User profiles for Jérôme Waldispühl
Jérôme WaldispühlAssociate Professor of Computer Science, McGill University Verified email at mcgill.ca Cited by 2320 |
Design of RNAs: comparing programs for inverse RNA folding
Computational programs for predicting RNA sequences with desired folding properties have
been extensively developed and expanded in the past several years. Given a secondary …
been extensively developed and expanded in the past several years. Given a secondary …
A method for probing the mutational landscape of amyloid structure
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 …
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
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 …
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 …
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
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 …
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
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, …
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
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 …
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’ …
games are among the most played categories. These games capitalize on the players’ …
Augmented base pairing networks encode RNA-small molecule binding preferences
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 …
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
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 …
serious goals include crucial activities for scientists: outreach, teaching and research. The …