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Jérôme Waldispühl

@waldispuhl.bsky.social

Associate Professor of Computer Science at McGill University. Bioinformatics & Video Games.

4 Posts62 Follower39 Folgt
Edoardo Gianni@edogia.bsky.social · 6mo ago

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n

A small polymerase ribozyme that can synthesize itself and its complementary strand

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

science.org

McGill Research + Innovation@mcgill-research.bsky.social · 10mo 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

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...

mcgill.ca

Elena Rivas@rivaselenarivas.bsky.social · 10mo 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...

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.

link.springer.com

Paul Gardner@ppgardne.bsky.social · 11mo 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.

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Otago Biochemistry@otagobiochemist.bsky.social · 11mo ago

We're looking for a new lecturer, here at the Department of Biochemistry in Dunedin, New Zealand. "Applications are invited in all areas of biochemistry, molecular genetics, and bioinformatics." otago.taleo.net/careersectio...

Jérôme Waldispühl@waldispuhl.bsky.social · 11mo ago

@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...

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...

mcgill.ca

Paul Gardner@ppgardne.bsky.social · 12mo ago

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

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 ...

nature.com

McGill News Magazine@mcgillnewsmag.bsky.social · last yr.

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...

Former Facebook VP champions Canadian digital sovereignty   - University Affairs

CIFAR AI Chair Joelle Pineau believes ethics and the common good must guide technological development.

universityaffairs.ca

D2R | DNA to RNA@d2rmcgill.bsky.social · last yr.

🚨 @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:

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…

buff.ly

McGill Science@mcgillscience.bsky.social · last yr.

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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Sean Eddy@cryptogenomicon.bsky.social · last yr.

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?

Jérôme Waldispühl@waldispuhl.bsky.social · last yr.

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

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...

nature.com