Comparative genomics and RNA informatics
MAGNOLIA: multiple alignment multiple alignment of protein-coding and structural RNA sequences A. Fontaine, A. de Monte and H. Touzet, in Nucleic Acids Research - web server issue 2008 [full text]
Alignment of RNA Structures G. Blin, A. Denise, S. Dulucq, C. Herrbach and H. Touzet in IEEE/ACM Transactions on Computational biology and Bioinformatics, 2008 [abstract]
Computational identification of protein-coding sequences by comparative analysis. A. Fontaine and H. Touzet, in 1st IEEE international conference on Bioinformatics and Biomedecine (BIBM), pages 95-102. IEEE Computer Society, 2007
How to compare arc-annotated sequences: The alignment hierarchy. G. Blin and H. Touzet, in 13th International Symposium on String Processing and Information Retrieval (SPIRE), volume 4209 of Lecture Notes in Computer Science, pages 291-303. Springer Verlag, 2006 [bib]
How to detect non-coding RNAs? Arnaud Fontaine, Hélène Touzet, in JOBIM 2005 [ bib|PDF|supplementary material]
A linear tree edit distance algorithm for similar ordered trees. Hélène Touzet, in Combinatorial Pattern Matching (CPM), volume 3537 of Lecture Notes in Computer Science, pages 334-345, 2005 [ bib |PDF ]
Decomposition algorithms for tree editing distance. Serge Dulucq and Hélène Touzet, in Journal of Discrete Algorithms, volume 3, issue 2-4, pages 448-471, 2005 [ bib|PDF]
CARNAC: folding families of related non coding RNAs. Hélène Touzet, Olivier Perriquet, in Nucleic Acids Research 142 , 2004 [ bib|PDF]
Finding the common structure shared by two homologous RNAs. Olivier Perriquet, Hélène Touzet, Max Dauchet, Bioinformatics 19, pages 108-116, 2003 [ bib|PDF]
Analysis of tree edit distance algorithms. Serge Dulucq and Hélène Touzet, in Combinatorial Pattern Matching (CPM), volume 2676 of Lecture Notes in Computer Science, pages 83-95, 2003 [PDF]
Tree edit distance with gaps. Hélène Touzet, Information Processing Letters 85 (3), pages 123 - 129, 2003 [ bib|PDF ]
Motifs and Cis-regulatory elements
Efficient and accurate P-value computation for position weight matrices. H. Touzet and J.S. Varré, Algorithms for Molecular Biology, 2(15), 2007 [full text]
Predicting transcription factor binding sites using local over-representation and comparative genomics. M. Defrance and H. Touzet, BMC Bioinformatics, 2006 [ bib|http ]
Large scale matching for position weight matrices. A. Liefooghe, H. Touzet, and J.-S. Varré, in 17th Annual Symposium on Combinatorial Pattern Matching (CPM), volume 4009 of Lecture Notes in Computer Science, pages 401-412. Springer Verlag, 2006 [ bib ]
Recherche d'éléments régulateurs communs, application aux gènes cibles des facteurs de transcription Rel-kappaB. Matthieu Defrance, Hélène Touzet, Karo Gosselin et Corinne Abbadie, in JOBIM, 2004 [ bib|PDF ]
L'Analyse bio-informatique des régions régulatrices. Séminaire IRI "Transcriptome et régulation transcriptionnelle", 2004 [PDF]
Logic and rewriting theory
A Characterisation of Multiply Recursive Functions with Higman's Lemma. Hélène Touzet, Information and Computation 178, pages 534-544, 2002 [ bib|PDF]
Algorithms with Polynomial Interpretation Termination Proof. Guillaume Bonfante, Adam Cichon, Jean-Yves Marion and Hélène Touzet, Journal of Functional Programming, 11 (1), pages 33-53, 2001 [PS]
A Characterisation of Multiply Recursive Functions with Higman's Lemma. Hélène Touzet, in proceedings of Rewriting Techniques and Applications (RTA), volume 1631 of Lecture Notes in Computer Science, pages 163-174, 1999 [PS]
Encoding the Hydra Battle as a Rewrite System. Hélène Touzet, in proceedings of Mathematical Foundations of Computer Science (MFCS), volume 1450 of Lecture Notes in Computer Science, pages 267-276, 1998 [PS]
Complexity Classes and Rewrite Systems with Polynomial Interpretation. Guillaume Bonfante, Adam Cichon, Jean-Yves Marion and Hélène Touzet, in proceedings of Computer Science Logic (CSL), volume 1584 of Lecture Notes in Computer Science, pages 372-384, 1998 [PS]
A Complex Example of a Simplifying Rewrite System. Hélène Touzet, in proceedings of International Colloquium on Automata, Languages and Programming (ICALP), volume 1143 of Lecture Notes in Computer Science, pages 507-517, 1998 [PS]
An Ordinal Calculus for Proving Termination in Term Rewriting. Adam Cichon and Hélène Touzet, in proceedings of Colloquium on trees in Algebra And Programming (CAAP), volume 1059 of Lecture Notes in Computer Science, volume 1059, pages 226-240, 1996 [PS]
Thesis
PhD thesis : Propriétés combinatoires pour la terminaison de systèmes de réécriture
[postscript in French]
Habilitation thesis : Structures combinatoires pour l'analyse de génomes
[PDF, defense in French]