Julien Allali

Research interests: algorithmic and bioinformatics

My research interests cover the algorithmic on strings and trees, and their applications in bioinformatics.

In particular, I work on string comparison (edit distance, alignement) and indexes such as suffix tree, suffix array, etc...

In bioinformatics, I'm focused on RNA secondary structure comparison.

Ph.D.

subject: "RNA secondary structures comparison" supervised by Maxime Crochemore and Marie-France Sagot

Obtained the 23 Décembre 2004, the jury:

• Alain Denise (reviewer)
• Christine Gaspin (reviewer)
• Robert Giegerich (reviewer)
• Dominique Perrin (president).
• Claude Thermes

The thesis (french) and presentation slides (french).

Publications

Journals and Conferences:

• In submission: "A multiple layer model to compare RNA secondary structures".
  J. Allali, M-F. Sagot.
  Software - Practice and Experience.
• "The Gapped-Factor Tree".
  P. Peterlongo, J. Allali, M-F. Sagot.
  PSC'06
• "A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison".
  J. Allali and M-F. Sagot.
  String Processing and Information Retrieval (SPIRE) 2005.
  article, bibtex
• "Novel tree edit operations for RNA secondary structure comparison".
  J. Allali and M-F. Sagot.
  Workshop on Algorithms in Bioinformatics (WABI) 2004.
  article, bibtex
• "A new distance for high level RNA secondary structure comparison".
  J. Allali and M-F. Sagot.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 2005.
  article, bibtex
• In submission: "The at most k-deep factor tree".
  J. Allali and M-F. Sagot.
  Theory of Computing Systems / Springer-Verlag.
  article, bibtex

Research report:

• "The at most k-deep factor tree".
  J. Allali and M-F. Sagot.
  article, bibtex

Software: (see the software section)

• migal: toolkit to compare RNA secondary structure.
• kfact: library to build the k-factor tree and the suffix tree.