Vanessa Dumeaux 🇨🇦
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vdumeaux.bsky.social
Vanessa Dumeaux 🇨🇦
@vdumeaux.bsky.social
210 followers 260 following 37 posts
Assistant Professor, Anatomy & Cell Biology, Western University, Canada. Computational Biology, Genomics, Microbes and Human Health https://lab-dumeaux.science/
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vdumeaux.bsky.social
Vanessa Dumeaux 🇨🇦 @vdumeaux.bsky.social · 17h
Happy to see this work finally published in Microbiome!
link.springer.com/article/10.1...
Reposted by Vanessa Dumeaux 🇨🇦
rodrahimi.bsky.social
This is fascinating

“Furthermore, these findings raise questions about whether anti-PD-1 blockade during cancer immunotherapy provides a short-term anti-tumour effect at the cost of diminishing efficacy due to progressive loss of these critical high-affinity precursors.” #Immunology
labwaggoner.bsky.social Waggoner Lab @labwaggoner.bsky.social · 20h
Inhibitory PD-1 axis maintains high-avidity stem-like CD8+ T cells @nature.com #Germain @niaidnews.bsky.social
www.nature.com/articles/s41...
November 26, 2025 at 10:18 PM
vdumeaux.bsky.social
Happy to see this work finally published in Microbiome!
link.springer.com/article/10.1...
November 26, 2025 at 8:20 PM
Reposted by Vanessa Dumeaux 🇨🇦
impactt-microbiome.bsky.social
The Canadian Bioinformatics Hub is accepting applications for their recognition awards. Three awards are available: CBH Research & Innovation Award, Francis Ouellette Community Award, and CBH Impact Trainee Award. Apply by Dec 8, 2025: www.iscb.org/cbhc2026/cal...
Canadian Bioinformatics Hub Conference 2026. May 27-29, 2026, MaRS Discovery District, Toronto, Canada. Nominate Outstanding Contributors to Canada's Bioinformatics Community! Help us recognize the researchers and community builders shaping the future of bioinformatics in Canada! CBHC 2026 is accepting nominations for awards celebrating innovation, leadership, inclusivity, and trainee excellence across the BCBDS community. Eligible nominees include trainees, early-career, and mid-career professionals. Self-nominations welcome!
November 25, 2025 at 10:22 PM
Reposted by Vanessa Dumeaux 🇨🇦
bhaibeka.bsky.social
🚀 Ready to lead the next frontier of AI in health care and research?

UHN is hiring a Coordinator to spearhead the Blue Vest #AI Initiative at @PMResearch_UHN @PM_CDI to train student volunteers and empower clinicians & scientists.

📍 Toronto
🔗 Apply: smrtr.io/vC7zh
smrtr.io
November 24, 2025 at 7:25 PM
Reposted by Vanessa Dumeaux 🇨🇦
cs-dcc.bsky.social
The Canadian Bioinformatics Hub Training Award application deadline is coming up soon on Dec 1, 2025! Successful applicants will receive up to $2,500 CAD to attend a workshop, tutoral, or other training event in 2026. Learn more and apply: bioinformatics.ca/hub/training...
CBH Training Awards. About the Awards: CBH Training Awards fund up to $2,500 CAD for professional development for trainees in Canada. Apply to attend workshops, tutorials, and training events that address your training needs in Bioinformatics, Computational Biology, and Data Science. Application Deadline: Dec 1, 2025. Questions? training@bioinformatics.ca
November 24, 2025 at 8:19 PM
Reposted by Vanessa Dumeaux 🇨🇦
mucusman.bsky.social
I'm happy to share a perspective that
@soniamodilevsky.bsky.social
and I wrote about a new and exciting paper in @science.org
with big implications for IBD.
Check it out:
A bacterial toxin disarms gut defenses against inflammation | Science
www.science.org/doi/10.1126/...
A bacterial toxin disarms gut defenses against inflammation
Macrophage-toxic bacteria from patients with ulcerative colitis worsen gut inflammation in mice
www.science.org
November 20, 2025 at 8:28 PM
Reposted by Vanessa Dumeaux 🇨🇦
peeperlab.bsky.social
Our new paper is out in Nature - online today!
Huge congrats to shared first authors Sofía Ibáñez-Molero & Johanna Veldman, the whole team & all collaborators.
📄 Open-access paper: www.nature.com/articles/s41...
Tumour-reactive heterotypic CD8 T cell clusters from clinical samples - Nature
Tumour-reactive CD8+ T cells are enriched in functional clusters with tumour cells and/or antigen-presenting cells and can be isolated and expanded from clinical samples.
www.nature.com
November 19, 2025 at 9:00 PM
Reposted by Vanessa Dumeaux 🇨🇦
maryseberkhout.bsky.social
Akkermansia muciniphila has potential as a next-generation #probiotic, but can it claim a niche and persist in a pre-existing, complex microbial community (in vitro)? 🦠🔍

#microsky
#microbiomesky
#glycotime

link.springer.com/article/10.1...
Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community - Microbial Ecology
Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. Howe...
link.springer.com
November 20, 2025 at 11:27 AM
vdumeaux.bsky.social
Tier 2 Canada Research Chair in Cancer Biotherapeutics @westernu.ca London Canada!
Join our world-class cancer research initiative developing novel therapies that transform patient outcomes. @schulichmeddent.bsky.social www.uwo.ca/facultyrelat...
#AcademicJobs #AcademicSky #AcademicChatter
www.uwo.ca
November 16, 2025 at 4:30 PM
Reposted by Vanessa Dumeaux 🇨🇦
yuriquintana.com
MIT book Introduction to Machine Learning Systems by Vijay Janapa Reddi:
• PDF www.mlsysbook.ai/assets/downl...
• EPUB www.mlsysbook.ai
Data Engineering
Model Development
Optimization
Deployment
Infrastructure
Monitoring
Security, Privacy, Safety
Scaling
Responsible AI
Future
November 16, 2025 at 10:07 AM
Reposted by Vanessa Dumeaux 🇨🇦
victorgreiff.bsky.social
The AIRR-ML-2025 challenge is LIVE on @kaggle.com!
We’re challenging the best in #MachineLearning & #DataScience to decode the immune system.

💰 $10,000 prize pool
📄 Co-author a NatureMethods paper
November 15, 2025 at 3:31 PM
Reposted by Vanessa Dumeaux 🇨🇦
harriswang.bsky.social
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 13, 2025 at 8:53 PM
Reposted by Vanessa Dumeaux 🇨🇦
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Vanessa Dumeaux 🇨🇦
drjkhokhar.bsky.social
Come join us @westernu.ca @schulichmeddent.bsky.social as Canada Research Chair (CRC) Tier 2 in Cancer Biotherapeutics: uwo.ca/facultyrelat... DM me with questions. As a CRC 2 recruit to ACB, I highly recommend it!
uwo.ca
November 11, 2025 at 9:57 PM
Reposted by Vanessa Dumeaux 🇨🇦
cancersociety.bsky.social
Introducing Cancer Trials Canada - a new website to make it easier than ever to find cancer clinical trials happening across Canada.

Clinical trials test new ways to prevent, detect and treat cancer. They help advance research that can lead to better care and save lives.
November 10, 2025 at 2:37 PM
Reposted by Vanessa Dumeaux 🇨🇦
natmicrobiol.nature.com
#NewResearch

Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes

@rstepanauskas.bsky.social & co

#microsky

www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes - Nature Microbiology
Environmental micro-compartment genomics provides efficient and high-throughput single-particle DNA sequencing that captures overlooked members of microbial communities.
www.nature.com
November 7, 2025 at 11:19 AM
Reposted by Vanessa Dumeaux 🇨🇦
jeffspence.github.io
How do GWAS and rare variant burden tests rank gene signals?

In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!

🧬🧪🧵

www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
Reposted by Vanessa Dumeaux 🇨🇦
tsbschm.bsky.social
Great to see this finally published!

Metalog: curated and harmonised contextual data for global metagenomics samples

now out in @narjournal.bsky.social

academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
vdumeaux.bsky.social
very cool paper: t.co/mxObUMC8R4 Cancer cells can transfer their mitochondria to T-cells which impairs the immune response t.co/dkEv5L5Bb0
October 31, 2025 at 8:26 PM
Reposted by Vanessa Dumeaux 🇨🇦
ace-gtdb.bsky.social
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Reposted by Vanessa Dumeaux 🇨🇦
tommytang.bsky.social
Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors www.nature.com/articles/s4...
October 21, 2025 at 2:15 PM
Reposted by Vanessa Dumeaux 🇨🇦
westernu.ca
We’ve entered a new era in health care, driven by collaboration across disciplines and powerful tools like artificial intelligence and big data.

Your support will accelerate breakthroughs and improve patient care. #AllinWesternU

Learn more: allin.westernu.ca/optimizing-h...
Flag pole banners on Western's campus, one reads "All in", the other "Optimizing health for all"
October 21, 2025 at 7:30 PM
Reposted by Vanessa Dumeaux 🇨🇦
plosbiology.org
#Candida albicans is a leading opportunistic fungal #pathogen of humans. Ci Fu, Leah Cowen &co expand the GRACE #Calbicans #FunctionalGenomics resource, identifying genes important for temperature-dependent fitness & highlighting its power to reveal vulnerabilities @plosbiology.org 🧪 plos.io/3Wft0Xg
Screening of expanded GRACE mutant collection at six temperatures reveals distinct functional enrichment in genes clustered by fitness profile. Top left: Schematic of GRACE mutant construction. Bottom left: Summary of GRACE mutant collection expansion based on manual curation of biological process gene ontology annotation on Candida Genome Database (CGD). Pie chart with four concentric rings visualizes the relative proportion of genes from various versions of the GRACE collection with biological process descriptions completely unannotated or annotated based on: experimentally characterization, S. cerevisiae ortholog, S. pombe ortholog, orthologs in other fungal species, conserved protein domains, or unannotated; see Materials and methods for full details. Right: Heatmap of genes ordered by hierarchical clustering of essentiality scores across screening temperatures. A score of 4 (red) represents no growth and 0 (yellow) represents growth comparable to wild type.
October 20, 2025 at 12:55 PM
Reposted by Vanessa Dumeaux 🇨🇦
hutlab.bsky.social
Congrats to Yancong, Amrisha, Xochitl, Eric and all co-authors!!!
October 17, 2025 at 3:36 PM
Reposted by Vanessa Dumeaux 🇨🇦
natmethods.nature.com
MrVI, based on deep generative modeling, is a unified framework for integrative, exploratory, and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets. @justjhong.bsky.social @canergen.bsky.social @elhamazizi.bsky.social

www.nature.com/articles/s41...
Deep generative modeling of sample-level heterogeneity in single-cell genomics - Nature Methods
MrVI, based on deep generative modelling, is a unified framework for integrative, exploratory and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets.
www.nature.com
October 14, 2025 at 4:44 PM