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Publications co-authored by members from at least two countries

We indicate first the publications that included members of at least 2 of the 3 countries participating in MAIA.


Andrade, R., Wannagat, M., Klein, C.C., Acuña, V., Marchetti-Spaccamela, A., Milreu, P. V., Stougie, L., Sagot, M.-F. Enumeration of minimal stoichiometric precursor sets in metabolic networks. Algorithms for Molecular Biology, 11(1):25, 2016.

Acuña, V., Grossi, R., Italiano, G., Lima, L., Rizzi, R., Sacomoto, G., Sagot, M.-F., Sinaimeri, B. On Bubble Generators in Directed Graphs. 43rd International Workshop on Graph-Theoretic Concepts in Computer Science (WG 2017), Lecture Notes in Computer Science, volume 10520, pp.18-31, 2017.

Di Genova, A. Assembly of complex genome by the integration of the Bruijn and the string graph. PhD, defended Nov 2017, University Adolfo Ibañez, Chile.

Di Genova, A., Ruz, G.A., Sagot, M.-F., Maass, A. Fast-SG: An alignment-free algorithm for hybrid assembly, accepted in GigaScience.


Andrade, R., Doostmohammadi, M., Santos, J. L., Sagot, M.-F., Mira, N., S. Vinga. MOMO – Multi-Objective Metabolic mixed integer Optimization: Application to yeast strain engineering.

In preparation

Andrade, A, Baudet, C., Mary, A., Sagot, M.-F., Sinaimeri, B. A new model for cophylogenetic reconciliations.

Andrade, R., Bulteau, L., Ferrarini, M., Julien-Laferrière, A., Mary, A., Sagot, M.-F. Quantitative Metabolic Stories.

Andrade, R., Ferrarini, M., Julien-Laferrière, A., Mary, A., Sagot, M.-F. TOTORO: A new method on Qualitative Metabolic Stories.

Publications related to the project

Apart from the above, the following publications were related to the project and accepted or submitted within its duration.


Acuña, V., Aravena, A., Guziolowski, C., Eveillard, D., Siegel, A., Maass, A. Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinformatics. 17(1):35, 2016.

Ferrarini, M. G., Siqueira, F. M., Mucha, S. G., Palama, T. L., Jobard, E., Elena-Herrmann, B., Ribeiro de Vasconcelos, A. T., Tardy, F., Schrank, I. S., Zaha, A., Sagot, M.-F. Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modelling. BMC Genomics, 17(1):353, 2016.

Lopez-Maestre, H., Brinza, L., Marchet, C., Kielbassa, J., Bastien, S., Boutigny, M., Monnin, D., El Filali, A., Carareto. C. M., Vieira, C., Picard, F., Kremer, N., Vavre, F., Sagot, M.-F., Lacroix, V. SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. Nucleic Acids Research, 2016.

Julien-Laferrière, A., Bulteau, L., Parrot, D., Marchetti-Spaccamela, A., Stougie, L., Vinga, S., Mary, A., Sagot, M.-F. A Combinatorial Algorithm for Microbial Consortia Synthetic Design. Scientific Reports, Nature Publishing Group, 2016.

Siqueira, F., Loss de Morais, G., Higashi, S., Scherer Beier, L., Merker Breyer, G., Padoan de Sá Godinho, C., Sagot, M.-F., Silveira Schrank, I., Zaha, A., Ribeiro de Vasconcelos, A. T. Mycoplasma non-coding RNA: identification of small RNAs and targets. Mycoplasma non-coding RNA: identification of small RNAs and targets. BMC Genomics, 23:1289, 2016.

Urbini, L., Sinaimeri, S., Matias, C., Sagot, M.-F. Robustness of the Parsimonious Reconciliation Method in Cophylogeny. Algorithms for Computational Biology, Lecture Notes in Computer Science. volume 9702, pp.12, 2016.

Veríssimo, A., Oliveira, A. L., Sagot, M.-F., Vinga, S. DegreeCox – a network-based regularization method for survival analysis. BMC Bioinformatics, 17(Suppl 16):109-121, 2016.

Ashlock, D., Ruz, G.A. A novel representation for Boolean networks designed to enhance heritability and scalability. The 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2017), Manchester, U.K., 23-25 August, pp. 1-8, 2017.

Bailly-Bechet, M., Martins-Simões, P., Szöllosi, G., Mialdea, G., Sagot, M.-F., Charlat, S. How Long Does Wolbachia Remain on Board? Mol Biol Evol. 34(5):1183-1193, 2017.

Hartmann, A., Vila-Santa, A., Kallscheuer, N., Vogt, M., Julien-Laferrière, A., Sagot, M.-F., Marienhagen, J., Vinga, S. OPTPIPE – a pipeline for optimizing metabolic engineering targets. BMC Syst Biol, 11(1):143, 2017.

Lima, L., Sinaimeri, B., Sacomoto G., Lopez-Maestre, H., Marchet, C., Miele, V., Sagot, M.-F., Lacroix, V. Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. Algorithms Mol Biol. 12:2, 2017.

Ruz, G.A., Timmermann, T., Goles, E. Neutral space analysis of gene regulatory network models of salt stress response in Arabidopsis using evolutionary computation, The 2016 IEEE Congress on Evolutionary Computation (IEEE CEC 2016), Vancouver, Canada, July 24-29, pp. 4281-4288, 2016.

Ruz, G.A, Ashlock, D., Ledger, T., Goles, E. Inferring bistable lac operon Boolean regulatory networks using evolutionary computation. The 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2017), Manchester, U.K., 23-25 August, pp. 1-8, 2017.

Zúñiga, A., Donoso, R.A., Ruiz, D., Ruz, G.A., González, B. Quorum-sensing systems in the plant growth-promoting bacterium Paraburkholderia phytofirmans PsJN exhibit cross-regulation and are involved in biofilm formation, Molecular Plant-Microbe Interactions, 30:557-565, 2017.


Ruz, G.A., Zúñiga, A., Goles, E. A Boolean network model of bacterial quorum-sensing systems. Int. J. Data Mining and Bioinformatics (Under review, second round, submitted Oct-16).

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