Luis L Fonseca

Luis L Fonseca, Ph.D.

Research Assistant Professor

Department: MD-PULMONARY SYSTEMS MEDICINE
Business Phone: (352) 273-7903
Business Email: llfonseca@medicine.ufl.edu

About Luis L Fonseca

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.

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Accomplishments

Thanks for Being a Great Teacher!
2019 · Center for Teaching and Learning at Georgia Tech
Postdoctoral Fellowship
2009 · Portuguese Science and Technology Foundation
Postdoctoral Fellowship
2006 · Portuguese Science and Technology Foundation
Doctoral Fellowship
2000 · Portuguese Science and Technology Foundation
TOP10 Freshman in the Faculty of Sciences
1995 · Faculty of Sciences, University of Lisbon

Clinical Profile

Areas of Interest
  • Anemia
  • Aspergillosis
  • Malaria
  • Thrombocytopenia

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0002-7902-742X

Areas of Interest
  • Metabolic Flux Analysis
  • NMR Spectroscopy
  • Systems Medicine
  • Systems biology

Publications

2024
Control of Medical Digital Twins with Artificial Neural Networks.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2024.03.18.585589. [PMID] 38562787.
2024
Control of Medical Digital Twins with Artificial Neural Networks.
ArXiv. [PMID] 38562447.
2024
Forum on immune digital twins: a meeting report
npj Systems Biology and Applications. 10(1) [DOI] 10.1038/s41540-024-00345-5. [PMID] 38365857.
2024
Toward mechanistic medical digital twins: some use cases in immunology.
Frontiers in digital health. 6 [DOI] 10.3389/fdgth.2024.1349595. [PMID] 38515550.
2022
Computational Modeling of Macrophage Iron Sequestration during Host Defense against Aspergillus.
mSphere. 7(4) [DOI] 10.1128/msphere.00074-22. [PMID] 35862797.
2022
MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques
Scientific Data. 9(1) [DOI] 10.1038/s41597-022-01755-y. [PMID] 36433985.
2021
A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression
PLOS Computational Biology. 17(5) [DOI] 10.1371/journal.pcbi.1008956. [PMID] 33970902.
2021
Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi.
Malaria journal. 20(1) [DOI] 10.1186/s12936-021-03925-6. [PMID] 34969401.
2021
Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections.
Scientific reports. 11(1) [DOI] 10.1038/s41598-021-98024-6. [PMID] 34593836.
2019
Plasmodium vivax Parasite Load Is Associated With Histopathology in Saimiri boliviensis With Findings Comparable to P vivax Pathogenesis in Humans.
Open forum infectious diseases. 6(3) [DOI] 10.1093/ofid/ofz021. [PMID] 30937329.
2019
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) [DOI] 10.1098/rsif.2019.0187. [PMID] 31455163.
2018
A dynamic model of lignin biosynthesis in Brachypodium distachyon.
Biotechnology for biofuels. 11 [DOI] 10.1186/s13068-018-1241-6. [PMID] 30250505.
2018
A Mathematical Model of the Phosphoinositide Pathway
Scientific Reports. 8(1) [DOI] 10.1038/s41598-018-22226-8. [PMID] 29500467.
2018
Analysis of erythrocyte dynamics in Rhesus macaque monkeys during infection with Plasmodium cynomolgi.
Malaria journal. 17(1) [DOI] 10.1186/s12936-018-2560-6. [PMID] 30400896.
2018
Integrative metabolomics and transcriptomics signatures of clinical tolerance to Plasmodium vivax reveal activation of innate cell immunity and T cell signaling.
Redox biology. 17:158-170 [DOI] 10.1016/j.redox.2018.04.011. [PMID] 29698924.
2018
Mathematical models of lignin biosynthesis.
Biotechnology for biofuels. 11 [DOI] 10.1186/s13068-018-1028-9. [PMID] 29449882.
2018
Metabolic modeling helps interpret transcriptomic changes during malaria.
Biochimica et biophysica acta. Molecular basis of disease. 1864(6 Pt B):2329-2340 [DOI] 10.1016/j.bbadis.2017.10.023. [PMID] 29069611.
2018
PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family.
Parasitology. 145(1):71-84 [DOI] 10.1017/S0031182017001329. [PMID] 28720171.
2018
Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria.
Parasitology. 145(1):85-100 [DOI] 10.1017/S0031182017001135. [PMID] 28712361.
2018
The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling.
AIMS microbiology. 4(2):289-303 [DOI] 10.3934/microbiol.2018.2.289. [PMID] 31294216.
2017
A model of Plasmodium vivax concealment based on Plasmodium cynomolgi infections in Macaca mulatta.
Malaria journal. 16(1) [DOI] 10.1186/s12936-017-2008-4. [PMID] 28923058.
2017
Case Report: Severe and Complicated Cynomolgi Malaria in a Rhesus Macaque Resulted in Similar Histopathological Changes as Those Seen in Human Malaria
The American Journal of Tropical Medicine and Hygiene. 97:548-555
2017
Integrative analysis associates monocytes with insufficient erythropoiesis during acute Plasmodium cynomolgi malaria in rhesus macaques.
Malaria journal. 16(1) [DOI] 10.1186/s12936-017-2029-z. [PMID] 28938907.
2016
Analysis of the Involvement of Different Ceramide Variants in the Response to Hydroxyurea Stress in Baker’s Yeast.
PloS one. 11(1) [DOI] 10.1371/journal.pone.0146839. [PMID] 26784947.
2016
Dynamic models of the complex microbial metapopulation of lake mendota
npj Systems Biology and Applications. 2(1) [DOI] 10.1038/npjsba.2016.7. [PMID] 28725469.
2016
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):23-36 [DOI] 10.1039/c5mb00331h. [PMID] 26609637.
2016
New insights into the complex regulation of the glycolytic pathway in Lactococcus lactis. II. Inference of the precisely timed control system regulating glycolysis.
Molecular bioSystems. 12(1):37-47 [DOI] 10.1039/c5mb00726g. [PMID] 26609780.
2016
Plasmodium cynomolgi infections in rhesus macaques display clinical and parasitological features pertinent to modelling vivax malaria pathology and relapse infections.
Malaria journal. 15(1) [DOI] 10.1186/s12936-016-1480-6. [PMID] 27590312.
2016
Quantifying the removal of red blood cells in Macaca mulatta during a Plasmodium coatneyi infection.
Malaria journal. 15(1) [DOI] 10.1186/s12936-016-1465-5. [PMID] 27520455.
2015
Comparison of mathematical frameworks for modeling erythropoiesis in the context of malaria infection.
Mathematical biosciences. 270(Pt B):224-36 [DOI] 10.1016/j.mbs.2015.08.020. [PMID] 26362230.
2015
Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum.
Biotechnology for biofuels. 8 [DOI] 10.1186/s13068-015-0334-8. [PMID] 26388938.
2015
Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast.
PLoS computational biology. 11(8) [DOI] 10.1371/journal.pcbi.1004373. [PMID] 26241868.
2014
Carbon flux analysis by 13C nuclear magnetic resonance to determine the effect of CO2 on anaerobic succinate production by Corynebacterium glutamicum.
Applied and environmental microbiology. 80(10):3015-24 [DOI] 10.1128/AEM.04189-13. [PMID] 24610842.
2014
Production of glycolipid biosurfactants, mannosylerythritol lipids, from pentoses and D-glucose/D-xylose mixtures by Pseudozyma yeast strains
Process Biochemistry. 49:1790-1799
2013
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 : EBJ. 42(7):503-19 [DOI] 10.1007/s00249-013-0899-8. [PMID] 23563802.
2013
Coordination of rapid sphingolipid responses to heat stress in yeast.
PLoS computational biology. 9(5) [DOI] 10.1371/journal.pcbi.1003078. [PMID] 23737740.
2013
Metabolic and transcriptional analysis of acid stress in Lactococcus lactis, with a focus on the kinetics of lactic acid pools.
PloS one. 8(7) [DOI] 10.1371/journal.pone.0068470. [PMID] 23844205.
2012
Canonical modeling of the multi-scale regulation of the heat stress response in yeast.
Metabolites. 2(1):221-41 [DOI] 10.3390/metabo2010221. [PMID] 24957376.
2011
Complex coordination of multi-scale cellular responses to environmental stress.
Molecular bioSystems. 7(3):731-41 [DOI] 10.1039/c0mb00102c. [PMID] 21088798.
2011
Statistical inference methods for sparse biological time series data.
BMC systems biology. 5 [DOI] 10.1186/1752-0509-5-57. [PMID] 21518445.
2011
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. 48:518-525
2009
Characterization of the individual glucose uptake systems of Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU permease.
Molecular microbiology. 71(3):795-806 [DOI] 10.1111/j.1365-2958.2008.06564.x. [PMID] 19054326.
2009
Estimation of metabolic pathway systems from different data sources.
IET systems biology. 3(6):513-22 [DOI] 10.1049/iet-syb.2008.0180. [PMID] 19947777.
2009
The turnover of the H3 deuterons from (2-13C) glutamate and (2-13C) glutamine reveals subcellular trafficking in the brain of partially deuterated rats.
Journal of neurochemistry. 109 Suppl 1:63-72 [DOI] 10.1111/j.1471-4159.2009.05962.x. [PMID] 19393010.
2008
Role of periplasmic trehalase in uptake of trehalose by the thermophilic bacterium Rhodothermus marinus.
Journal of bacteriology. 190(6):1871-8 [DOI] 10.1128/JB.01616-07. [PMID] 18192391.
2007
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):3244-53 [PMID] 17600826.
2006
The redox switch/redox coupling hypothesis.
Neurochemistry international. 48(6-7):523-30 [PMID] 16530294.
2005
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):286-96 [PMID] 15834952.
2005
Culturing primary brain astrocytes under a fully controlled environment in a novel bioreactor.
Journal of neuroscience research. 79(1-2):26-32 [PMID] 15602759.
2001
Effect of ethanol on the metabolism of primary astrocytes studied by (13)C- and (31)P-NMR spectroscopy.
Journal of neuroscience research. 66(5):803-11 [PMID] 11746405.
2000
NMR studies on energy metabolism of immobilized primary neurons and astrocytes during hypoxia, ischemia and hypoglycemia.
NMR in biomedicine. 13(8):438-48 [PMID] 11252029.
A Mathematical Model of the Phosphoinositide Pathway
. [DOI] 10.1101/182634.

Education

Ph.D. in Biochemistry
2006 · Instituto de Tecnologia Química e Biológica, New University of Lisbon, Portugal
BS/MS in Biochemistry
1998 · University of Lisbon, Portugal

Contact Details

Phones:
Business:
(352) 273-7903
Emails:
Administrative Specialist I:
Barbara J Martin
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