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I was trained as a biochemist, and I am familiar with most common biochemical assays. I wrote my Ph.D. thesis on the elucidation of the metabolism of primary cultures of brain cells (astrocytes and neurons) and had two postdoctoral positions studying the metabolism of trehalose in Saccharomyces cerevisiae and the metabolic response to acid stress in Lactococcus lactis. Most of the metabolic studies were done by NMR (1H, 2H, 7Li, 13C, 15N, 19F, 23Na and 31P) either in vivo (with cells perfused through or immobilized in the NMR tube) or in vitro (isotopomeric analysis or metabolic flux analysis). During these postdoctoral positions I changed the focus of my research from the wet-lab to the computational side to which I now devote all of my research time. My main interest is still on the fundamental elucidation of cellular metabolism, which I undertake with computational models using both continuous and discrete frameworks with mechanistic and canonical formulations. I have also been involved in teaching Computational Systems Biology to undergraduates in biomedical engineering.
Identificação

Identificação pessoal

Nome completo
Luís Maria de Figueiredo Mascarenhas Lopes da Fonseca

Nomes de citação

  • Luis L. Fonseca

Identificadores de autor

Ciência ID
CC13-0B59-25B6
ORCID iD
0000-0002-7902-742X
AuthenticusID
R-000-9P0
Google Scholar ID
W2znhD4AAAAJ
Researcher Id
B-2265-2009
Scopus Author Id
8940764800

Endereços de correio eletrónico

  • llfonseca@medicine.ufl.edu (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Ciências da Computação e da Informação
  • Ciências Naturais - Ciências Biológicas - Bioquímica

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Espanhol; Castelhano Utilizador independente (B1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador independente (B1)
Francês Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1)
Formação
Grau Classificação
2006/09/11
Concluído
Bioquímica (Doutoramento)
Especialização em Especialidade: Bioquímica
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Metabolism of Primary Astrocytes Studied by Nmr: Metabolic Trafficking and Neuroprotection" (TESE/DISSERTAÇÃO)
1993 - 1998
Concluído
Bioquimica (Licenciatura)
Universidade de Lisboa, Portugal
"Brain cell culture studied by in vivo nuclear magnetic resonance techniques." (TESE/DISSERTAÇÃO)
17
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento
Empregador
2020/08/01 - Atual Investigador Contratado (Investigação) University of Florida, Estados Unidos
2012/05/02 - 2020/07/31 Investigador Contratado (Investigação) Georgia Institute of Technology, Estados Unidos
2009/10 - 2012/04 Pós-doutorado (Investigação) Fundação para a Ciência e a Tecnologia, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006/10 - 2009/09 Pós-doutorado (Investigação) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1998/11 - 1999/12 Investigador (Investigação) Universidade Nova de Lisboa, Portugal
1997/09 - 1998/10 Estagiário de Investigação (Investigação) Universidade Nova de Lisboa, Portugal
Produções

Publicações

Artigo em revista
  1. DeBarry, Jeremy D.; Nural, Mustafa V.; Pakala, Suman B.; Nayak, Vishal; Warrenfeltz, Susanne; Humphrey, Jay; Lapp, Stacey A.; et al. "MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques". Scientific Data 9 1 (2022): http://dx.doi.org/10.1038/s41597-022-01755-y.
    10.1038/s41597-022-01755-y
  2. Adhikari, Bandita; Scindia, Yogesh; Sordo Vieira, Luis; de Assis Lopes Ribeiro, Henrique; Masison, Joseph; Yang, Ning; Luis L. Fonseca; et al. Autor correspondente: Laubenbacher, Reinhard. "Computational Modeling of Macrophage Iron Sequestration during Host Defense against Aspergillus". mSphere e00074-22 (2022): http://dx.doi.org/10.1128/msphere.00074-22.
    10.1128/msphere.00074-22
  3. Peterson, Mariko S.; Joyner, Chester J.; Lapp, Stacey A.; Brady, Jessica A.; Wood, Jennifer S.; Cabrera-Mora, Monica; Saney, Celia L.; et al. "Plasmodium knowlesi Cytoadhesion Involves SICA Variant Proteins". Frontiers in Cellular and Infection Microbiology 12 (2022): http://dx.doi.org/10.3389/fcimb.2022.888496.
    Publicado • 10.3389/fcimb.2022.888496
  4. Peterson, Mariko S.; Joyner, Chester J.; Brady, Jessica A.; Wood, Jennifer S.; Cabrera-Mora, Monica; Saney, Celia L.; Fonseca, Luis L.; et al. "Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi". Malaria Journal 20 1 (2021): 486. http://dx.doi.org/10.1186/s12936-021-03925-6.
    10.1186/s12936-021-03925-6
  5. Gupta, Anuj; Styczynski, Mark P.; Galinski, Mary R.; Voit, Eberhard O.; Luis L. Fonseca. "Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections". (2021):
    Publicado • 10.1038/s41598-021-98024-6
  6. Dalvi-Garcia, Felipe; Fonseca, Luis L.; Vasconcelos, Ana Tereza R.; Hedin-Pereira, Cecilia; Voit, Eberhard O.. "A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression". PLOS Computational Biology 17 5 (2021): e1008956. http://dx.doi.org/10.1371/journal.pcbi.1008956.
    Publicado • 10.1371/journal.pcbi.1008956
  7. Olivença, Daniel V.; Fonseca, Luis L.; Voit, Eberhard O.; Pinto, Francisco R.. "Thickness of the airway surface liquid layer in the lung is affected in cystic fibrosis by compromised synergistic regulation of the ENaC ion channel". Journal of The Royal Society Interface 16 157 (2019): 20190187. http://dx.doi.org/10.1098/rsif.2019.0187.
    Acesso aberto • Publicado • 10.1098/rsif.2019.0187
  8. Faraji, Mojdeh; Fonseca, Luis L; Escamilla-Treviño, Luis; Barros-Rios, Jaime; Engle, Nancy; Yang, Zamin K.; Tschaplinski, Timothy J.; Dixon, Richard A.; Voit, Eberhard O. "Mathematical models of lignin biosynthesis". Biotechnology for Biofuels 11 1 (2018): 34-34.
    Publicado • 10.1186/s13068-018-1028-9
  9. Olivença, Daniel V.; Uliyakina, Inna; Fonseca, Luis L; Amaral, Margarida D.; Voit, Eberhard O; Pinto, Francisco R.. "A Mathematical Model of the Phosphoinositide Pathway". Scientific Reports 8 1 (2018): 3904-0.
    Publicado • 10.1038/s41598-018-22226-8
  10. M. Downs, Diana; V. Bazurto, Jannell; Gupta, Anuj; L. Fonseca, Luis; O. Voit, Eberhard. "The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling". AIMS Microbiology 4 2 (2018): 289-303.
    Publicado • 10.3934/microbiol.2018.2.289
  11. Faraji, Mojdeh; Fonseca, Luis L; Escamilla-Treviño, Luis; Barros-Rios, Jaime; Engle, Nancy L.; Yang, Zamin K.; Tschaplinski, Timothy J.; Dixon, Richard A.; Voit, Eberhard O. "A dynamic model of lignin biosynthesis in Brachypodium distachyon". Biotechnology for Biofuels 11 1 (2018): 253-253.
    Publicado • 10.1186/s13068-018-1241-6
  12. Fonseca, Luis L; Joyner, Chester J.; Saney, Celia L.; Moreno, Alberto; Barnwell, John W.; Galinski, Mary R.; Voit, Eberhard O. "Analysis of erythrocyte dynamics in Rhesus macaque monkeys during infection with Plasmodium cynomolgi". Malaria Journal 17 1 (2018): 410-0.
    Publicado • 10.1186/s12936-018-2560-6
  13. Galinski MR; Lapp SA; Peterson MS; Ay F; Joyner CJ; LE Roch KG; Fonseca LL; Voit EO; MAHPIC CONSORTIUM. "Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria.". Parasitology 0 0 (2017): 1-16. http://europepmc.org/abstract/med/28712361.
    Publicado • 10.1017/S0031182017001135
  14. Fonseca, Luis L; Joyner, Chester J.; Galinski, Mary R.; Voit, Eberhard O. "A model of Plasmodium vivax concealment based on Plasmodium cynomolgi infections in Macaca mulatta". Malaria Journal 16 1 (2017): 375-0.
    Publicado • 10.1186/s12936-017-2008-4
  15. Tang, Yan; Gupta, Anuj; Garimalla, Swetha; Galinski, Mary R.; Styczynski, Mark P.; Fonseca, Luis L; Voit, Eberhard O. "Metabolic modeling helps interpret Transcriptomic changes during malaria". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 0 (2017): 0-0.
    Publicado • 10.1016/j.bbadis.2017.10.023
  16. Fonseca, Luis L; Alezi, Harnel S.; Moreno, Alberto; Barnwell, John W.; Galinski, Mary R.; Voit, Eberhard O. "Quantifying the removal of red blood cells in Macaca mulatta during a Plasmodium coatneyi infection". Malaria Journal 15 1 (2016): 410-425.
    Publicado • 10.1186/s12936-016-1465-5
  17. Phuongan Dam; Luis L Fonseca; Konstantinos T Konstantinidis; Eberhard O Voit. "Dynamic models of the complex microbial metapopulation of lake mendota". npj Systems Biology and Applications 2 0 (2016): 16007-16. https://doi.org/10.1038%2Fnpjsba.2016.7.
    Publicado • 10.1038/npjsba.2016.7
  18. Chen, Po-Wei; Fonseca, Luis L; Hannun, Yusuf A.; Voit, Eberhard O; Witt, Stephan Neil. "Analysis of the Involvement of Different Ceramide Variants in the Response to Hydroxyurea Stress in Baker's Yeast". PLOS ONE 11 1 (2016): e0146839-e0146839.
    Publicado • 10.1371/journal.pone.0146839
  19. Dolatshahi, Sepideh; Fonseca, Luis L.; Voit, Eberhard O.. "New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. I. Construction and diagnosis of a comprehensive dynamic model". Molecular Biosystems 12 1 (2016): 23-36.
    Publicado • 10.1039/c5mb00331h
  20. Dolatshahi, Sepideh; Fonseca, Luis L; Voit, Eberhard O. "New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. II. Inference of the precisely timed control system regulating glycolysis". Mol. BioSyst. 12 1 (2016): 37-47.
    Publicado • 10.1039/c5mb00726g
  21. Fonseca, Luis L; Voit, Eberhard O. "Comparison of mathematical frameworks for modeling erythropoiesis in the context of malaria infection". Mathematical Biosciences 270 1 (2015): 224-236.
    Publicado • 10.1016/j.mbs.2015.08.020
  22. Faraji, Mojdeh; Fonseca, Luis L; Escamilla-Treviño, Luis; Dixon, Richard A.; Voit, Eberhard O. "Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum". Biotechnology for Biofuels 8 1 (2015): 151-0.
    Publicado • 10.1186/s13068-015-0334-8
  23. Chen, Po-Wei; Fonseca, Luis L; Hannun, Yusuf A.; Voit, Eberhard O; Stelling, Jorg. "Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast". PLOS Computational Biology 11 8 (2015): e1004373-e1004373.
    Publicado • 10.1371/journal.pcbi.1004373
  24. Radoš D; Turner DL; Fonseca LL; Carvalho AL; Blombach B; Eikmanns BJ; Neves AR; Santos H. "Carbon flux analysis by 13C nuclear magnetic resonance to determine the effect of CO2 on anaerobic succinate production by Corynebacterium glutamicum.". (2014): http://europepmc.org/abstract/med/24610842.
    10.1128/AEM.04189-13
  25. Faria, N.T.; Santos, M.V.; Fernandes, P.; Fonseca, L.L.; Fonseca, C.; Ferreira, F.C.. "Production of glycolipid biosurfactants, mannosylerythritol lipids, from pentoses and d-glucose/d-xylose mixtures by Pseudozyma yeast strains". Process Biochemistry 49 11 (2014): 1790-1799. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908267677&partnerID=MN8TOARS.
    10.1016/j.procbio.2014.08.004
  26. Carvalho, Ana Lúcia; Turner, David L.; Fonseca, Luís L.; Solopova, Ana; Catarino, Teresa; Kuipers, Oscar P.; Voit, Eberhard O; et al. "Metabolic and Transcriptional Analysis of Acid Stress in Lactococcus lactis, with a Focus on the Kinetics of Lactic Acid Pools". PLoS ONE 8 7 (2013): e68470-e68470.
    Publicado • 10.1371/journal.pone.0068470
  27. Chen, Po-Wei; Fonseca, Luis L.; Hannun, Yusuf A.; Voit, Eberhard O.; Stelling, Jorg. "Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast". PLoS Computational Biology 9 5 (2013): e1003078-e1.
    Publicado • 10.1371/journal.pcbi.1003078
  28. Fonseca, Carla P.; Fonseca, Luís L.; Montezinho, Liliana P.; Alves, Paula M.; Santos, Helena; Castro, M. Margarida C. A.; Geraldes, Carlos F. G. C.. "23Na multiple quantum filtered NMR characterisation of Na+ binding and dynamics in animal cells: a comparative study and effect of Na+/Li+ competition". European Biophysics Journal 42 7 (2013): 503-519. http://dx.doi.org/10.1007/s00249-013-0899-8.
    Publicado • 10.1007/s00249-013-0899-8
  29. Fonseca, Luis L.; Chen, Po-Wei; Voit, Eberhard O.. "Canonical Modeling of the Multi-Scale Regulation of the Heat Stress Response in Yeast". Metabolites 2 4 (2012): 221-241. http://dx.doi.org/10.3390/metabo2010221.
    Publicado • 10.3390/metabo2010221
  30. Fonseca, Luis L.; Sánchez, Claudia; Santos, Helena; Voit, Eberhard O.. "Complex coordination of multi-scale cellular responses to environmental stress". Molecular BioSystems 7 3 (2011): 731-731. http://dx.doi.org/10.1039/c0mb00102c.
    Publicado • 10.1039/c0mb00102c
  31. Fonseca, César; Olofsson, Kim; Ferreira, Carla; Runquist, David; Fonseca, Luís L.; Hahn-Hägerdal, Bärbel; Lidén, Gunnar. "The glucose/xylose facilitator Gxf1 from Candida intermedia expressed in a xylose-fermenting industrial strain of Saccharomyces cerevisiae increases xylose uptake in SSCF of wheat straw". Enzyme and Microbial Technology 48 6-7 (2011): 518-525.
    Publicado • 10.1016/j.enzmictec.2011.02.010
  32. Ndukum, Juliet; Fonseca, Luís L.; Santos, Helena; Voit, Eberhard O; Datta, Susmita. "Statistical Inference Methods for Sparse Biological Time Series Data". BMC Systems Biology 5 1 (2011): 57-57. http://dx.doi.org/10.1186/1752-0509-5-57.
    Publicado • 10.1186/1752-0509-5-57
  33. Voit, E.O.; Goel, G.; Chou, I.-C.; Fonseca, L.L.. "Estimation of metabolic pathway systems from different data sources". IET Systems Biology 3 6 (2009): 513-513. http://dx.doi.org/10.1049/iet-syb.2008.0180.
    Publicado • 10.1049/iet-syb.2008.0180
  34. Castro, Rute; Neves, Ana R.; Fonseca, Luís L.; Pool, Wietske A.; Kok, Jan; Kuipers, Oscar P.; Santos, Helena. "Characterization of the individual glucose uptake systems of Lactococcus lactis /: mannose-PTS, cellobiose-PTS and the novel GlcU permease". Molecular Microbiology 71 3 (2009): 795-806. http://dx.doi.org/10.1111/j.1365-2958.2008.06564.x.
    Publicado • 10.1111/j.1365-2958.2008.06564.x
  35. Cerdán, Sebastián; Sierra, Alejandra; Fonseca, Luis L; Ballesteros, Paloma; Rodrigues, Tiago B.. "The turnover of the H3 deuterons from (2- 13 C) glutamate and (2- 13 C) glutamine reveals subcellular trafficking in the brain of partially deuterated rats". Journal of Neurochemistry 109 S1 (2009): 63-72.
    Publicado • 10.1111/j.1471-4159.2009.05962.x
  36. C. Jorge; L. L. FONSECA; W. Boos; H. SANTOS. "Role of periplasmic trehalase in uptake of trehalose by the thermophilic bacterium Rhodothermus marinus". JOURNAL OF BACTERIOLOGY 74 6 (2008): 1871-1878.
    Publicado • 10.1128/JB.01616-07
  37. Ramírez, Belén G.; Rodrigues, Tiago B.; Violante, Inês R.; Cruz, Fátima; Fonseca, Luís L.; Ballesteros, Paloma; Castro, M. Margarida C.A.; García-Martín, María L.; Cerdán, Sebastián. "Kinetic properties of the redox switch/redox coupling mechanism as determined in primary cultures of cortical neurons and astrocytes from rat brain". Journal of Neuroscience Research 85 15 (2007): 3244-3253.
    Publicado • 10.1002/jnr.21386
  38. Cerdán, Sebastián; Rodrigues, Tiago B.; Sierra, Alejandra; Benito, Marina; Fonseca, Luis L; Fonseca, Carla P.; García-Martín, María L.. "The redox switch/redox coupling hypothesis". Neurochemistry International 48 6-7 (2006): 523-530.
    Publicado • 10.1016/j.neuint.2005.12.036
  39. Fonseca, Luís L.; Monteiro, Miguel A.R.; Alves, Paula M.; Carrondo, Manuel J.T.; Santos, Helena. "Cultures of rat astrocytes challenged with a steady supply of glutamate: New model to study flux distribution in the glutamate-glutamine cycle". Glia 51 4 (2005): 286-296.
    Publicado • 10.1002/glia.20209
  40. Santos, S¿nia S¿; Fonseca, Lu¿s L.; Monteiro, Miguel A.R.; Carrondo, Manuel J.T.; Alves, Paula M.. "Culturing primary brain astrocytes under a fully controlled environment in a novel bioreactor". Journal of Neuroscience Research 79 1-2 (2005): 26-32.
    Publicado • 10.1002/jnr.20279
  41. Fonseca, Luis L.; Alves, Paula M.; Carrondo, Manuel J.T.; Santos, Helena. "Effect of ethanol on the metabolism of primary astrocytes studied by13C- and31P-NMR spectroscopy". Journal of Neuroscience Research 66 5 (2001): 803-811. http://dx.doi.org/10.1002/jnr.10039.
    Publicado • 10.1002/jnr.10039
  42. Alves, P.M.; Fonseca, L.L.; Peixoto, C.C.; Almeida, A.C.; Carrondo, M.J.T.; Santos, H.. "NMR studies on energy metabolism of immobilized primary neurons and astrocytes during hypoxia, ischemia and hypoglycemia". NMR in Biomedicine 13 8 (2000): 438-448. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034493853&partnerID=MN8TOARS.
    10.1002/nbm.665
Capítulo de livro
  1. Fonseca, Luís L.; Yin, Weiwei; Kemp, Melissa L.; Voit, Eberhard O. "Metabolic Systems Modeling, Power-Law Functions". In Encyclopedia of Systems Biology, 1272-1275. New York, NY: Springer New York, 2013.
    Publicado • 10.1007/978-1-4419-9863-7_1156
Poster em conferência
  1. Dalvi-Garcia, Felipe; Fonseca, Luis Lopes Da; Hedin-Pereira, Cecilia; Vasconcelos, Ana Tereza Ribeiro De; Voit, Eberhard. "Modeling the Effects of Cortisol in Serotonergic-Kynurenic Pathways in the Etiology of Depressive Behavior". 2019.
    10.1016/j.ibror.2019.07.1302
Atividades

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2019/09 - 2019/12 Biomedical Systems and Modeling Biomedical Systems and Modeling (Bachelor) Georgia Institute of Technology, Estados Unidos
2015/01 - 2015/05 Biomedical Systems and Modeling Biomedical Systems and Modeling (Bachelor) Georgia Institute of Technology, Estados Unidos
2014/01/06 - 2014/05/04 Biomedical Systems and Modeling Biomedical Engineering (Bachelor) Georgia Institute of Technology, Estados Unidos
Distinções

Prémio

2019 Thanks for Being a Great Teacher!
Georgia Institute of Technology, Estados Unidos