## 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.