Associated Team HELIX-USP

Publications

This page contains references to the publications of participants to the associated team that have been accepted, published or submitted after Jan. 2005, as well as pointers to the publicly available (through a web interface) software corresponding to some of the algorithms described in the papers.

International journals

• V. Lacroix, C. G. Fernandes, M.-F. Sagot, Motif Search in Graphs: Application to Metabolic Networks, accepted at IEEE/ACM Trans. on Comp. Biology and Bioinformatics, 3:360-368, 2006.
• E.M. Rodrigues, M.-F. Sagot, and Y. Wakabayashi, The Maximum Agreement Forest Problem: approximation algorithms and computational experiments, Theoretical Computer Science, 374:91-110, 2007.
• P. Peterlongo, N. Pisanti, F. Boyer, A. P. do Lago, M.-F. Sagot, Lossless filter for multiple repetitions, Journal of Discrete Algorithms, in press, 2007.

International conferences with program committee

• V. Lacroix, C. G. Fernandes, and M.-F. Sagot, Reaction motifs in metabolic networks, Proceedings of WABI 2005 (Workshop on Algorithms in BioInformatics) (R. Casadio and G. Myers, eds.),Lecture Notes in BioInformatics (LNBI), topical subseries of Lecture Notes in Computer Siences, vol. 3692, Springer-Verlag, pp. 178-191, 2005.
• S. S. Adi, M. D. V. Braga, C. G. Fernandes, C. Ferreira, F. Martinez, M.-F. Sagot, M. A. Stefanes, C. Tjandraatmadja and Y. Wakabayashi, Repetition-free LCS with few reversals., IV Latin-American Algorithms, Graphs and Optimization Symposium (LAGOS'07), Electronic Notes in Discrete Mathematics, in press, 2007

Submitted

• R. Tavares, S. S. Adi, P. Blayo, and M.-F. Sagot, Utopia: an exact generic core algorithm for gene prediction using homology.

In preparation

• V. Lacroix, O. Rogier, L. Cottret, F. Jourdan, C. G. Fernandes M.-F. Sagot, Paper on the Motus software.
• P. Peterlongo, G. A. T. Sacomoto, N. Pisanti, A. P. do Lago, M.-F. Sagot, Extension of the paper on a lossless filter allowing for an edit instead of a Hamming distance and presentation of the corresponding Tuiuiu algorithm.

Internal reports

• P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot, Lossless Filter for Long Multiple Repetitions with Edit Distance., .

Software

• V. Lacroix, O. Rogier, L. Cottret, F. Jourdan, C. G. Fernandes M.-F. Sagot: Motus.
• P. Peterlongo, N. Pisanti, A. P. do Lago, M.-F. Sagot: Ed'Nimbus.