Jérôme Waldispühl

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 31

Top Topics

Ensemble Learning

Saccharomyces Cerevisiae

Comparative Genomics

Top Venues

J. Comput. Biol.

Nucleic Acids Res.

Publications

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)
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)
Carlos G. Oliver, Vincent Mallet, Jérôme Waldispühl
3D-based RNA function prediction tools in rnaglib. CoRR (2024)
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)
J. White Bear, Grégoire De Bisschop, Eric Lécuyer, Jérôme Waldispühl
Localized, Non-parametric Detection of RNA Structural Modification using Nanopore Basecalling. BCB (2023)
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)
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)
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) (2022)
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) (2022)
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)
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)
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) (2020)
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) (2020)
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) (2020)
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) (2020)
Ali Atiia, Corbin Hopper, Katsumi Inoue, Silvia Vidal, Jérôme Waldispühl
Computational intractability law molds the topology of biological networks. Appl. Netw. Sci. 5 (1) (2020)
Carlos G. Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl
VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA. CoRR (2020)
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) (2019)
Vincent Mallet, Carlos G. Oliver, Nicolas Moitessier, Jérôme Waldispühl
Leveraging binding-site structure for drug discovery with point-cloud methods. CoRR (2019)
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)
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) (2018)
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)
Ali Atiia, Corbin Hopper, Jérôme Waldispühl
Computational Intractability Generates the Topology of Biological Networks. BCB (2017)
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) (2017)
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) (2017)
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 (2017)
Zheng Dai, David Becerra, Jérôme Waldispühl
On Stable States in a Topologically Driven Protein Folding Model. J. Comput. Biol. 24 (9) (2017)
Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl
Lessons from an Online Massive Genomics Computer Game. HCOMP (2017)
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 (2016)
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) (2016)
Olivier Tremblay Savard, Alexander Butyaev, Jérôme Waldispühl
Collaborative Solving in a Human Computing Game Using a Market, Skills and Challenges. CHI PLAY (2016)
Mohammed Shamrani, François Major, Jérôme Waldispühl
Evolution by Computational Selection. CoRR (2015)
Mohamed Raef Smaoui, Henri Orland, Jérôme Waldispühl
Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes. Bioinform. 31 (14) (2015)
Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl
Preface. J. Comput. Biol. 22 (3) (2015)
Jérôme Waldispühl, Arthur Kam, Paul P. Gardner
Crowdsourcing RNA Structural Alignments with an Online Computer Game. Pacific Symposium on Biocomputing (2015)
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)
Jérôme Waldispühl, Mathieu Blanchette
Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. HCOMP (2014)
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) (2014)
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)
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) (2013)
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) (2013)
Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. RECOMB (2013)
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) (2013)
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) (2012)
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) (2011)
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) (2011)
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) (2011)
Jérôme Waldispühl, Yann Ponty
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. J. Comput. Biol. 18 (11) (2011)
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)
Jérôme Waldispühl, Yann Ponty
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. RECOMB (2011)
Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
Simultaneous Alignment and Folding of Protein Sequences. RECOMB (2009)
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) (2009)
Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. 4 (8) (2008)
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) (2007)
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) (2006)
Jérôme Waldispühl, Jean-Marc Steyaert
Modeling and predicting all-alpha transmembrane proteins including helix-helix pairing. Theor. Comput. Sci. 335 (1) (2005)
Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert
-point mutants of an RNA molecule. Bioinform. 21 (22) (2005)
Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert
An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. ECCB (2002)