SIMBIOSI

Published

V. Acuña, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie. A note on the complexity of finding and enumerating elementary modes. BioSystems, 99(3):210-214, 2010.

L. Cottret, P.V. Milreu, V. Acuña, A. Marchetti-Spaccamela, L. Stougie, H. Charles, M.-F. Sagot. Graph based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata, PLoS Computational Biology, 6(9):307-316, 2010.

P. Milreu, V. Acuña, E. Birmelé, P. Crescenzi, A. Marchetti-Spaccamela, M.-F. Sagot, L. Stougie and V. Lacroix Enumerating chemical organisations in consistent metabolic networks: Complexity and algorithms. WABI'2010, LNBI/LNCS, vol. 6293, pages 226-237, 2010.

Selected conference presentation without proceedings

V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. Milreu, M.-F. Sagot, L Stougie. Telling stories. Workshop of ICALP Graph Algorithms and Applications, 2011.

Invited presentation with abstract in proceedings

A. Marchetti-Spaccamela. Structures and hyperstructures in metabolic networks. Invited presentation at 37th International Workshop on Graph-Theoretic Concepts in Computer Science (WG) 2011, Tepla, Czech Rep., abstract to appear in LNCS, Springer, 2011 – work in common with other members of SIMBIOSI.

In submission

V. Acuña, P. Milreu, L. Cottret, A. Marchetti-Spaccamela, L. Stougie, M.-F. Sagot. Enumerating all minimal metabolic precursor sets: complexity analysis and efficient network compression algorithm.

A. Freire, V. Acuña, P. Crescenzi, C.E. Ferreira, V. Lacroix, P. Milreu, E. Moreno, M.-F. Sagot. Covering reactions of a metabolic network by elementary modes (tentative title).

V. Acuña V., E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. Milreu, M.-F. Sagot, L. Stougie. Telling stories (tentative title).

In preparation

P. Milreu, V. Acuña, E. Birmelé, A. Marino, L. Cottret, V. Lacroix, A. Marchetti-Spaccamela, L. Stougie, F. Jourdan, M.-F. Sagot, P. Crescenzi. Telling metabolic stories (tentative title).

Paper on Kelly-width with application to metabolic networks.

Paper on algorithm for NGS data analysis, more specifically, RNAseq analysis.

Paper on algorithm for inferring the genetic architecture of a parasite infection.