Journal articles:

• 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 (Web Server Issue), to appear, 2006.
• 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, to appear, 2006.
• 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, 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.

Patents :

• J. Waldispühl et J.-M. Steyaert,
  Method for modeling the three-dimensionnal topological structure of proteins.
  international patent, in process, 2004.

PHD's Thesis :

• J. Waldispühl,
  Modélisation et prédiction de la structure des protéines transmembranaires,
  Ph.D. thesis, École Polytechnique, 2004, to appaer

Poster papers:

• 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-alpha 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.

Reports :

• An Introduction to multi-tape S-attributed grammars (from F. Lefebvre's works)
  download : [ps.gz] [pdf]
• Étude combinatoire de la qualité de repliement des protéines,
  M.S. thesis
• Polynome d'Herhart, Matrice de cooccurence et applications à la reconnaissance de formes,
  B.S. thesis