Jérôme Waldispühl
Jérôme Waldispühl
Associate Professor of Computer Science, McGill University
Verified email at - Homepage
Cited by
Cited by
American gut: an open platform for citizen science microbiome research
D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ...
Msystems 3 (3), 10.1128/msystems. 00031-18, 2018
Phylo: a citizen science approach for improving multiple sequence alignment
A Kawrykow, G Roumanis, A Kam, D Kwak, C Leung, C Wu, E Zarour, ...
PloS one 7 (3), e31362, 2012
A method for probing the mutational landscape of amyloid structure
CW O'Donnell, J Waldispühl, M Lis, R Halfmann, S Devadas, S Lindquist, ...
Bioinformatics 27 (13), i34-i42, 2011
Design of RNAs: comparing programs for inverse RNA folding
A Churkin, MD Retwitzer, V Reinharz, Y Ponty, J Waldispühl, D Barash
Briefings in bioinformatics 19 (2), 350-358, 2018
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 chemistry 168, 414-425, 2019
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 28 (12), i207-i214, 2012
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery
J Boitreaud, V Mallet, C Oliver, J Waldispuhl
Journal of Chemical Information and Modeling 60 (12), 5658-5666, 2020
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution
V Reinharz, Y Ponty, J Waldispühl
Bioinformatics 29 (13), i308-i315, 2013
Efficient algorithms for probing the RNA mutation landscape
J Waldispühl, S Devadas, B Berger, P Clote
PLoS computational biology 4 (8), e1000124, 2008
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families
V Reinharz, A Soulé, E Westhof, J Waldispühl, A Denise
Nucleic acids research 46 (8), 3841-3851, 2018
Predicting transmembrane β‐barrels and interstrand residue interactions from sequence
J Waldispühl, B Berger, P Clote, JM Steyaert
PROTEINS: Structure, Function, and Bioinformatics 65 (1), 61-74, 2006
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates
MR Smaoui, F Poitevin, M Delarue, P Koehl, H Orland, J Waldispühl
Biophysical journal 104 (3), 683-693, 2013
A global sampling approach to designing and reengineering RNA secondary structures
A Levin, M Lis, Y Ponty, CW O’Donnell, S Devadas, B Berger, ...
Nucleic acids research 40 (20), 10041-10052, 2012
Leveling up citizen science
J Waldispühl, A Szantner, R Knight, S Caisse, R Pitchford
Nature Biotechnology 38 (10), 1124-1126, 2020
Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment
D Kwak, A Kam, D Becerra, Q Zhou, A Hops, E Zarour, A Kam, ...
Genome biology 14, 1-12, 2013
Ten simple rules to create a serious game, illustrated with examples from structural biology
M Baaden, O Delalande, N Ferey, S Pasquali, J Waldispühl, A Taly
PLoS computational biology 14 (3), e1005955, 2018
Augmented base pairing networks encode RNA-small molecule binding preferences
C Oliver, V Mallet, RS Gendron, V Reinharz, WL Hamilton, N Moitessier, ...
Nucleic acids research 48 (14), 7690-7699, 2020
Modeling ensembles of transmembrane β‐barrel proteins
J Waldispühl, CW O'Donnell, S Devadas, P Clote, B Berger
Proteins: Structure, Function, and Bioinformatics 71 (3), 1097-1112, 2008
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels
J Waldispühl, B Berger, P Clote, JM Steyaert
Nucleic acids research 34 (suppl_2), W189-W193, 2006
Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model
J Waldispühl, P Clote
Journal of Computational Biology 14 (2), 190-215, 2007
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