#MLCB2026 will be November 16-17 at (once again) @nygenome.org, NYC! Paper/abstract deadline is July 1st, more deets at mlcb.org. We'll be opening in-person registration alongside paper decisions. Mailing list to stay in the loop: groups.google.com/g/mlcb. Keynotes TBA! Please RP!

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...

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...

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.

nature.com

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!

Helena Lucia Crowell@helucro.bsky.social · 11mo ago

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

Has anyone tried antigravity w/ Gemini 3 yet? What'd you build? antigravity.google

Google Antigravity

Google Antigravity - Build the new way

antigravity.google

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...

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.

buildcanada.com

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

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

Eric Swindell@gradschooldean.bsky.social · 12mo ago

Van Andel Institute PhD program application is OPEN! youtu.be/o79eqd1Ui0s?...

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...

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

ox.ac.uk

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.

⏰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

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...

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.

nature.com

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...

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...

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

The grand vision of the AI university. Professors design curricula, lecture notes and exam questions using genAI. Students read the notes and submit essays and exam answers using LLMs. Massive efficiency and speed gains ensue. Students can go play pool, professors write grants in the saved time.

Check out how we tackled one of the fundamental challenges in immunology, out today @cp-cellsystems.bsky.social: www.cell.com/cell-systems.... Our major innovations are BATCAVE and BATMAN, two new players to get us closer to solving TCR-pMHC predictions!

T cell receptor cross-reactivity prediction improved by a comprehensive mutational scan database

Banerjee et al. present a comprehensive T cell receptor cross-reactivity database and a hierarchical Bayesian framework to predict T cell receptor targets. Together, they reveal structural and biochem...

cell.com

The DNA of pure DCIS. We look at prognosis (invasive & in situ local recurrence) & benefit to radiotherapy in a unique cohort of Ontarians. A manuscript with my long term collaborators Eileen Rakovitch (Sunnybrook) & @vdumeaux.bsky.social breast-cancer-research.biomedcentral.com/articles/10....

Mutational landscape of pure ductal carcinoma in situ and associations with disease prognosis and response to radiotherapy - Breast Cancer Research

Background Managing Ductal Carcinoma in Situ (DCIS) remains challenging due to the lack of reliable biomarkers to predict radiotherapy (RT) response, leading to both overtreatment of indolent disease ...

breast-cancer-research.biomedcentral.com

I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with the Lowe lab. The paper sheds light on benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53. -> www.biorxiv.org/content/10.1...

Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis

The transition from benign to malignant growth is a pivotal yet poorly understood step in cancer progression that marks the shift from a pathologically inert condition to a clinically lethal disease. ...

biorxiv.org