User profiles for Jérôme Waldispühl

Jérôme Waldispühl

Associate Professor of Computer Science, McGill University
Verified email at mcgill.ca
Cited by 2320

Design of RNAs: comparing programs for inverse RNA folding

…, V Reinharz, Y Ponty, J Waldispühl… - Briefings in …, 2018 - academic.oup.com
Computational programs for predicting RNA sequences with desired folding properties have
been extensively developed and expanded in the past several years. Given a secondary …

A method for probing the mutational landscape of amyloid structure

CW O'Donnell, J Waldispühl, M Lis, R Halfmann… - …, 2011 - academic.oup.com
Motivation: Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates
known as amyloid fibrils, important both biologically and clinically. However, the specific …

Challenges and current status of computational methods for docking small molecules to nucleic acids

J Luo, W Wei, J Waldispühl, N Moitessier - European journal of medicinal …, 2019 - Elsevier
Since the development of the first docking program in 1982, the use of docking-based in silico
screening for potentially bioactive molecule discovery has become a common strategy in …

[HTML][HTML] Leveling up citizen science

J Waldispühl, A Szantner, R Knight, S Caisse… - Nature …, 2020 - nature.com
To the Editor—Over the past decade, online science discovery games (SDGs) have become
an increasingly popular practice for engaging the public in research activities. This …

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

…, A Soulé, E Westhof, J Waldispühl… - Nucleic acids …, 2018 - academic.oup.com
The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to
assemble into sophisticated interaction networks, which are used to create complex 3D …

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

V Reinharz, F Major, J Waldispühl - Bioinformatics, 2012 - academic.oup.com
Motivation: The prediction of RNA 3D structures from its sequence only is a milestone to RNA
function analysis and prediction. In recent years, many methods addressed this challenge, …

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

V Reinharz, Y Ponty, J Waldispühl - Bioinformatics, 2013 - academic.oup.com
Motivations: The design of RNA sequences folding into predefined secondary structures is a
milestone for many synthetic biology and gene therapy studies. Most of the current software …

Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems?

…, M Blanchette, A Szantner, J Waldispühl - Proceedings of the …, 2023 - dl.acm.org
With nearly three billion players, video games are more popular than ever. Casual puzzle
games are among the most played categories. These games capitalize on the players’ …

Augmented base pairing networks encode RNA-small molecule binding preferences

…, WL Hamilton, N Moitessier, J Waldispühl - Nucleic acids …, 2020 - academic.oup.com
RNA-small molecule binding is a key regulatory mechanism which can stabilize 3D structures
and activate molecular functions. The discovery of RNA-targeting compounds is thus a …

[HTML][HTML] Ten simple rules to create a serious game, illustrated with examples from structural biology

…, N Ferey, S Pasquali, J Waldispühl… - PLoS computational …, 2018 - journals.plos.org
Serious scientific games are games whose purpose is not just fun. In the field of science, the
serious goals include crucial activities for scientists: outreach, teaching and research. The …