Jérôme Waldispühl
Jérôme Waldispühl
Associate Professor of Computer Science, McGill University
Verified email at mcgill.ca - Homepage
Cited by
Cited by
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
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), e00031-18, 2018
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
Efficient algorithms for probing the RNA mutation landscape
J Waldispühl, S Devadas, B Berger, P Clote
PLoS Comput Biol 4 (8), e1000124, 2008
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
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
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
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
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
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
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
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 (10), R116, 2013
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
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure
J Waldispühl, Y Ponty
Journal of Computational Biology 18 (11), 1465-1479, 2011
Modeling and predicting all-α transmembrane proteins including helix–helix pairing
J Waldispühl, JM Steyaert
Theoretical Computer Science 335 (1), 67-92, 2005
Energy landscape of k-point mutants of an RNA molecule
P Clote, J Waldispühl, B Behzadi, JM Steyaert
Bioinformatics 21 (22), 4140-4147, 2005
An approximate matching algorithm for finding (sub-) optimal sequences in S-attributed grammars
J Waldispühl, B Behzadi, JM Steyaert
Bioinformatics 18 (suppl_2), S250-S259, 2002
SPARCS: a web server to analyze (un) structured regions in coding RNA sequences
Y Zhang, Y Ponty, M Blanchette, E Lecuyer, J Waldispühl
Nucleic acids research 41 (W1), W480-W485, 2013
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
J Waldispühl, S Devadas, B Berger, P Clote
Nucleic acids research 37 (suppl_2), W281-W286, 2009
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