 0    📌 8

Mid-Career to Senior Principal Investigator About OICR   OICR is Ontario’s cancer research institute. We bring together people from across the province and around the world to improve the lives of everyone affected by cancer. We take on the big...

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!

04.02.2025 16:05 — 👍 36    🔁 58    💬 0    📌 0

Enhancer scrambling strategy

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...

15.01.2025 20:32 — 👍 182    🔁 77    💬 3    📌 2

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology The naked mole-rat (NMR; Heterocephalus glaber ) is a eusocial subterranean rodent with a highly unusual set of physiological traits that has attracted great interest amongst the scientific community....

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

29.11.2024 13:58 — 👍 34    🔁 7    💬 1    📌 1

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...

29.02.2024 14:59 — 👍 22    🔁 8    💬 2    📌 0