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ORCIDJérôme Waldispühl
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2020 – today
- 2024
[j36]Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette
, Jérôme Waldispühl:
PERFUMES: pipeline to extract RNA functional motifs and exposed structures. Bioinform. 40(2) (2024)- [j35]Chrisostomos Drogaris, Yanlin Zhang, Eric Zhang, Elena Nazarova, Roman Sarrazin-Gendron, Sélik Wilhelm-Landry, Yan Cyr, Jacek Majewski, Mathieu Blanchette, Jérôme Waldispühl:
ARGV: 3D genome structure exploration using augmented reality. BMC Bioinform. 25(1): 277 (2024) - [c18]Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghasemloo Gheidari, Alexander Butyaev, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl:
Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. FDG 2024: 31 - [i5]Carlos G. Oliver, Vincent Mallet, Jérôme Waldispühl:
3D-based RNA function prediction tools in rnaglib. CoRR abs/2402.09330 (2024) - 2023
- [c17]J. White Bear, Grégoire De Bisschop, Eric Lécuyer, Jérôme Waldispühl:
Localized, Non-parametric Detection of RNA Structural Modification using Nanopore Basecalling. BCB 2023: 38:1-38:8 - [c16]Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl:
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? CHI 2023: 679:1-679:15 - [c15]Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl:
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. CI 2023: 53-62 - 2022
- [j34]Carlos G. Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl:
Vernal: a tool for mining fuzzy network motifs in RNA. Bioinform. 38(4): 970-976 (2022) - [j33]Vincent Mallet, Carlos G. Oliver, Jonathan Broadbent, William L. Hamilton, Jérôme Waldispühl:
RNAglib: a python package for RNA 2.5 D graphs. Bioinform. 38(5): 1458-1459 (2022) - [c14]Elena Nazarova, Alexander Butyaev, Mohamed Youssef Bouaouina, Dominic Filion, Jérôme Waldispühl:
Adaptive Instructional System for Complex Equipment Trainings in the Post-covid Era: Breaking the Ice of Time-Consuming Tasks. HCI (31) 2022: 207-225 - 2021
- [j32]Antoine Soulé, Vladimir Reinharz, Roman Sarrazin-Gendron, Alain Denise, Jérôme Waldispühl:
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. PLoS Comput. Biol. 17(5) (2021) - 2020
- [j31]Ali Atiia, Corbin Hopper, Katsumi Inoue, Silvia Vidal, Jérôme Waldispühl:
Computational intractability law molds the topology of biological networks. Appl. Netw. Sci. 5(1): 34 (2020) - [j30]David Becerra, Alexander Butyaev, Jérôme Waldispühl:
Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation. Bioinform. 36(5): 1420-1428 (2020) - [j29]Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash:
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. Bioinform. 36(9): 2920-2922 (2020) - [j28]Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl:
A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. J. Comput. Biol. 27(3): 390-402 (2020) - [j27]Jacques Boitreaud, Vincent Mallet, Carlos G. Oliver, Jérôme Waldispühl:
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery. J. Chem. Inf. Model. 60(12): 5658-5666 (2020) - [c13]Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl:
Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. RECOMB 2020: 186-201 - [i4]Carlos G. Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl:
VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA. CoRR abs/2009.00664 (2020)
2010 – 2019
- 2019
- [j26]Wanlei Wei, Jiaying Luo, Jérôme Waldispühl, Nicolas Moitessier:
Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes. J. Chem. Inf. Model. 59(6): 2941-2951 (2019) - [i3]Vincent Mallet, Carlos G. Oliver, Nicolas Moitessier, Jérôme Waldispühl:
Leveraging binding-site structure for drug discovery with point-cloud methods. CoRR abs/1905.12033 (2019) - 2018
- [j25]Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash:
Design of RNAs: comparing programs for inverse RNA folding. Briefings Bioinform. 19(2): 350-358 (2018) - [j24]Marc Baaden, Olivier Delalande, Nicolas Férey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly:
Ten simple rules to create a serious game, illustrated with examples from structural biology. PLoS Comput. Biol. 14(3) (2018) - [c12]Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl:
A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. RECOMB 2018: 177-193 - 2017
- [j23]Zheng Dai, David Becerra, Jérôme Waldispühl:
On Stable States in a Topologically Driven Protein Folding Model. J. Comput. Biol. 24(9): 851-862 (2017) - [j22]Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl:
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. Nucleic Acids Res. 45(Webserver-Issue): W440-W444 (2017) - [j21]Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl:
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. Nucleic Acids Res. 45(Webserver-Issue): W573 (2017) - [c11]Ali Atiia, Corbin Hopper, Jérôme Waldispühl:
Computational Intractability Generates the Topology of Biological Networks. BCB 2017: 500-509 - [c10]Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl:
Lessons from an Online Massive Genomics Computer Game. HCOMP 2017: 177-186 - [i2]Marc Baaden, Olivier Delalande, Nicolas Férey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly:
10 simple rules to create a serious game, illustrated with examples from structural biology. CoRR abs/1708.04176 (2017) - 2016
- [j20]Mohamed Raef Smaoui, Cody Mazza-Anthony, Jérôme Waldispühl:
Investigating Mutations to Reduce Huntingtin Aggregation by Increasing Htt-N-Terminal Stability and Weakening Interactions with PolyQ Domain. Comput. Math. Methods Medicine 2016: 6247867:1-6247867:12 (2016) - [j19]Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash:
incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res. 44(Webserver-Issue): W308-W314 (2016) - [c9]Olivier Tremblay Savard, Alexander Butyaev, Jérôme Waldispühl:
Collaborative Solving in a Human Computing Game Using a Market, Skills and Challenges. CHI PLAY 2016: 130-141 - 2015
- [j18]Mohamed Raef Smaoui, Henri Orland, Jérôme Waldispühl:
Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes. Bioinform. 31(14): 2294-2302 (2015) - [j17]Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl:
Preface. J. Comput. Biol. 22(3): 189 (2015) - [c8]Jérôme Waldispühl, Arthur Kam, Paul P. Gardner:
Crowdsourcing RNA Structural Alignments with an Online Computer Game. Pacific Symposium on Biocomputing 2015: 330-341 - [i1]Mohammed Shamrani, François Major, Jérôme Waldispühl:
Evolution by Computational Selection. CoRR abs/1505.02348 (2015) - 2014
- [j16]Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. 21(7): 477-491 (2014) - [j15]Eric A. Yen, Aaron Tsay, Jérôme Waldispühl, Jackie Vogel:
Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks. PLoS Comput. Biol. 10(5) (2014) - [c7]Jérôme Waldispühl, Mathieu Blanchette:
Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. HCOMP 2014: 73-74 - [e1]Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl:
Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), Strasbourg, France, September 7, 2014. McGill University 2014 [contents] - 2013
- [j14]Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinform. 29(13): 308-315 (2013) - [j13]Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. J. Comput. Biol. 20(11): 905-919 (2013) - [j12]Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl:
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res. 41(Webserver-Issue): 480-485 (2013) - [c6]Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise:
Flexible RNA design under structure and sequence constraints using formal languages. BCB 2013: 229 - [c5]Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. RECOMB 2013: 199-211 - 2012
- [j11]Vladimir Reinharz, François Major, Jérôme Waldispühl:
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinform. 28(12): 207-214 (2012) - 2011
- [j10]Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger:
A method for probing the mutational landscape of amyloid structure. Bioinform. 27(13): 34-42 (2011) - [j9]Jérôme Waldispühl, Yann Ponty:
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. J. Comput. Biol. 18(11): 1465-1479 (2011) - [j8]Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl:
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. J. Comput. Biol. 18(11): 1635-1647 (2011) - [j7]Edmund Lam, Alfred Kam, Jérôme Waldispühl:
corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs. Nucleic Acids Res. 39(Web-Server-Issue): 160-166 (2011) - [c4]Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl:
Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. RECOMB 2011: 408-423 - [c3]Jérôme Waldispühl, Yann Ponty:
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. RECOMB 2011: 501-515
2000 – 2009
- 2009
- [j6]Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Res. 37(Web-Server-Issue): 281-286 (2009) - [c2]Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger:
Simultaneous Alignment and Folding of Protein Sequences. RECOMB 2009: 339-355 - 2008
- [j5]Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote:
Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. 4(8) (2008) - 2007
- [j4]Jérôme Waldispühl, Peter Clote:
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. J. Comput. Biol. 14(2): 190-215 (2007) - 2006
- [j3]Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert:
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res. 34(Web-Server-Issue): 189-193 (2006) - 2005
- [j2]Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert:
Energy landscape of k-point mutants of an RNA molecule. Bioinform. 21(22): 4140-4147 (2005) - [j1]Jérôme Waldispühl, Jean-Marc Steyaert:
Modeling and predicting all-alpha transmembrane proteins including helix-helix pairing. Theor. Comput. Sci. 335(1): 67-92 (2005) - 2002
- [c1]Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert:
An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. ECCB 2002: 250-259
Coauthor Index
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