iiinova — where your digital self keeps evolving

Reposted by Jared Simpson

Jüri Reimand @reimand.bsky.social · 16/09/2026

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]

nature.com

Integrated signatures define mutational processes in prostate cancer - Nature

Eight integrated mutational footprints collectively explain the mutational processes in 85% of primary prostate cancer genomes.

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Reposted by Jared Simpson

Quaid Morris @quaidmorris.bsky.social · 21/07/2026

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

biorxiv.org

Ensembles of in silico structures enable T cell peptide-MHC binding prediction

Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data rem...

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Reposted by Jared Simpson

Collins Genomics Lab @collinsgenomics.bsky.social · 10/07/2026

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

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Reposted by Jared Simpson

Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026

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...

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Reposted by Jared Simpson

Martin Taylor @mstaylor.bsky.social · 26/05/2026

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

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Reposted by Jared Simpson

Leopold Parts @leopoldparts.bsky.social · 27/03/2026

🧬 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.

partslab.bio

Parts team

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Reposted by Jared Simpson

Marcin Imieliński @skimomiks.bsky.social · 01/12/2025

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/🧵

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Reposted by Jared Simpson

Jim Shaw @jimshaw.bsky.social · 08/09/2025

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

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Reposted by Jared Simpson

Daniel Durocher @durocher1.bsky.social · 28/08/2025

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!

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Jared Simpson @jaredsimpson.bsky.social · 04/02/2025

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!

oicr.bamboohr.com

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...

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Reposted by Jared Simpson

Leopold Parts @leopoldparts.bsky.social · 15/01/2025

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...

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Jared Simpson @jaredsimpson.bsky.social · 29/02/2024

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...

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