⏰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...

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!

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....

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...

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

Six days left to apply!

Please check out our new approach to modeling somatic mutation signatures. DAMUTA has independent Damage and Misrepair signatures whose activities are more interpretable and more predictive of DNA repair defects, than COSMIC SBS signatures 🧬🖥️🧪 www.biorxiv.org/content/10.1...

Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma 🧪 www.biorxiv.org/content/10.1...

🧬 We're hiring - join our lab in Toronto, Canada! 🇨🇦 Exciting postdoc joint with @hartjackson.bsky.social developing machine learning methods for the next generation of spatial histopathology technologies joint with industry partners in the Bay Area. 👉 apply.interfolio.com/168307

Just wrote up a quick blog post on why p-values are uniformly distributed under the null hypothesis! cindyfang70.github.io/posts/2025-0...

Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!

Interested in how to infer tumour microenvironment ecosystems from scRNA-seq atlases? I'll be at #AACR25 presenting in the ED06 session this Friday 3-4.30pm. Otherwise would love to meet to chat science for anyone on here attending Preprint: www.biorxiv.org/content/10.1...

Interested in how to infer tumour microenvironment ecosystems from scRNA-seq atlases? I'll be at #AACR25 presenting in the ED06 session this Friday 3-4.30pm. Otherwise would love to meet to chat science for anyone on here attending Preprint: www.biorxiv.org/content/10.1...

CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling genomebiology.biomedcentral.com/articles/10....

We have an opening in our #DataScience core @icr.ac.uk. The post will work on a breadth of topics across #cancer biology, but expertise in spatial data, single cell and data integration are priorities. Details here: jobs.icr.ac.uk/vacancies/11... @jobrxiv.bsky.social

Got our first chatGPT paper review that was really positive...the future is bright 🙃

Foundation Models -- A Panacea for Artificial Intelligence in Pathology? Interesting paper-training on top of FMs quickly gets you close to asymptotic performance -> could be useful to quickly assess how solvable a prediction problem is before assembling full dataset arxiv.org/abs/2502.21264

🧬 Join our lab in Toronto, Canada 🇨🇦! Exciting postdoc opening joint with @durocher1.bsky.social at the intersection of machine learning and cancer genomics-develop next-gen models to predict genetic interactions with in-the-loop validation. Apply ➡️ apply.interfolio.com/162929 or DM with questions!

🧬 Join our lab in Toronto, Canada 🇨🇦! Exciting postdoc opening joint with @durocher1.bsky.social at the intersection of machine learning and cancer genomics-develop next-gen models to predict genetic interactions with in-the-loop validation. Apply ➡️ apply.interfolio.com/162929 or DM with questions!

I’m super excited to share what I’ve been working on for the last (many) years: a spatial + genomic + transcriptomic characterization of how the breast cancer microenvironment evolves through immunotherapy! (1/x) 🧪🧬 🖥️ #AcademicSky #MLSky #ImmunoSky www.biorxiv.org/content/10.1...

Mean of the training data still absolutely crushing it for perturbation prediction. www.biorxiv.org/content/10.1...

It's quite insulting when posed with a research question you've been pondering for >2 years DeepSeek-R1 hits the major points with "Thought for 9 seconds"

Are you an #AI #digitalpathology developer struggling to make sense of all the pathology lingo? Don't worry because @sohmandal.bsky.social & @pathologop.bsky.social are here to help with their "Histopathology glossary for AI devs" journals.plos.org/ploscompbiol... published today - congrats both

"In this review. We highlight the role of DCs in lymph nodes and tumors in maintaining stem-like CD8+ T cells, which are critical for durable antitumor immune responses" www.science.org/doi/10.1126...

🎙️ Simply Oncology Episode 33 on high grade brain tumours is now live🚨 🎙️@ProfAJChalmers is a must listen -superb🔊 📻 Available on any podcast platform or on link 👇 "Episode 33: In the Clinic - Discussing high grade brain tumours with Professor Anthony Chalmers" at www.buzzsprout.com/2342317/epis...

Really excellent blog post on the ESM3 architecture and how it computes forward passes despite missing modalities: ericmjl.github.io/blog/2024/8/...

New work from the lab on comparing patient-derived GBM organoids & spheroids. TLRD: Surprisingly very similar across genetic, transcriptomics and epigenetic levels!

When asked about knockout vs knockdown, Google AI wonderfully bet-hedges on whether you're interested in genetics or boxing

Anyone have pointers to publications/datasets with large numbers of patient-matched scRNA-seq + WES?

How can we quantify single cell expression from multiplexed imaging datasets given segmentation errors? To help tackle this, we introduce evaluation metrics, a gold-standard dataset, and STARLING—a new probabilistic machine learning method (1/4) www.nature.com/articles/s41...

New year, new job? A position of 🧪 🦠 Clinical Diagnostics Project Manager 🦠 🧪 is available with our pandemic preparedness project PRECISE at Sinai Health in Toronto (closes Jan 12) - have a look at the position and apply here: apply.interfolio.com/160789.

Expert's Dilemma: the more specialized you become, the less open you are to creative solutions from other fields. But the more you explore other fields, the more you risk losing credibility in your home field. Interdisciplinary work is still not really embraced by academia.

1/n Some time ago my colleague, excellent cook, and friend Ivan told me: "Cacio e pepe is the recipe that I screw up more often. Let's make a project studying systematically the physics of that sauce". Prepare to get cheesy, I'm glad to share the Cacio e paper preprint: arxiv.org/abs/2501.00536

Thrilled to share the results in Cancer Cell of years of hard work to develop classifiers for all major TCGA cancer subtypes, enabling assessment of differential drug response among cancer subtypes in clinical trials. www.cell.com/cancer-cell/...

Happy New Year! 🎉 If your 2025 resolution is to finally get your lab life together (read: #NewPIs), you’re not alone. A few people have requested I share how we use automation to survive: 1️⃣ Recruitment & Scheduling 👩‍🔬 2️⃣ Finance & Ordering 💸 3️⃣ Alerts & Emergencies 🚨 So here goes!—A 🧵... 1/n...

Happy New Year!! I wrote a career retrospective on my past 10 years. tl;dr gotta pivot. ekernf01.github.io/retrospective/

Google AI describing triple sec as “cloyingly artificial” is the real AGI milestone everyone missed

A deep-learning tool for species-agnostic integration of cancer cell states

Genetic ancestry and population structure in the All of Us Research Program cohort https://www.biorxiv.org/content/10.1101/2024.12.21.629909v1 🧬🖥️🧪

Rethinking cancer drug synergy prediction: a call for standardization in machine learning applications https://www.biorxiv.org/content/10.1101/2024.12.24.630216v1

U.S. District Court Awards 10x Genomics Permanent Injunction in Patent Infringement Lawsuit Against Bruker Corporation's GeoMx Products