Kieran Campbell

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!

Inferring cancer type-specific patterns of metastatic spread using Metient - Nature Methods Metient is a statistical framework that infers patterns of metastatic spread and reconstructs cancer migration histories.

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

Poster showing speakers for the TPN seminar series

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!

Graphic featuring pictures of the five presenters and the event details: Health Informatics & Data Science Awards pt. 1 Seminar: Thursday, Dec. 18, 2025. 9am PT / 10am MT / 11am CT / 12pm ET / 1pm AT / 1:30pm NT.

📣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!

Google Antigravity Google Antigravity - Build the new way

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 SR&ED credits are the largest federal support for R&D. But the process is complex, often rewards the wrong companies, and doesn’t support business value.

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

Screenshot of paper title

Great collaboration with @gingraslab.bsky.social
& congrats to lead author Vesal.

Paper: www.nature.com/articles/s41...

Thanks to @sinaihealth.bsky.social

Figure showing overview of genetic search algorithm and evaluation strategy

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

Fundamentals of AI (EIT CDT) | University of Oxford About the courseFundamentals of AI (EIT CDT) is a research-based DPhil course focused on foundational AI, machine learning, and computational statistics. Students will help shape the future of AI and

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...

Overview of the MPAC workflow. MPAC calculates inferred pathway levels (IPLs) from real and permuted CNA and RNA data. It filters real IPLs using the permuted IPLs to remove spurious IPLs. Then, MPAC focuses on the largest pathway subset network with filtered IPLs to compute GO term enrichment, predict patient groups, and identify key group-specific proteins.

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!

Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

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

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!

A Segmentation errors in highly multiplexed imaging experiments induce clusters formed by the composition of multiple true cell types. B Our probabilistic model STARLING for clustering highly multiplexed imaging data models whether each cell is observed segmentation error free, and if not models the composition of cell types leading to the observed cell. The loss function jointly maximies the likelihood of the data and the ability to discriminate on-the-fly simulated segmentation errors. C STARLING takes as input summarized single-cell expression and cell sizes as output by common pipelines for multiplexed imaging, along with a cluster initialization either user-defined or derived from multiple existing algorithms. D The output includes both the denoised cell types along with a per-cell estimate of segmentation errors.

"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...