Publications

The members from Capoeira appear indicated in italics.

Papers accepted with members from both teams

• • M. Ferrarini, L. Nisimura, R. Girard, M. Alencar, M. Fragoso, C. Araújo-Silva, A. Veiga, A. P. Abud, S.Nardelli, R. Vommaro, A. Silber, M.-F. Sagot, and A. Ávila. DCA and Pyruvate metabolism: Dehydrogenase kinases as targets worth investigating for effective therapy of toxoplasmosis. mSphere, 6(1), 2021, doi:10.1128/mSphere.01002-20.
  • M. Ferrarini, I. Ziska, R. Andrade, A. Julien-Laferrière, L. Duchemin, R. Marcondes César Jr., A. Mary, S. Vinga, M.-F. Sagot. TOTORO: Identifying active reactions during the transient state for metabolic perturbations. Frontiers in Genetics, 13, 2022, doi:10.3389/fgene.2022.815476.

  Papers accepted with members from one of the two sides only

  These papers are indicated nevertheless as the work realised was intended to be used and extended in the collaboration with Brazil.
  • C. Moraga, E. Sanchez, M. Ferrarini, R. A. Gutierrez, E. A. Vidal, M.-F. Sagot. BRUMIR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. GigaScience, 11, 2022, doi:10.1093/gigascience/giac093.
  • Grover E. C. Guzman, André Fujita. A fast algorithm to approximate the spectral density of locally tree-like networks with assortativity. J. of Complex Networks. 11(2):cnad005, 2023, doi:10.1093/comnet/cnad005.
  • Y. Wang, A. Mary, M.-F. Sagot, B. Sinaimeri. A General Framework for Enumerating Equivalence Classes of Solutions. Algorithmica, 85(10):3003-3023, 2023, doi:10.1007/s00453-023-01131-1, which was a generalisarion of the work done more specifically on co-phylogeny presented in these two papers who involved the same authors:
    • Y. Wang, A. Mary, M.-F. Sagot, B. Sinaimeri. Efficiently sparse listing of classes of optimal cophylogeny reconciliations. Algorithms for Molecular Biology, 2022, 17(1):1-16, 2022, doi:10.1186/s13015-022-00206-y.
    • Y. Wang, A. Mary, M.-F. Sagot, B. Sinaimeri. A General Framework for Enumerating Equivalence Classes of Solutions. ESA 2021 – 29th Annual European Symposium on Algorithms, 2021, Virtual, Portugal, doi:10.4230/LIPIcs.ESA.2021.80.