Work in progress

Work done in 2020

• Paper accepted (in italics, members from Capoeira):
  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.
• Approved UdL-Fapesp project between the Brazilian and the French teams. The approval was communicated only at the end of October 2020, and the project ends in December 2021.

Work done in 2021

• Organisation of two virtual events.
  • The first event was a workshop that involved mainly the participants in Brazil and France of Capoeira. It took place on June 10 and 11, 2021. The program may be found here.
  • The second event was the “Workshop Metabolism and mathematical models: Two for a tango” that was co-organised by Ariel M. Silber and Marie-France Sagot. This workshop was open to the outside (with registration required but free) and involved six Keynote Speakers at the international level. It took place on November 18 and 19, 2021. A full information on its content, including the program may be found here.
• Initial discussion for the submission of a CNRS IRP project to be submitted in 2021.
• Reinforcement of an informal three-way link we started establishing between Erable, the Brazilian members of Capoeira, and the Portuguese members of the H2020 Twinning project Olissipo which started in 2021. The “Workshop Metabolism and mathematical models: Two for a tango” was organised also with Olissipo.
• Visit of Ariel M. Silber to France from November 1 to 23, 2021 to progress on the work related to the PhD of Gabriela Torres Montanaro who is co-supervised by Ariel M. Silber and Marie-France Sagot. Gabriela joined the Brazilian team of Capoeira in May 2021. Both she and Ariel have already various visits planned for 2022, two by Gabriela of respectively approximately two months for the first and one month for the second, and three by Ariel of between two and three weeks each with an overlap of the visits by Gabriela. The flights for such trips has already been covered by funds from the French team from 2021.
• Overlapping with the visit of Ariel M. Silber to Lyon from November 1 to 23, the French team had the visit of Andrea Ávila and Helisson Faoro from the Instituto Carlos Chagas – Fiocruz, Curitiba, Brazil, in the context of a Capes-Cofecub project called Ahimsa. Notably with Andrea Ávila, this visit enabled to advance with the work on toxoplasmosis (see the accepted publication above).

Work done in 2022

• Paper accepted (in italics, members from Capoeira):
  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.
• Co-organisation by A. Silber and M.-F. Sagot of the Second Edition of the “Workshop Metabolism and mathematical models: Two for a tango” that was held virtually on October 25-26, 2022. This organisation involved also Portuguese members of the H2020 Twinning project Olissipo started in 2021. A full information on its content, including the program may be found here.
• Initiation of the Ph.D. of Gabriela T. Montanaro, co-supervised by A. Silber and M.-F. Sagot, and who was added to the list of participants of Capoeira. This involved two visits of Gabriela to Lyon, from to and from to. During these visits, Gabriela worked mostly on the reconstruction of the metabolic network of Trypanosoma brucei which will be crucial for understanding some differences at the level of metabolism between this species of Trypanosoma and Trypanosoma cruzi, the main parasite investigated by the group of A. Silber. Although two reconstructions had been done, none is satisfactory.
• Continuation of the discussions initiated between A. Silber, V. Lacroix and A. Mary during A. Silber’s visit to Erable in Nov. 2021 on the inference of variants in non-model parasite or vector species.

Work done in 2023

• Paper accepted (in italics, members from Capoeira):
  Carol Moraga, Evelyn Sanchez, Mariana Galvão Ferrarini, Rodrigo A Gutierrez, Elena A Vidal, Marie-France Sagot. BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. GigaScience, 11, 2022, doi:10.1093/gigascience/giac093.
• Co-organisation by A. Silber and M.-F. Sagot of the Third Edition of the “Workshop Metabolism and mathematical models: Two for a tango” that was held virtually on November 14-15, 2023. This organisation involved also Portuguese members of the H2020 Twinning project Olissipo which started in 2021. A full information on its content, including the program may be found here.
• Discussions with the PhD student Gabriela T. Montanaro who is co-supervised by A. Silber and M.-F. Sagot. Such discussions concerned mostly the reconstruction of the metabolic network of Trypanosoma brucei which will be crucial for understanding some differences at the level of metabolism between this species of Trypanosoma and Trypanosoma cruzi, the main parasite investigated by the group of A. Silber.
• Continuation of the discussions initiated between A. Silber, V. Lacroix and A. Mary during A. Silber’s visit to Erable in Nov. 2021 on the inference of variants in non-model parasite or vector species.