Below are indicated the publications of Compasso, plus their associated software.
Papers accepted plus software
Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga. MOMO – Multi-Objective Metabolic mixed integer Optimization: application to yeast strain engineering, BMC Bioinformatics, 21(1):69, 2020. A version of this paper is also available in BioRxiv and the code of MOMO is available here (soon to be transferred to GitLab Erable due to the closure of GForge).
Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri. CAPYBARA: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions. Bioinformatics, 36(14):4197-4199. The code of CAPYBARA is available here. Although there is no participation of a member of Portuguese team, the work in this paper is important for the discussions we have had with Mário Figueiredo.
Papers submitted plus software
Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha, Marie-France Sagot. A comprehensive evaluation of binning methods to recover human gut microbial pan-genomes from a non-redundant reference gene catalog.
Irene Ziska, Ricardo Andrade, Mariana Galvão Ferrarini, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César Jr., Arnaud Mary, Susana Vinga, Marie-France Sagot. TOTORO: Identifying active reactions during the transient state for metabolic perturbations. The code of TOTORO is available here.
Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri. Lazy listing of equivalence classes — A paper on dynamic programming and tropical circuits. A version of this paper is available in arXiv. Although there is no participation of a member of Portuguese team, the work in this paper is important for the discussions we have had with Mário Figueiredo.
Papers in preparation plus software
André Veríssimo, Eunice Carrasquinha, Marta B. Lopes, Arlindo L. Oliveira, Marie-France Sagot, Susana Vinga. Sparse network-based regularization for the analysis of patientomics high-dimensional survival data. A preliminary version of this paper is available in BioRxiv. The code of GLMSparseNet is available here.
Irene Ziska, Mariana Galvão Ferrarini, Nuno Mira, Susana Vinga, Arnaud Mary, Marie-France Sagot. Identifying knockouts when the target chemical is toxic for the organism (provisional title).
With Marianne Borderes, two more papers are in preparation that should be submitted before the PhD defence in March-April 2021, or just after. A patent should also be submitted related to one of the two papers still in preparation together with the private company MaatPharma (main person involved, Lilia Boucinha) funded by an ANR Technology, project SPOCK.
PhD manuscripts
Irene Ziska, Models and algorithms for investigating and exploiting the metabolism of microorganisms. Defence planned for November 24, 2020. PhD supervisors: Arnaud Mary, Marie-France Sagot, Susana Vinga.
André Veríssimo, Network-based sparse regularization for the identification of disease signatures. Defence planned for the end of 2020. PhD supervisors: Arlindo Oliveira, Marie-France Sagot, Susana Vinga.
PhD to be defended in March-April 2021
Marianne Borderes, funded by ANR Technology, project Spock, with MaatPharma, Lyon. PhD supervisors: Marie-France Sagot, Susana Vinga, MaatPharma supervisor: initially Lilia Boucinha and since 2019 Emmanuel Prestat.
