default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDJérôme Waldispühl
Person information
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
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
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from 
.
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-10-07 22:23 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
