Jérôme Waldispühl

62 papers A* 1B 8C 2Misc 2Journal 43Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Improving the Reliability of Molecular String Representations for Generative Chemistry. J. Chem. Inf. Model. Etienne Reboul, Zoe Wefers, Harish Prabakaran, Jérôme Waldispühl, Antoine Taly
2025	J	`jnl`	What's so hard about RNA-targeting drug discovery? Nat. Comput. Sci. Carlos Oliver, Jérôme Waldispühl
2024	J	`jnl`	3D-based RNA function prediction tools in rnaglib. CoRR Carlos G. Oliver, Vincent Mallet, Jérôme Waldispühl
2024	J	`jnl`	ARGV: 3D genome structure exploration using augmented reality. BMC Bioinform. Chrisostomos Drogaris, Yanlin Zhang, Eric Zhang, Elena Nazarova, Roman Sarrazin-Gendron, Sélik Wilhelm-Landry, Yan Cyr, Jacek Majewski, Mathieu Blanchette, Jérôme Waldispühl
2024	C	`conf`	Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. FDG Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghasemloo Gheidari, Alexander Butyaev, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2024	J	`jnl`	PERFUMES: pipeline to extract RNA functional motifs and exposed structures. Bioinform. Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl
2023	—	`conf`	Localized, Non-parametric Detection of RNA Structural Modification using Nanopore Basecalling. BCB J. White Bear, Grégoire De Bisschop, Eric Lécuyer, Jérôme Waldispühl
2023	—	`conf`	Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. CI Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2023	A*	`conf`	Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? CHI Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2022	—	`conf`	Adaptive Instructional System for Complex Equipment Trainings in the Post-covid Era: Breaking the Ice of Time-Consuming Tasks. HCI (31) Elena Nazarova, Alexander Butyaev, Mohamed Youssef Bouaouina, Dominic Filion, Jérôme Waldispühl
2022	J	`jnl`	RNAglib: a python package for RNA 2.5 D graphs. Bioinform. Vincent Mallet, Carlos G. Oliver, Jonathan Broadbent, William L. Hamilton, Jérôme Waldispühl
2022	J	`jnl`	Vernal: a tool for mining fuzzy network motifs in RNA. Bioinform. Carlos G. Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl
2021	J	`jnl`	Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. PLoS Comput. Biol. Antoine Soulé, Vladimir Reinharz, Roman Sarrazin-Gendron, Alain Denise, Jérôme Waldispühl
2020	J	`jnl`	A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. J. Comput. Biol. Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl
2020	J	`jnl`	Computational intractability law molds the topology of biological networks. Appl. Netw. Sci. Ali Atiia, Corbin Hopper, Katsumi Inoue, Silvia Vidal, Jérôme Waldispühl
2020	J	`jnl`	Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation. Bioinform. David Becerra, Alexander Butyaev, Jérôme Waldispühl
2020	J	`jnl`	OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery. J. Chem. Inf. Model. Jacques Boitreaud, Vincent Mallet, Carlos G. Oliver, Jérôme Waldispühl
2020	B	`conf`	Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. RECOMB Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl
2020	J	`jnl`	VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA. CoRR Carlos G. Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jérôme Waldispühl
2020	J	`jnl`	incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. Bioinform. Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash
2019	J	`jnl`	Leveraging binding-site structure for drug discovery with point-cloud methods. CoRR Vincent Mallet, Carlos G. Oliver, Nicolas Moitessier, Jérôme Waldispühl
2019	J	`jnl`	Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes. J. Chem. Inf. Model. Wanlei Wei, Jiaying Luo, Jérôme Waldispühl, Nicolas Moitessier
2018	B	`conf`	A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. RECOMB Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl
2018	J	`jnl`	Design of RNAs: comparing programs for inverse RNA folding. Briefings Bioinform. Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2018	J	`jnl`	Ten simple rules to create a serious game, illustrated with examples from structural biology. PLoS Comput. Biol. Marc Baaden, Olivier Delalande, Nicolas Férey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly
2017	J	`jnl`	10 simple rules to create a serious game, illustrated with examples from structural biology. CoRR Marc Baaden, Olivier Delalande, Nicolas Férey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly
2017	—	`conf`	Computational Intractability Generates the Topology of Biological Networks. BCB Ali Atiia, Corbin Hopper, Jérôme Waldispühl
2017	B	`conf`	Lessons from an Online Massive Genomics Computer Game. HCOMP Akash Singh, Faizy Ahsan, Mathieu Blanchette, Jérôme Waldispühl
2017	J	`jnl`	On Stable States in a Topologically Driven Protein Folding Model. J. Comput. Biol. Zheng Dai, David Becerra, Jérôme Waldispühl
2017	J	`jnl`	RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. Nucleic Acids Res. Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl
2017	J	`jnl`	RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. Nucleic Acids Res. Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldispühl
2016	Misc	`conf`	Collaborative Solving in a Human Computing Game Using a Market, Skills and Challenges. CHI PLAY Olivier Tremblay-Savard, Alexander Butyaev, Jérôme Waldispühl
2016	J	`jnl`	Investigating Mutations to Reduce Huntingtin Aggregation by Increasing Htt-N-Terminal Stability and Weakening Interactions with PolyQ Domain. Comput. Math. Methods Medicine Mohamed Raef Smaoui, Cody Mazza-Anthony, Jérôme Waldispühl
2016	J	`jnl`	incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res. Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2015	Misc	`conf`	Crowdsourcing RNA Structural Alignments with an Online Computer Game. Pacific Symposium on Biocomputing Jérôme Waldispühl, Arthur Kam, Paul P. Gardner
2015	J	`jnl`	Evolution by Computational Selection. CoRR Mohammed Shamrani, François Major, Jérôme Waldispühl
2015	J	`jnl`	Preface. J. Comput. Biol. Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl
2015	J	`jnl`	Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes. Bioinform. Mohamed Raef Smaoui, Henri Orland, Jérôme Waldispühl
2014	J	`jnl`	Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks. PLoS Comput. Biol. Eric A. Yen, Aaron Tsay, Jérôme Waldispühl, Jackie Vogel
2014	B	`conf`	Phylo and Open-Phylo: A Human-Computing Platform for Comparative Genomics. HCOMP Jérôme Waldispühl, Mathieu Blanchette
2014	—	`ed.`	Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), Strasbourg, France, September 7, 2014. CMSR@ECCB Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl
2014	J	`jnl`	Simultaneous Alignment and Folding of Protein Sequences. J. Comput. Biol. Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2013	B	`conf`	A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. RECOMB Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2013	J	`jnl`	A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinform. Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2013	—	`conf`	Flexible RNA design under structure and sequence constraints using formal languages. BCB Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise
2013	J	`jnl`	SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res. Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl
2013	J	`jnl`	Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. J. Comput. Biol. Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2012	J	`jnl`	Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinform. Vladimir Reinharz, François Major, Jérôme Waldispühl
2011	J	`jnl`	A method for probing the mutational landscape of amyloid structure. Bioinform. Charles W. O'Donnell, Jérôme Waldispühl, Mieszko Lis, Randal Halfmann, Srinivas Devadas, Susan Lindquist, Bonnie Berger
2011	J	`jnl`	An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. J. Comput. Biol. Jérôme Waldispühl, Yann Ponty
2011	B	`conf`	An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. RECOMB Jérôme Waldispühl, Yann Ponty
2011	B	`conf`	Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. RECOMB Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
2011	J	`jnl`	Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models. J. Comput. Biol. Solomon Shenker, Charles W. O'Donnell, Srinivas Devadas, Bonnie Berger, Jérôme Waldispühl
2011	J	`jnl`	corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs. Nucleic Acids Res. Edmund Lam, Alfred Kam, Jérôme Waldispühl
2009	J	`jnl`	RNAmutants: a web server to explore the mutational landscape of RNA secondary structures. Nucleic Acids Res. Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
2009	B	`conf`	Simultaneous Alignment and Folding of Protein Sequences. RECOMB Jérôme Waldispühl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen, Bonnie Berger
2008	J	`jnl`	Efficient Algorithms for Probing the RNA Mutation Landscape. PLoS Comput. Biol. Jérôme Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote
2007	J	`jnl`	Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model. J. Comput. Biol. Jérôme Waldispühl, Peter Clote
2006	J	`jnl`	transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res. Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert
2005	J	`jnl`	Energy landscape of Bioinform. Peter Clote, Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert
2005	J	`jnl`	Modeling and predicting all-alpha transmembrane proteins including helix-helix pairing. Theor. Comput. Sci. Jérôme Waldispühl, Jean-Marc Steyaert
2002	C	`conf`	An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. ECCB Jérôme Waldispühl, Behshad Behzadi, Jean-Marc Steyaert