Vanessa Dumeaux

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution Nature Microbiology, Published online: 06 March 2026; doi:10.1038/s41564-026-02286-7Bulk polyadenylation improves the capture of microbial RNA, enabling host–microorganism interactions to be visualized at a high resolution when combined with commercially available spatial transcriptomics platforms.

Out Now! Spatial transcriptomics maps host–gut microbiome biogeography at high resolution #MicroSky

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

Given that clonal biofilms of single bacterial species rapidly diversify into niche specialists, how do biofilms of multiple species evolve?
A 🧵 featuring new collaborative pubs:
1. www.biorxiv.org/content/10.6...
2. www.nature.com/articles/s41...

We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: biorxiv.org/content/10.1...

🧵👇1/n

Had a wonderful time last week at the From Cells to Ecosystems meeting at the Bellairs Research Institute in Barbados!

Thanks to @vdumeaux.bsky.social and @hallettmiket.bsky.social for the invitation. It was a unique experience that brought together researchers from vastly different disciplines.

Thank you for coming and for your participation throughout the week. The workshop participants are the ones making this a great event! Cheers

Individualized mRNA vaccines evoke durable T cell immunity in adjuvant TNBC - Nature In a phase 1 trial, personalized mRNA vaccines tailored to individual tumour mutations in triple-negative breast cancer induced robust, long-lasting T cell responses and improved prognosis.

More hope from mRNA vaccines. In this instance, individualized vaccines were given to women with triple negative breast cancer following surgery and adjuvant therapy. The results are quite remarkable. Despite cancer finding a ‘T cell-evading’ work-around in some patients.
#Science 🧪

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...

Our latest is out today in @plosbiology.org:

"Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials"

@isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social

doi.org/10.1371/jour...

Culturing microbiome therapeutics with big data www.nature.com/articles/s41...

CIHR funding rate: 13.6%.
Early 2000s: 30%+.

Canada’s new $1.7B Impact+ program recruits talent — but without increased Tri-Council base funding, we risk further strain on an already stretched system.

We’re calling for $1B over 5 years.
Support here: tinyurl.com/33c5av46

Check out this new & very promising method for differential analysis in microbiomes from @antagomir.bsky.social et al.

Heading home after an enlightening couple of days at the Cells to Ecosystems Meeting at the rather scenic Bellairs Research Institute in Barbados! Thanks to @vdumeaux.bsky.social and @hallettmiket.bsky.social for the invite and bringing together people from diametrically opposite research fields!

Thank you for coming and giving such an excellent talk, Glen! A true keystone species in this year’s ecosystem of rich idea and scientific exchange. No foragers here. Safe travels back home!

Our paper in @science.org 👉🏽 www.science.org/doi/10.1126/...

is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽
www.science.org/doi/10.1126/...

How AI assistance impacts the formation of coding skills www.anthropic.com/research/AI-...

PhD position in my team at @pasteur.fr ! The selected canddiate will work on the development of new methods combining biophysicial and machine learning modelling for single-cell multi-omics spatiotemporal data.

emploi.cnrs.fr/Offres/Docto...

I've started my own lab 🎉
PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders.

We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.

Now with a bioinformatics/genomics label 🖥️🧬

AlphaGenome is out in @nature.com today along with model weights! 🧬

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

💻 Weights: github.com/google-deepm...

Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial - Nature Medicine In a phase 2 trial evaluating healthy donor fecal microbial transplantation plus either anti-PD-1 in patients with non-small cell lung cancer or anti-PD-1 and anti-CTLA-4 in patients with melanoma, en...

First evidence that healthy donor fecal microbiota transplant, added to immunotherapy, can enhance efficacy vs cancer
3 clinical trial reports (renal, small cell lung, melanoma)
nature.com/articles/s41...
nature.com/articles/s41...
nature.com/articles/s41...
Holy 💩!

Strain displacement in microbiomes via ecological competition - Nature Microbiology Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

At the University of Guelph, in the College of Arts, Philosophy is hiring in AI ethics.

#philsky

careers.uoguelph.ca/job/Guelph-A...

Postdoctoral Fellow - Innate Lymphoid Cells and Spatial Genomics in Type 1 Diabetes, Crome Lab, Terry Fox Laboratory - BC Cancer Vancouver | Working at Provincial Health Services Authority | Careers a... Postdoctoral Fellow - Innate Lymphoid Cells and Spatial Genomics in Type 1 Diabetes, Crome Lab, Terry Fox Laboratory BC Cancer Vancouver, BC We are recruiting a highly motivated Postdoctoral Fellow to...

The new Crome Lab at BC Cancer is up and running — and we’re hiring!

We’re recruiting a PDF for a newly funded project on ILCs & NK cells in Type 1 Diabetes, using spatial genomics and single-cell approaches.

🔗 jobs.phsa.ca/job/postdoct...

#Immunology #SingleCell #SpatialGenomics #Type1Diabetes

Decoding the spatial dynamics of tumor and immune cell interactions in solid cancers www.cell.com/cancer-cell...

Scientific Director - Biomedical Research Institute in Montreal, Canada - Montréal, Quebec (CA) job with Centre d'innovation biomédicale - Université de Montréal | 12851492 The Courtois Institute for Biomedical Innovation (CI²B) is seeking a distinguished scientist to steer its development.

🌟🫱🏼‍🫲🏻Join the fun & scientific excellence of Montreal and become a primary partner of Centre de recherche du CHUM (CRCHUM) [please repost].

www.nature.com/naturecareer...

Western University is looking for a Canada Research Chair (CRC)
Tier 1 in Metabolomics. We are intent on building capacity in this system and the ideal candidate will help build infrastructure and mentor junior faculty.

Please see the job ad at: uwo.ca/facultyrelat...

The microbial keystone concept is a very cool topic in microbiome ecology. This review summarises mechanisms, prediction methods and implications, with "keystoneness" being highly context/time dependent + new methods approaches suggested. Very nice read!
www.nature.com/articles/s41...

My First Look at Claude Code Not behind, but at the forefront: On feeling overwhelmed by AI progress, and why that means you're exactly where you need to be.

Adding to the slew of recent articles about Claude Code. Not behind, but at the forefront: On feeling overwhelmed by AI progress, and why that means you're exactly where you need to be. doi.org/10.59350/gdj...

🤯 Another tumour immune evasion strategy uncovered. This times it's MHC molecules that acts as decoys to distract cytotoxic T cells.

Our new @nature.com Rev Clin Oncol Review maps how computational oncology is pushing predictive biomarker discovery forward: multimodal ML, transformers and foundation models, and frameworks that aim to match each patient to the therapies most likely to work.

doi.org/10.1038/s415...