Jérôme Waldispühl
@waldispuhl.bsky.social
📤 52
📥 34
📝 3
Associate Professor of Computer Science at McGill University. Bioinformatics & Video Games.
McGill is recruiting talents from abroad through the Canada Impact+ Research Chairs program. The deadline is tight (Late Jan). Learn more about it at:
www.mcgill.ca/research/res...
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Canada Impact+ Research Chairs Competition
McGill University, a world-renowned research intensive institution, invites applications for the Canada Impact+ Research Chairs (Impact+) Program, open to the rank of Associate or Full Professor. The ...
https://www.mcgill.ca/research/research/funding/mcgill-recruitment-canada-impact-research-chairs
21 days ago
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Jérôme Waldispühl
Elena Rivas
2 months ago
RNA BENASQUE July 05-17 2026
add a skeleton here at some point
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Jérôme Waldispühl
McGill Research + Innovation
3 months ago
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
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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...
https://mcgill.ca/x/izt
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Jérôme Waldispühl
Elena Rivas
3 months ago
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).
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Jérôme Waldispühl
Elena Rivas
3 months ago
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...
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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.
https://link.springer.com/article/10.1038/s41592-025-02833-w
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Jérôme Waldispühl
Paul Gardner
4 months ago
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.
add a skeleton here at some point
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@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...
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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...
https://www.mcgill.ca/dna-to-rna/channels/news/event-seminar-computer-based-predictions-rna-structures-where-do-we-stand-367001
4 months ago
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reposted by
Jérôme Waldispühl
Elena Rivas
5 months ago
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...
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https://doi.org/10.1101/2025.07.31.668042
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Jérôme Waldispühl
Paul Gardner
5 months ago
www.nature.com/articles/s41...
From remote matches to
@rfamdb.bsky.social
models to the discovery of novel *vertebrate* riboswitches!
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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 ...
https://www.nature.com/articles/s41467-025-62815-6
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Jérôme Waldispühl
McGill News Magazine
6 months ago
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...
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Former Facebook VP champions Canadian digital sovereignty - University Affairs
CIFAR AI Chair Joelle Pineau believes ethics and the common good must guide technological development.
https://universityaffairs.ca/features/former-facebook-vp-champions-canadian-digital-sovereignty/
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Jérôme Waldispühl
D2R | DNA to RNA
7 months ago
🚨
@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:
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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…
https://buff.ly/i91YdJK
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Jérôme Waldispühl
Génome Québec
7 months ago
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
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Jérôme Waldispühl
McGill Science
7 months ago
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
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Jérôme Waldispühl
Sean Eddy
7 months ago
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?
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Jérôme Waldispühl
Génome Québec
9 months ago
🧬🌊 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
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YouTube
Share your videos with friends, family, and the world
https://rb.gy/sakf14
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Jérôme Waldispühl
Microbiome Virtual International Forum
9 months ago
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
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reposted by
Jérôme Waldispühl
Microbiome Virtual International Forum
9 months ago
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
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reposted by
Jérôme Waldispühl
Microbiome Virtual International Forum
9 months ago
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
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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
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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...
https://www.nature.com/articles/s41467-025-57852-0
10 months ago
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Jérôme Waldispühl
McGill Science
10 months ago
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...
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Jérôme Waldispühl
Jonathan Eisen
12 months ago
Another really interesting microbiome paper worth checking out
www.cell.com/cell/fulltex...
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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...
https://www.cell.com/cell/fulltext/S0092-8674(24)01430-2
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Jérôme Waldispühl
Nature Biotechnology
12 months ago
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
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Jérôme Waldispühl
Paul Gardner
about 1 year ago
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...
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