Vanessa Dumeaux 🇨🇦

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

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-...

very cool paper: t.co/mxObUMC8R4 Cancer cells can transfer their mitochondria to T-cells which impairs the immune response t.co/dkEv5L5Bb0

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

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-...

Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors www.nature.com/articles/s4...

Flag pole banners on Western's campus, one reads "All in", the other "Optimizing health for all"

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...

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.

#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

Congrats to Yancong, Amrisha, Xochitl, Eric and all co-authors!!!

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.

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...

Want to be our colleague? We have a faculty position in microbial systems biology looking for candidates. Please share. www.rh.ulaval.ca/emplois-disp...

SciLifeLab launches major recruitment call for staff scientists in computational biology, data science and AI Computational methods and artificial intelligence on large-scale molecular data are transforming the study of biological systems and processes, ranging from molecular structures and cellular processes...

We’re launching a major #recruitment call for staff scientists in #ComputationalBiology, #DataScience, and #AI to strengthen Sweden’s life science research. 🧪🖥️

Positions are based at SciLifeLab sites across Sweden’s leading universities.

Learn more and apply ↓
www.scilifelab.se/news/scilife...

Microbiology & Immunology at Western University is hiring a tenure-track Assistant Professor in the area of Neurovirology. Read the description here: www.uwo.ca/facultyrelat...

Microbiology & Immunology at Western University is hiring a tenure-track Assistant Professor in the area of T cell Biology and Neuroimmunology - one of two positions available. Full description here: www.uwo.ca/facultyrelat...

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.

Scvi-hub is a versatile and efficient platform for model-based analysis of single-cell sequencing studies with access to a diverse array of datasets and downstream analysis. @canergen.bsky.social

www.nature.com/articles/s41...

High costs motivate efforts to predict spatial transcriptomics from H&E images w/ deep learning. In our recent preprint, we show that noise, sparsity & resolution in ST data impact performance, highlighting the importance of training data quality: www.biorxiv.org/content/10.1...

🧵1/n

Now is the time to sign up for the Run for the Cure!

From now until 11:59 p.m. PST on September 10, 2025, all donations in support of the #CIBCRunForTheCure will be matched by CIBC, dollar for dollar, up to $500,000.

Conditional generation of real antigen-specific T cell receptor sequences @natmachintell.nature.com
www.nature.com/articles/s42...

GloMiNe2025

Atlantic session

Pacific session

Tomorrow begins #GloMiNe2025 organized by @microbiotavault.bsky.social & #MVIF

Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior

Both sessions will be LIVE!

Check the details: cassyni.com/s/mvif-glomi...

This is the absolute beauty coming from @rayanchikhi.bsky.social et al! 🔥😍 If you don't quite yet fully know what Logan is and what it is capable of: check the 🧵 and most importantly the updated preprint 📑. One of those things to print and simply admire 🧠🩷

Scientists in training should be taught the creative scientific process, to gain confidence in their self-efficacy for research and identity as a scientist, & also for greater work satisfaction and a better chance of remaining in science long-term. Join our community at www.night-science.org

New review 🔥 Single-cell RNA-Seq has been revolutionary for studying eukaryotic cells and now it's time for it to do the same for microbes! We describe the technology for single-bacterium RNA-Seq & the questions now studied using it.🧵⬇️
science.org/doi/10.1126/...
@andrewpountain.bsky.social

mvif season 5 keynotes

Season 5 is going to start 🔜

Check out the program and
feel free to join the keynotes by presenting your work–abstract submission is open www.microbiome-vif.org/en-US/-/info...

@kathlemon.bsky.social ‬ @saramitri.bsky.social @simrouxvirus.bsky.social @halllab.bsky.social @deepaagashe.bsky.social

Mutational landscape of triple-negative breast cancer in African American women - Nature Genetics This study explores the genomic and transcriptomic landscapes of triple-negative breast cancer in African American women. The authors show that the mutational profile is broadly similar to that observ...

Mutational landscape of triple-negative breast cancer in African American women
www.nature.com/articles/s41...

Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data - Nature Communications Spatial expression assays are affected by segmentation errors leading to difficulty interpreting cell types. Here, the authors introduce a machine learning model to infer cell types accounting for suc...

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...

FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance Nature Microbiology - An online, manually curated and continually updating database of fungal antimicrobial resistance mutations provides a starting point for further research in fungal AMR.

#Resource

An online, manually curated, and continually updating database of fungal antimicrobial resistance mutations that provides a starting point for further research in fungal AMR

@christianlandry.bsky.social @camillebed17.bsky.social @nmquijada.bsky.social

#MicroSky 🦠🍄💉

rdcu.be/eAUZm

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...

The creative process in science has a set of thinking tools that we could do a better job teaching. Here are the 12 articles that Martin and I wrote about them, including "It takes two to think", "A hypothesis is a liability" and "The two languages of science". night-science.org/home/learn/r...

RNAi epimutations conferring antifungal drug resistance are inheritable - Nature Communications Epimutations mediated by RNA interference can confer antifungal drug resistance and affect virulence in fungi. Here, the authors show that these epigenetic modifications can be transmitted across gene...

Epi-adapting to adverse conditions www.nature.com/articles/s41...

Logo for the Canadian fungal research Network meeting

CanFunNet25 🍄🇨🇦 starts tomorrow!
So excited for all the presentations!

Check out the conference website for more info: canfunnet.conferences.uwo.ca

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

New in @natbiotech.nature.com: a team led by scientists at MSK and ‪University of Toronto have developed a new platform to facilitate the study of RNA-biding proteins (RBPs) across hundreds of species of plants, insects, and animals.