Jérôme Waldispühl

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Vladimir ReinharzAssistant Professor, Computer Science Department, Université du Québec à MontréalVerified email at uqam.ca
Mathieu BlanchetteProfessor of Computer Science, McGill UniversityVerified email at cs.mcgill.ca
Yann PontyResearch director at CNRS & Ecole PolytechniqueVerified email at lix.polytechnique.fr
Bonnie BergerMITVerified email at mit.edu
Carlos OliverAssistant Professor of Molecular Physiology and Biophysics, Vanderbilt UniversityVerified email at vanderbilt.edu
Peter CloteBoston CollgeVerified email at bc.edu
Roman Sarrazin-GendronAssistant Professor of Computer Science, UQAMVerified email at uqam.ca
Srinivas DevadasEdwin Sibley Webster Professor of Electrical Engineering and Computer Science, MITVerified email at mit.edu
Vincent MalletCBIO, Mines Paris - PSL, Institut CurieVerified email at mail.mcgill.ca
Charles W. O'DonnellPostdoctoral Fellow - MIT, HarvardVerified email at mit.edu
Alfred KamSchool of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, CanadaVerified email at mail.mcgill.ca
Nicolas MoitessierMcGill UniversityVerified email at mcgill.ca
Eleyine ZarourRadiology resident, University of MontrealVerified email at umontreal.ca
Mohamed Raef SmaouiAssociate Professor, Computer Science Dept., Kuwait UniversityVerified email at ku.edu.kw
Clarence LeungMcGill UniversityVerified email at mail.mcgill.ca
Francois MajorUniversite de MontrealVerified email at umontreal.ca
Mieszko LisThe University of British ColumbiaVerified email at ece.ubc.ca
Matan Drory RetwitzerAssoc. Director, Data ScienceVerified email at mammothbiosci.com
Danny BarashBen-Gurion UniversityVerified email at bgu.ac.il
Rob KnightWolfe Family Chair at Rady Children's; Director, Center for Microbiome Innovation; Professor, UCSDVerified email at ucsd.edu

Jérôme Waldispühl

Associate Professor of Computer Science, McGill University

Verified email at mcgill.ca - Homepage

RNA Bioinformatics Citizen Science Crowdsourcing Algorithms Video Games


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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	751	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	297	2012
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	95	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	84	2011
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	75	2019
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	69	2013
`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	68	2020
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	61	2012
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	58	2018
Efficient algorithms for probing the RNA mutation landscape J Waldispühl, S Devadas, B Berger, P Clote PLoS computational biology 4 (8), e1000124, 2008	58	2008
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	49	2012
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	48	2020
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	48	2013
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	48	2006
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	46	2018
Leveling up citizen science J Waldispühl, A Szantner, R Knight, S Caisse, R Pitchford Nature Biotechnology 38 (10), 1124-1126, 2020	45	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	42	2013
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	37	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	36	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	35	2007

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