2023
  • Salles, L. F. P., de Aguiar, M. A. M., & Marquitti, F. M. D. 2023. Evolution of cooperation in a two-species system with a common resource pool. Journal of Theoretical Biology, 111670.
  • Vasconcelos, V. V., Marquitti, F., Ong, T., McManus, L. C., Aguiar, M., Campos, A. B., ... & Zhan, Q. 2023. Rate-Induced Transitions in Networked Complex Adaptive Systems: Exploring Dynamics and Management Implications Across Ecological, Social, and Socioecological Systems. arXiv preprint arXiv:2309.07449.
  • Princepe, D., Czarnobai, S., Caetano, R. A., Marquitti, F. M. D., de Aguiar, M. A. M., & Araujo, S. B. L. 2023. Intermittent migration can induce pulses of speciation in a two-island system. In press in Evolution.
  • D’Bastiani, E., Princepe, D., Marquitti, F. M., Boeger, W. A., Campião, K. M., & Araujo, S. B. 2023. Effect of host-switching on the ecological and evolutionary patterns of parasites. Systematic Biology, syad022.
  • Ferreira, L.S.,Marquitti, F.M.D., da Silva, R.L.P., Borges, M.E., Gomes, M.F., Cruz, O.G., Kraenkel, R.A., Coutinho, R.M., Prado, P.I. & Bastos, L.S. 2023. Estimating the impact of implementation and timing of the COVID-19 vaccination programme in Brazil: a counterfactual analysis. The Lancet Regional Health–Americas, 17.

2022
  • Ferreira, L.S.,Marquitti, F.M.D., da Silva, R.L.P., Borges, M.E., Gomes, M.F., Cruz, O.G., Kraenkel, R.A., Coutinho, R.M., Prado, P.I. & Bastos, L.S. Estimating the impact of implementation and timing of the COVID-19 vaccination programme in Brazil: a counterfactual analysis. In press in Lancet Regional Health Americas (PrePrint at: medRxiv:2021.12.24.21268384). 
  • Princepe, D., Czarnobai, S., Pradella, T.M., Caetano, R.A., Marquitti, F.M.D., de Aguiar, M.A.M. & Araujo, S.B.L. Diversity patterns and speciation processes in a two-island system with continuous migration. Evolution. 2022. 76: 2260-2271 
  • Botelho, L. L., Marquitti, F. M. D., & de Aguiar, M. A. (2022). Extinction and hybridization in a neutral model of speciation. Journal of Physics A: Mathematical and Theoretical 55(38), 385601.
  • Lima, T. R. A., Martins, F. R., Menezes, B. S., Marquitti, F. M. D., Sfair, J. C., Silveira, A. P., & Araújo, F. S. (2022). The stress gradient hypothesis explains plant-plant interaction networks in edapho climatic gradients. Acta Oecologica 115, 103831.
  • Souto Ferreira, L., Canton, O., da Silva, R. L. P., Poloni, S., Sudbrack, V., Borges, M. E., ... & Coutinho, R. M. (2022). Assessing the best time interval between doses in a two-dose vaccination regimen to reduce the number of deaths in an ongoing epidemic of SARS-CoV-2. PLoS Computational Biology 18(3), e1009978.

2021
  • Coutinho, R. M., Marquitti, F. M. D., Ferreira, L. S., Borges, M. E., da Silva, R. L. P., Canton, O., ... & Prado, P. I. (2021). Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P. 1 variant. Communications Medicine 1(1), 1-8.
  • Maia, K. P., Marquitti, F. M., Vaughan, I. P., Memmott, J., & Raimundo, R. L. (2021). Interaction generalisation and demographic feedbacks drive the resilience of plant–insect networks to extinctions. Journal of Animal Ecology 90(9), 2109-2121.
  • Franco, G. D., Marquitti, F. M. D., Fernandes, L. D., Braha, D. & de Aguiar, M. A. M. 2021. Shannon information criterion for low-high diversity transition in Moran and voter models. Physical Review E 104(2), 024315.
  • Marquitti, F. M. D., Coutinho, R. M., Ferreira, L. S., Borges, M. E., Portella, T. P., Silva, R. L. P. D., Canton, O. , Poloni, S., Franco, C., Coelho, V., Barberia, L., de Bolle, M., Boing, A. C., Donalisio, M. R., Boing, A. F.,  da Silva, A. A. M., Prado, P. I., Veras, M. A. S. M. & Kraenkel, R. A. (2021). Brazil in the face of new SARS-CoV-2 variants: emergencies and challenges in public health. Revista Brasileira de Epidemiologia 24.
​
2020
  • Marquitti, F.M.D.; Fernandes, L.D. & de Aguiar, M.A.M. 2020. Allopatry increases the balance of phylogenetic trees during radiation under neutral speciation. Ecography 43 (10), 1487-1498. doi:10.1111/ecog.04937 
  • Araújo Lima, T., Marquitti, F., & de Aguiar, M. A. 2020. Measuring Tree Balance with Normalized Tree Area. arXiv e-prints, arXiv-2008.
  • Raimundo, R., Maia, K., Muniz, D., Cantor, M., Guimarães Jr, P., Lemos-Costa, P., Santana, E., Gaiarsa, M., Santana, P., Giacobelli, L., Assis, A.P., Birskis-Barros, I., Medeiros, L., Marquitti, F., Dáttilo, W., Andreazzi, C., Pires, M.,Velásquez, V. & Migon, E. 2020. Vulnerabilidade das microrregiões do Nordeste brasileiro à pandemia do novo coronavírus (SARS-CoV-2). SciELO Preprints: https://preprints.scielo.org/index.php/ scielo/preprint/view/35/version/39
  • Gaiarsa, M.P., Marquitti, F.M.D., Lemos-Costa, P., Burin, G., Medeiros, L.P., Velásquez, V.M., Santana, P.C., Santana, E.M., Maia, K.P., Muniz, D, Cosmo, L.G., Assis,A.P.A., Birskis-Barros, I., Cantor, M., Emer, C., Andreazzi, C.S., Pires, M.M., Côrtes, M.C., Melo, D., D áttilo, W.F., Raimundo, R.L.G., Migon, E. X. F.G. & Guimarães, P.R. 2020. Vulnerabilidade estrutural dos hospitais e cemitérios e crematórios da cidade de São Paulo à COVID-19.SciELO Preprints: https://doi.org/10.1590/SciELOPreprints.381
  • Emer, C., Maia, K. P., Santana, P. C., Santana, E. M., da Silva, D. G., Cosmo, L. G., Assis, A. P. A., Burin, G, Cantor M., Lemos-Costa, P. Velásquez, V. M., Birskis-Barros, I., Gaiarsa, M. P., Medeiros, L. P.; Marquitti, F. M. D.; Côrtes, M. C.; Dáttilo, W. F, Andreazzi, C. S., Pires, M. M.; Melo, D, Migon, E. X. F. G.; Raimundo, R. L, G. & Guimarães Jr, P. 2020. Vulnerability of the micro-regions of the South of Brazil to the new coronavirus (SARS-CoV-2) pandemic. SciELO Preprints: https://doi.org/10.1590/SciELOPreprints.128. 
​
2019
  • Costa, C. L., Lemos-Costa, P., Marquitti, F. M., Fernandes, L. D., Ramos, M. F., Schneider, D. M., ... & de Aguiar, M. A. 2019. Signatures of microevolutionary processes in phylogenetic patterns. Systematic Biology 68(1), 131-144. https://doi.org/10.1093/sysbio/syy049.

2018
  • Costa, C.L.N, F.M.D. Marquitti, S.I. Perez, M.F. Ramos, D.M. Schneider, M.A.M. de Aguiar. 2018. Registering the evolutionary history in individual-based models of speciation. Physica A: Statistical Mechanics and its Applications 510:1-14.
  • Raimundo, R.L.G., F.M.D. Marquitti, C.S. de Andreazzi, M.M. Pires, P.R. Guimarães 2018. Ecology and evolution of species-rich interaction networks. In Ecological Networks in the Tropics (pp. 43-58). Springer, Cham.

2017
  • Pires, M. M., F.M.D. Marquitti, P. R. Guimaraes. 2017. The friendship paradox in species-rich ecological networks: implications for conservation and monitoring. Biological Conservation 209: 245-252.
  • Barreto, W.P., F.M.D. Marquitti, and M. A. M .de Aguiar. 2017. A genetic approach to the Rock-Paper-Scissors game. Journal of Theoretical Biology 421: 146–152.
  • Cantor, M., Pires, M.M., Marquitti, F.M.D., Raimundo, R. L., Sebastián-González, E., Coltri, P. P., Ivan-Perez, S., Barneche, D.R., Brandt, D.Y. C. , Nunes, K, Daura-Jorge, F. G., Floeter, S.R. & Guimarães Jr., P.R. 2017. Nestedness across biological scales. PloS One 12(2): e0171691.

2016
  • Guimarães, P.R., Pires, M.M., Marquitti, F.M.D., & Raimundo, R. L. 2016. Ecology of mutualisms. eLS: 1–9.

2015
  • Ashikaga, H., Aguilar-Rodríguez, J., Gorsky, S., Lusczek, E., Marquitti, F.M.D., Thompson, B. Wu, D., Garland, J. 2015. Modeling the heart as a communication system. Journal Royal Society Interface 12(2): 20141201.
  • Mello, M. A. R., Rodrigues, F. A., Costa, L. D. F., Kissling, W. D., Şekercioğlu, Ç. H., Marquitti, F. M. D., & Kalko, E. K. V. 2015. Keystone species in seed dispersal networks are mainly determined by dietary specialization. Oikos 124: 1031-1039.

2014
  • Marquitti, F. M. D., P. R. Guimaraes, M. M. Pires, L. F. Bittencourt. 2014. MODULAR: Software for the Autonomous Computation of Modularity in Large Network Sets. Ecography 37: 221–224.
  • Dáttilo, W., F. M. D. Marquitti, P. R. Guimaraes, T. J. Izzo. 2014. The structure of ant-plant ecological networks: is abundance enough?. Ecology 95: 475–485.

2012
  • Hagen, M., W. D. Kissiling, C. Rasmussen, M. A. M. de Aguiar, L. Brown, D. W. Carstensen, I. Alves-dos-Santos, Y. L. Dupont, F. K. Edwards, J. Genini, P. R. Guimaraes, G. B. Jenkins, P. Jordano, C. N. Kaiser-Bunbury, M. Ledger, K. P. Maia,F. M. D. Marquitti, O. McLaughlin, L. P. C. Morellato, E. J. O'Gorman, K. Trojelsgaard, J. M. Tylianakis, M. M. Vidal, G. Woodward, J. Olesen. 2012. Biodiversity, species interactions and ecological networks in a fragmented world. Advances in Ecological Research 46: 89-210.
  • Tinker, M. T., P. R. Guimaraes, M. Novak, F. M. D. Marquitti, J. Bodkin, M. Staedler, G. Bentall, J. Estes. 2012. Structure and mechanism of diet specialization: testing models of individual variation in resource use with sea otters. Ecology Letters15: 475-483.

2011
  • Donatti, C.I., P. R. Guimaraes, M. Galetti, M. A. Pizo, F. M. D. Marquitti, R. Dirzo. 2011. Analysis of a hyper-diverse seed dispersal network: modularity and underlying mechanisms. Ecology Letters 14:773-781.
  • Mello, M. A.R, F. M. D. Marquitti, P. R. Guimaraes, E. K. V. Kalko, P. Jordano, M. A. M. de Aguiar. 2011.The missing part of seed dispersal networks: structure and robustness of bat-fruit interactions. PLoS ONE 6: e17395.
  • Mello, M. A.R, F. M. D. Marquitti, P. R. Guimaraes, E. K. V. Kalko, P. Jordano, M. A. M. de Aguiar. 2011. The modularity of seed dispersal: differences in structure and robustness between bat - and bird - fruit networks. Oecologia 167: 131-140.

2008-2010
  • Mello, M. A.R., F.M. D. Marquitti, P. R. Guimaraes, E.K.V. Kalko, P. Jordano. 2008. Small differences may lead to big consequences: bat and bird seed dispersal networks (Abstract, Luis F Barcardi Award 2008). Biotropica 40: 777-777.