Jérôme Waldispühl

Nineteen new or renewed Canada Research Chairs awarded to McGill Federal investment boosts McGill’s research leadership with over $13 million for Canada Research Chairs Today, the Honourable Mélanie Joly, Minister of Industry and Minister responsible for Canada Eco...

A big boost for cutting-edge research at #McGill 🙌

19 McGill researchers were awarded Canada Research Chairs (new + renewed) supported by a $13M investment from the Government of Canada through the #CRC program 🎉👏 mcgill.ca/x/izt

RNA3DB 2025-10-01 release
github.com/marcellszi/r...
#RNA #RNAsky

The database of all RNA chains in PDB arranged in structurally disimilar components, including Rfam annotation.

More chains (25,666), more independent components (144), more Rfam families represented (853).

All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods Structural RNAs exhibit a vast array of recurrent short three-dimensional (3D) elements found in loop regions involving non-Watson–Crick interactions that help arrange canonical double helices into tertiary structures. Here we present CaCoFold-R3D, a probabilistic grammar that predicts these RNA 3D motifs (also termed modules) jointly with RNA secondary structure over a sequence or alignment. CaCoFold-R3D uses evolutionary information present in an RNA alignment to reliably identify canonical helices (including pseudoknots) by covariation. Here we further introduce the R3D grammars, which also exploit helix covariation that constrains the positioning of the mostly noncovarying RNA 3D motifs. Our method runs predictions over an almost-exhaustive list of over 50 known RNA motifs (‘everything’). Motifs can appear in any nonhelical loop region (including three-way, four-way and higher junctions) (‘everywhere’). All structural motifs as well as the canonical helices are arranged into one single structure predicted by one single joint probabilistic grammar (‘all-at-once’). Our results demonstrate that CaCoFold-R3D is a valid alternative for predicting the all-residue interactions present in a RNA 3D structure. CaCoFold-R3D is fast and easily customizable for novel motif discovery and shows promising value both as a strong input for deep learning approaches to all-atom structure prediction as well as toward guiding RNA design as drug targets for therapeutic small molecules.

Integrated prediction of RNA secondary structure jointly with 3D motifs and pseudoknots guided by evolutionary information.
@aakaran31.bsky.social and @rivaselenarivas.bsky.social

link.springer.com/article/10.1...

Are you looking for a lectureship in biochemistry, molecular genetics, or bioinformatics? Come and enjoy the greatest place for kayak fishing and a fun research+teaching career.

*there are other fun things to do here too.

Event | Seminar, Computer-based Predictions of RNA Structures: Where do we stand? Join D2R for this hybrid seminar with Professor Eric Westhof from University of Strasbourg From its origins in the 1960s to today’s cutting-edge approaches, this keynote will highlight evolution of RN...

@d2rmcgill.bsky.social will host a seminar of Eric Westhof on Sep 24. Join us if you want to discuss where we stand in RNA structure prediction!
www.mcgill.ca/dna-to-rna/c...

we asked a simple question:
What does it take to learn the rules of RNA base pairing?

using standard deep-learning technics, got a simple answer:
don't need structures, nor alignments or many parameters
only a few RNA sequences and 21 parameters;
doi.org/10.1101/2025...

Guanidine aptamers are present in vertebrate RNAs associated with calcium signaling and neuromuscular function - Nature Communications 150 years ago, guanidine was found to affect muscle function via unknown mechanisms. Here, Kavita et al. provide evidence that guanine-sensing RNAs are present in many eukaryotic transcripts relevant ...

www.nature.com/articles/s41... From remote matches to @rfamdb.bsky.social models to the discovery of novel *vertebrate* riboswitches!

Former Facebook VP champions Canadian digital sovereignty   - University Affairs CIFAR AI Chair Joelle Pineau believes ethics and the common good must guide technological development.

McGill’s Joelle Pineau on the work she did as the VP of AI research at Meta, why Canada needs to plan for its digital sovereignty, and why she has little patience for “sensational claims” about how “we’re in imminent peril of a technological apocalypse” universityaffairs.ca/features/for...

Canada Excellence Research Chair (CERC) in RNA Neurotherapeutics Please refer to the How to Apply for a Job (for External Candidates) job aid for instructions on how to apply. If you are an active McGill employee (ie: currently in an active contract or position at…

🚨 @healthsciences.mcgill.ca‬ is recruiting: Canada Excellence Research Chair in #RNA Neurotherapeutics

Looking for an established leader in RNA research in the brain with an innovative research program in RNA-related research in neuropsychiatry.

✍ Apply by July 4:

Génome Québec est heureux de lancer le 5e cycle du Programme d’intégration de la #génomique – #agriculture et #bioalimentaire, #foresterie et #environnement.

La date limite pour soumettre une demande est le 20 octobre 2025. Pour plus d’information 👉 rb.gy/kjs0vq

Are you a McGill student interested in developing your science communications skills? We’re looking for a communications intern to help us build awareness of Faculty of Science research, students, publications, events, and other initiatives.

Apply by June 19 ➡️ mcgill.ca/x/iQK

Phage people: Rich Losick and I are combing the world looking for T4 rIIB mutant FC0 (also known as P13). FC0 was the starting point for Francis Crick's beautiful 1961 paper on the triplet nature of the genetic code. We want to sequence it. Anyone have it in an ancient stock collection?

🧬🌊 code Béluga : un projet de science participative pour mieux comprendre le fleuve Saint-Laurent.

Participez aux collectes d’eau de mai à août 2025!

🎥 Pour regarder notre capsule vidéo 👉 rb.gy/sakf14

📍 Infos et lieux d’échantillonnage 👉 rb.gy/vyk0n9

Our first panel talk is LIVE!

Jérôme Waldispühl kicks things off with Leveling Up Citizen Science for (meta)genomic research
@waldispuhl.bsky.social
Join #MVIF 38 👇
🔗 cassyni.com/s/mvif-38

#Microbiome #MeetTheSpeakers

MVIF 38

NEXT WEEK don't miss #MVIF 38 on Microbiome and Citizen Science
👉https://cassyni.com/s/mvif-38

& meet:
🇫🇷 @patrickveiga.bsky.social & Mathieu Almeida
🇮🇹Claudia Cappello

🇨🇦 @waldispuhl.bsky.social
🇺🇸Daniel McDonald
🇺🇸Mikayla A. Borton
🇧🇪Sarah Ahannach

🇳🇱Saara Suominen
🇺🇸 @gilbertjacka.bsky.social

MVIF 38

It’s Friday
...and a new #MVIF program is out! 🤩

Register👉 cassyni.com/s/mvif-38

Contributed talks by
🇫🇷 @patrickveiga.bsky.social
🇮🇹 Claudia Cappello

Keynotes:
🇨🇦 @waldispuhl.bsky.social
🇺🇸Daniel McDonald
🇺🇸Mikayla A. Borton
🇧🇪Sarah Ahannach

Moderators:
🇳🇱 Saara Suominen
🇺🇸 @gilbertjacka.bsky.social

RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning - Nature Communications RNA is a promising reservoir of new drug targets. Here, the authors introduce RNAmigos2, a structure-based deep learning model that speeds up screening by 10,000x while rivaling docking accuracy, show...

Our latest work in RNA bioinformatics was published today: www.nature.com/articles/s41...
If you are looking for a tool to speed up RNA virtual screening, this is for you.
Congrats to the team and thank you to @genomequebec.bsky.social , FRQNT, and NSERC for the support!
@mcgillscience.bsky.social

Visit the Faculty of Science crowdfunding page to learn about some of the great student-run initiatives raising money this #McGill24, like the McGill Biochemistry Undergraduate Society (BUGS)!

➡️ crowdfunding.mcgill.ca/ui/main/t/sc...

Integration of 168,000 samples reveals global patterns of the human gut microbiome The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

Another really interesting microbiome paper worth checking out www.cell.com/cell/fulltex...

The January issue is live nature.com/nbt/volumes/...

On our cover, a minigame integrated within a popular video game let more than 4 million players contribute to improving a multiple sequence alignment for microbial phylogeny estimations and association go.nature.com/4aSfOg6

Tertiary structure comparisons between 23 experimentally determined small RNA structures and the best structure prediction selected from 18 different groups.

The latest RNA-Puzzles paper is out (CASP for RNA structure prediction). Check how wild some of the best predictions are for these small RNAs. We're still a long way from a reliable AlphaFold for RNA.

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