Journal articles:

• J. Waldispühl*, S. Devadas, B. Berger and P. Clote*
  RNAmutants: A web server to explore the mutational landscape of RNA secondary structures,
  Nucleic Acids Research, Web Server issue, p. 281-286, 2009.
  [abstract] [bibtex-entry]
  doi:10.1093/nar/gkp477
  (* authors equally contributed)
• J. Waldispühl, S. Devadas, B. Berger and P. Clote,
  Efficient Algorithms for Probing the RNA Mutation Landscape,
  [abstract] [bibtex-entry]
  PLoS Computational Biology, 4(8):e1000124, 2008. doi:10.1371/journal.pcbi.1000124
  
• J. Waldispühl*, C.W. O'Donnell*, S. Devadas, P. Clote and B. Berger,
  Modeling Ensembles of Transmembrane β-barrel Proteins,
  [abstract] [bibtex-entry]
  PROTEINS: Structure, Function and Bioinformatics, Volume 71, Issue 3, p. 1097-1112, 2008. Published online 14 Nov. 2007.
  doi:10.1002/prot.21788
  (* authors equally contributed)
• J. Waldispühl and P. Clote,
  Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model,
  [abstract] [bibtex-entry]
  Journal of Computational Biology, Vol. 14, No. 2, p. 190-215, 2007. doi:10.1089/cmb.2006.0012
• J. Waldispühl, B. Berger, P. Clote and J.-M. Steyaert,
  Predicting Transmembrane β-barrels and Inter-strand Residue Interactions from Sequence,
  [abstract] [bibtex-entry]
  PROTEINS: Structure, Function and Bioinformatics, vol. 65, issue 1, p.61-74, 2006. doi:10.1002/prot.21046
• J. Waldispühl, B. Berger, P. Clote and J.-M. Steyaert,
  transFold: a web Server for Predicting the Structure and Residue Contacts of Transmembrane β-barrels,
  [abstract] [bibtex-entry]
  Nucleic Acids Research, vol 34, Web Server issue, p. W189-W193, 2006. doi:10.1093/nar/gkl205
• P. Clote, J. Waldispühl, B. Behzadi and J.-M. Steyaert,
  Energy landscape of k-point mutants of an RNA molecule,
  [abstract] [bibtex-entry]
  Bioinformatics Vol. 21, p. 4140-4147, 2005.
  doi:10.1093/bioinformatics/bti669
• J. Waldispühl and J.-M. Steyaert,
  Modeling and Predicting All-α Transmembrane Proteins Including Helix-helix Pairing,
  [abstract] [bibtex-entry]
  Theoretical Computer Science, special issue on Pattern Discovery in the Post Genome, p. 67-92, 2005.
  doi:10.1016/j.tcs.2004.12.018

Peer-refereed Proceedings:

• J. Waldispühl, C.W. O'Donnell, S. Will, S. Devadas, R. Backofen and B. Berger,
  Simultaneous Alignment and Folding of Proteins,
  13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), Tucson AZ.
  Lecture Notes in Computer Science, Research in Computational Molecular Biology, Vol. 5541/2009, p. 339-355, 2009.
  [preprint] [abstract] [bibtex-entry]
  doi:10.1007/978-3-642-02008-7_25
  
  
• J. Waldispühl, B. Behzadi and J.-M. Steyaert,
  An Approximate Matching Algorithm for Finding (Sub-)Optimal Sequences in S-attributed Grammars,
  [abstract] [bibtex-entry]
  Proc. ECCB 2002, Bioinformatics Vol. 18, p. 250-259, 2002.

Book Chapters:

• J. Waldispühl and B. Berger,
  Novel Perspectives on protein structure prediction,,
  The Problem Solving Handbook for Computational Biology and Bioinformatics,
  Heath, Lenwood S.; Ramakrishnan, Naren (Eds.), 2010.

Patents:

• J. Waldispühl and J.-M. Steyaert,
  Method for modelling the three-dimensionnal topological structure of a protein,
  Publication Number: WO/2006/032949, Publication Date: 30.03.2006, International Filing Date: 24.09.2004.

Thesis :

• J. Waldispühl,
  Modélisation et prédiction de la structure des protéines transmembranaires,
  Ph.D. thesis, École Polytechnique, Nov. 2004.
• J. Waldispühl,
  Étude combinatoire de la qualité de repliement des protéines,
  M.S. thesis
• J. Waldispühl and J. Familiari,
  Polynome d'Herhart, Matrice de cooccurence et applications à la reconnaissance de formes,
  B.S. thesis

Poster papers:

• J. Waldispühl, S. Devadas, B. Berger and P. Clote,
  Efficient Algorithms for Investigating the RNA Mutation Landscape,
  Poster at the at RNA in Biology, Bioengineering and Nanotechnology workshop at the Institute of Mathematics and Application (University of Minnesota, Minneapolis), November 2007.
• J. Waldispühl*, C.W. O'Donnell*, N. Palmer, S. Devadas, P. Clote and B. Berger,
  Modeling Ensembles of Transmembrane β-barrel Proteins,
  Poster at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 2007.
  (* authors equally contributed)
• J. Waldispühl, B. Berger, P. Clote and J.-M. Steyaert,
  Predicting Transmembrane β-barrels and Inter-strand Residue Interactions from Sequence: Application to OmpA of E. Coli,
  Poster at the Merck/MIT Poster Session, June 2006.
• J. Waldispühl and P. Clote,
  A Study of the Folding Energy Spectrum of RNAs,
  Poster at the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005) and extended abstract in the conference proceedings, 2005.
• J. Waldispühl, B. Behzadi and J.-M. Steyaert,
  Can RNA Super-Optimal Structure Improve Prediction ?
  Poster at the fourth Belgium Bioinformatics Conference (BBC 2003) and extended abstract in the conference proceedings, 2003.
• J. Waldispühl and J.-M. Steyaert,
  Modeling and Predicting All-α Transmembrane Proteins,
  Poster at the second European Conference on Computational Biology (ECCB 2003) and extended abstract in the conference proceedings, 2003.
• J. Waldispühl and J.-M. Steyaert,
  Modélisation du Repliement des Protéines Membranaires par une Grammaire S-attribuée,
  Poster at the troisièmes Journées Ouvertes en Biologie Informatique et Mathématique (JOBIM 2002) and extended abstract in the conference proceedings, 2002.

Technical reports:

• An Introduction to multi-tape S-attributed grammars (from F. Lefebvre's works)
  download : [ps.gz] [pdf]