An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. - Jérôme Waldispühl; Behshad Behzadi; Jean-Marc Steyaert (ECCB, 2002)

Energy landscape of k-point mutants of an RNA molecule. - Peter Clote; Jérôme Waldispühl; Behshad Behzadi; Jean-Marc Steyaert (Bioinform., 2005)

Modeling and predicting all-alpha transmembrane proteins including helix-helix pairing. - Jérôme Waldispühl; Jean-Marc Steyaert (Theor. Comput. Sci., 2005)

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. - Jérôme Waldispühl; Bonnie Berger; Peter Clote; Jean-Marc Steyaert (Nucleic Acids Res., 2006)

Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. - Jérôme Waldispühl; Peter Clote (J. Comput. Biol., 2007)

Efficient Algorithms for Probing the RNA Mutation Landscape. - Jérôme Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote (PLoS Comput. Biol., 2008)

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. - Jérôme Waldispühl; Srinivas Devadas; Bonnie Berger; Peter Clote (Nucleic Acids Res., 2009)

A method for probing the mutational landscape of amyloid structure. - Charles W. O'Donnell; Jérôme Waldispühl; Mieszko Lis; Randal Halfmann; Srinivas Devadas; Susan Lindquist; Bonnie Berger (Bioinform., 2011)

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. - Solomon Shenker; Charles W. O'Donnell; Srinivas Devadas; Bonnie Berger; Jérôme Waldispühl (J. Comput. Biol., 2011)

An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. - Jérôme Waldispühl; Yann Ponty (J. Comput. Biol., 2011)

corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs. - Edmund Lam; Alfred Kam; Jérôme Waldispühl (Nucleic Acids Res., 2011)

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. - Vladimir Reinharz; François Major; Jérôme Waldispühl (Bioinform., 2012)

Flexible RNA design under structure and sequence constraints using formal languages. - Yu Zhou 021; Yann Ponty; Stéphane Vialette; Jérôme Waldispühl; Yi Zhang 046; Alain Denise (BCB, 2013)

A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (RECOMB, 2013)

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (Bioinform., 2013)

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (J. Comput. Biol., 2013)

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. - Yang Zhang; Yann Ponty; Mathieu Blanchette; Eric Lécuyer; Jérôme Waldispühl (Nucleic Acids Res., 2013)

Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. - Jérôme Waldispühl; Mathieu Blanchette (HCOMP, 2014)

Simultaneous Alignment and Folding of Protein Sequences. - Jérôme Waldispühl; Charles W. O'Donnell; Sebastian Will; Srinivas Devadas; Rolf Backofen; Bonnie Berger (J. Comput. Biol., 2014)

Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks. - Eric A. Yen; Aaron Tsay; Jérôme Waldispühl; Jackie Vogel (PLoS Comput. Biol., 2014)

Crowdsourcing RNA Structural Alignments with an Online Computer Game. - Jérôme Waldispühl; Arthur Kam; Paul P. Gardner (Pacific Symposium on Biocomputing, 2015)

Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes. - Mohamed Raef Smaoui; Henri Orland; Jérôme Waldispühl (Bioinform., 2015)

Evolution by Computational Selection. - Mohammed Shamrani; François Major; Jérôme Waldispühl (CoRR, 2015)

Preface. - Fabrice Jossinet; Yann Ponty; Jérôme Waldispühl (J. Comput. Biol., 2015)

Collaborative Solving in a Human Computing Game Using a Market, Skills and Challenges. - Olivier Tremblay Savard; Alexander Butyaev; Jérôme Waldispühl (CHI PLAY, 2016)

Investigating Mutations to Reduce Huntingtin Aggregation by Increasing Htt-N-Terminal Stability and Weakening Interactions with PolyQ Domain. - Mohamed Raef Smaoui; Cody Mazza-Anthony; Jérôme Waldispühl (Comput. Math. Methods Medicine, 2016)

incaRNAfbinv: a web server for the fragment-based design of RNA sequences. - Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Nucleic Acids Res., 2016)

Computational Intractability Generates the Topology of Biological Networks. - Ali Atiia; Corbin Hopper; Jérôme Waldispühl (BCB, 2017)

Lessons from an Online Massive Genomics Computer Game. - Akash Singh; Faizy Ahsan; Mathieu Blanchette; Jérôme Waldispühl (HCOMP, 2017)

10 simple rules to create a serious game, illustrated with examples from structural biology. - Marc Baaden; Olivier Delalande; Nicolas Férey; Samuela Pasquali; Jérôme Waldispühl; Antoine Taly (CoRR, 2017)

On Stable States in a Topologically Driven Protein Folding Model. - Zheng Dai; David Becerra; Jérôme Waldispühl (J. Comput. Biol., 2017)

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. - Jason Yao; Vladimir Reinharz; François Major; Jérôme Waldispühl (Nucleic Acids Res., 2017)

A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. - Antoine Soulé; Jean-Marc Steyaert; Jérôme Waldispühl (RECOMB, 2018)

Design of RNAs: comparing programs for inverse RNA folding. - Alexander Churkin; Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Briefings Bioinform., 2018)

Ten simple rules to create a serious game, illustrated with examples from structural biology. - Marc Baaden; Olivier Delalande; Nicolas Férey; Samuela Pasquali; Jérôme Waldispühl; Antoine Taly (PLoS Comput. Biol., 2018)

Leveraging binding-site structure for drug discovery with point-cloud methods. - Vincent Mallet; Carlos G. Oliver; Nicolas Moitessier; Jérôme Waldispühl (CoRR, 2019)

Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes. - Wanlei Wei; Jiaying Luo; Jérôme Waldispühl; Nicolas Moitessier (J. Chem. Inf. Model., 2019)

Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. - Roman Sarrazin-Gendron; Hua-Ting Yao; Vladimir Reinharz; Carlos G. Oliver; Yann Ponty; Jérôme Waldispühl (RECOMB, 2020)

Computational intractability law molds the topology of biological networks. - Ali Atiia; Corbin Hopper; Katsumi Inoue; Silvia Vidal; Jérôme Waldispühl (Appl. Netw. Sci., 2020)

Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation. - David Becerra; Alexander Butyaev; Jérôme Waldispühl (Bioinform., 2020)

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. - Matan Drory Retwitzer; Vladimir Reinharz; Alexander Churkin; Yann Ponty; Jérôme Waldispühl; Danny Barash (Bioinform., 2020)

A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. - Antoine Soulé; Jean-Marc Steyaert; Jérôme Waldispühl (J. Comput. Biol., 2020)

OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery. - Jacques Boitreaud; Vincent Mallet; Carlos G. Oliver; Jérôme Waldispühl (J. Chem. Inf. Model., 2020)

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. - Antoine Soulé; Vladimir Reinharz; Roman Sarrazin-Gendron; Alain Denise; Jérôme Waldispühl (PLoS Comput. Biol., 2021)

Adaptive Instructional System for Complex Equipment Trainings in the Post-covid Era: Breaking the Ice of Time-Consuming Tasks. - Elena Nazarova; Alexander Butyaev; Mohamed Youssef Bouaouina; Dominic Filion; Jérôme Waldispühl (HCI (31), 2022)

RNAglib: a python package for RNA 2.5 D graphs. - Vincent Mallet; Carlos G. Oliver; Jonathan Broadbent; William L. Hamilton; Jérôme Waldispühl (Bioinform., 2022)

Vernal: a tool for mining fuzzy network motifs in RNA. - Carlos G. Oliver; Vincent Mallet; Pericles Philippopoulos; William L. Hamilton; Jérôme Waldispühl (Bioinform., 2022)

Localized, Non-parametric Detection of RNA Structural Modification using Nanopore Basecalling. - J. White Bear; Grégoire De Bisschop; Eric Lécuyer; Jérôme Waldispühl (BCB, 2023)

Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? - Renata Mutalova; Roman Sarrazin-Gendron; Eddie Cai; Gabriel Richard; Parham Ghasemloo Gheidari; Sébastien Caisse; Rob Knight 001; Mathieu Blanchette; Attila Szantner; Jérôme Waldispühl (CHI, 2023)

Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. - Renata Mutalova; Roman Sarrazin-Gendron; Parham Ghasemloo Gheidari; Eddie Cai; Gabriel Richard; Sébastien Caisse; Rob Knight 001; Mathieu Blanchette; Attila Szantner; Jérôme Waldispühl (CI, 2023)

Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. - Eddie Cai; Roman Sarrazin-Gendron; Renata Mutalova; Parham Ghasemloo Gheidari; Alexander Butyaev; Gabriel Richard; Sébastien Caisse; Rob Knight 001; Mathieu Blanchette; Attila Szantner; Jérôme Waldispühl (FDG, 2024)

3D-based RNA function prediction tools in rnaglib. - Carlos G. Oliver; Vincent Mallet; Jérôme Waldispühl (CoRR, 2024)

PERFUMES: pipeline to extract RNA functional motifs and exposed structures. - Arnaud Chol; Roman Sarrazin-Gendron; Eric Lécuyer; Mathieu Blanchette; Jérôme Waldispühl (Bioinform., 2024)

ARGV: 3D genome structure exploration using augmented reality. - Chrisostomos Drogaris; Yanlin Zhang; Eric Zhang; Elena Nazarova; Roman Sarrazin-Gendron; Sélik Wilhelm-Landry; Yan Cyr; Jacek Majewski; Mathieu Blanchette; Jérôme Waldispühl (BMC Bioinform., 2024)