31 citations · 67 across the 8 of their papers we have counts for
8 papers
3D-based RNA function prediction tools in rnaglib
Carlos Oliver, Vincent Mallet, Jérôme Waldispühl
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, build…
RNAglib: A Python Package for RNA 2.5D Graphs
Vincent Mallet, Carlos Oliver, Jonathan Broadbent +2
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficientl…
VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs
Carlos Oliver, Vincent Mallet, Pericles Philippopoulos +2
RNA 3D motifs are recurrent substructures, modelled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automat…
Leveraging binding-site structure for drug discovery with point-cloud methods
Vincent Mallet, Carlos G. Oliver, Nicolas Moitessier +1
Computational drug discovery strategies can be broadly placed in two categories: ligand-based methods which identify novel molecules by similarity with known ligands, and structure…
10 simple rules to create a serious game, illustrated with examples from structural biology
Marc Baaden, Olivier Delalande, Nicolas Ferey +3
Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and resea…
The Topology of Biological Networks from a Complexity Perspective
Ali Atiia, François Major, Jérôme Waldispühl
A complexity-theoretic approach to studying biological networks is proposed. A simple graph representation is used where molecules (DNA, RNA, proteins and chemicals) are vertices a…
Using structural and evolutionary information to detect and correct pyrosequencing errors in non-coding RNAs
Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in s…
Flexible RNA design under structure and sequence constraints using formal languages
Yu Zhou, Yann Ponty, Stéphane Vialette +3
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or…