How to deal with clinical flow cytometry data with batch effects, changing markers, multiple panels per sample, incomplete cell-type labelling and large differences in cell-type proportions across patients? Mike Phuycharoen developed the UVAE method to solve this problem www.cell.com/iscience/ful...
Nice one Quaid!
In a new paper, we introduce Metient, a new method to reconstruct the migration history of metastatic clones, and learn cancer-type specific patterns of metastatic spread, from bulk or single-cell sequencing data.
www.nature.com/articles/s41...
Does anyone with familiarity with Claude Skills have a sense of how to reliably test these things? I've seen it succeed by peeking at the code instead of just running the skills as-is, which defeats the purpose of managing the context window
🧠 Explore the latest from Bioinformatics Advances: “Multi-view deep learning of highly multiplexed imaging data improves association of cell states with clinical outcomes”.
Find the full study at https://doi.org/10.1093/bioadv/vbag010
Authors include: @kieranrcampbell.bsky.social
The Toronto Population Network @tpn-uoft.bsky.social Seminar Series is happening this semester, with a great line-up, including @lucampesando.bsky.social, Orsola Torrisi, @mdhayward.bsky.social, and @jnobles.bsky.social! Starts next Tuesday. If you're in Toronto please come along!
📣This Thursday!📣
Don’t miss this virtual event ft. plain-language presentations from 5 future precision oncology experts using Network-generated “big data data" and disruptive technologies to shape the future of cancer research and care!
Register now to secure your spot!🔗: tinyurl.com/58ts23ba
I am very excited to share this book! It has been so much to collaborate on the project. We hope you find it useful!
Has anyone tried antigravity w/ Gemini 3 yet? What'd you build? antigravity.google
My main thesis as a phd student was that certain unsupervised models used in biology work so well due to much tweaking of hyperparameters and we might as well bake informative priors into them...didn't always go down so well
Congratulations to @michaelgeuenich.bsky.social selected as the Canadian representative at the Young Investigator Symposium at SITC 2025.
He's presenting our work on tertiary lymphoid structures in pancreatic cancer tomorrow at 8.15am at SITC
Abstract ➡️ www.immunotherapycancer.ca/2025-michael...
"The advent of large language models have made this type of content relatively easy to churn out on demand, and the majority of the review articles we receive are little more than annotated bibliographies, with no substantial discussion of open research issues."
Fix Canada’s Primary R&D Program - excellent article on issues with federal support for R&D in Canada
www.buildcanada.com/en/memos/fix...
Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma https://www.biorxiv.org/content/10.1101/2025.10.23.684170v1
Great collaboration with @gingraslab.bsky.social
& congrats to lead author Vesal.
Paper: www.nature.com/articles/s41...
Thanks to @sinaihealth.bsky.social
How can we scale subcellular spatial proteomics across many experiments and conditions?
Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.
Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested
Applications are now open for entry in academic year 2026/27 for the Centre for Doctoral Training in Fundamentals of AI @ox.ac.uk with @eitoxford.bsky.social: www.ox.ac.uk/admissions/g...
The journal version of our Multi-omic Pathway Analysis of Cells (MPAC) software is now out: doi.org/10.1093/bioi...
MPAC uses biological pathway graphs to model DNA copy number and gene expression changes and infer activity states of all pathway members.
Congratulations!
⏰Reminder: There's still time to apply!
LTRI is hiring two outstanding Principal Investigators in Population Health Data Science.
Find out more and apply by October 20th, 2025 ➡️ apply.interfolio.com/172529
Congrats Trevor very exciting!
Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...
Full professor complaining to an assistant professor on how hard it is to get funding nowadays
Fantastic hosting @alexr.bsky.social in Toronto today discussing the hype of AI in cancer biology and a realistic route to leverage it for personalized immunotherapy
Cancer cells are notoriously plastic, but what triggers the changes in cell state? In our new Nature (@nature.com) paper, Miranda Hunter (@mrndhntr.bsky.social) found that mechanical pressure is a key to this switch. Check it out here: go.nature.com/47iwDm2
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!
"The perfect segmentation doesn't ex—"
—@kieranrcampbell.bsky.social. www.nature.com/articles/s41...
Hopefully there was free pizza!
Online now! Tumor dynamics & spatial proteomics-informed personalized predictions of growth & response
Beyond RECIST: mathematical modeling and Bayesian inference reveal the importance of immune parameters in metastatic breast cancer
www.biorxiv.org/content/10.1...
