Experimental Computational and Structural Biochemistry

Through the integration of mathematical foundation with computational programming in Matlab, R and Python we have been developing algorithms to process and represent complex neural systems regarding metabolism and NGS.

Our research involves the application of computational and mathematical techniques to problems in biomedicine.

We integrate novel techniques in computer science and programming to address multidisciplinary fields and approaches.

Our group is dedicated to the development of computational models for the understanding of complex neural systems including potential therapeutic molecules, neurobiochemistry, ion channels, neurosciences, and physiology and regulation systems.

ANSEP Astrocyte Neuron Simulation Environment Platform

We developed the free platform Ansep (Astrocyte-Neuron Simulation Enviroment), which is available for the scientific community for the model and analysis of metabolic Networks, offering tools that contribute to a better understanding of neurodegeneration processes.

Recent Publications

Brain lipidomics as a rising field in neurodegenerative contexts: Perspectives with Machine Learning approaches
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Abstract

Lipids are essential for cellular functioning considering their role in membrane composition, signaling, and energy metabolism. The brain is the second most abundant organ in terms of lipid concentration and diversity only after adipose tissue. However, in the central system (CNS) lipid dysregulation has been linked to the etiology, progression, and severity of neurodegenerative diseases such as Alzheimeŕs, Parkinson, and Multiple Sclerosis. Advances in the human genome and subsequent sequencing technologies allowed us the study of lipidomics as a promising approach to diagnosis and treatment of neurodegeneration. Lipidomics advances rapidly increased the amount and quality of data allowing the integration with other omic types as well as implementing novel bioinformatic and quantitative tools such as machine learning (ML). Integration of lipidomics data with ML, as a powerful quantitative predictive approach, led to improvements in diagnostic biomarker prediction, clinical data integration, network, and systems approaches for neural behavior, novel etiology markers for inflammation, and neurodegeneration progression and even Mass Spectrometry image analysis. In this sense, by exploiting lipidomics data with ML is possible to improve the identification of new biomarkers or unveil new molecular mechanisms associated with lipid impairment across neurodegeneration. In this review, we present the lipidomic neurobiology state-of-the-art highlighting its potential applications to study neurodegenerative conditions. Also, we present theoretical background, applications, and advances in the integration of lipidomics with ML. This review opens the door to new approaches in this rising field.

Advances in Astrocyte Computational Models: From Metabolic Reconstructions to Multi-omic Approaches View Publication

Abstract

The growing importance of astrocytes in the field of neuroscience has led to a greater number of computational models devoted to the study of astrocytic functions and their metabolic interactions with neurons. The modeling of these interactions demands a combined understanding of brain physiology and the development of computational frameworks based on genomic-scale reconstructions, system biology, and dynamic models. These computational approaches have helped to highlight the neuroprotective mechanisms triggered by astrocytes and other glial cells, both under normal conditions and during neurodegenerative processes. In the present review, we evaluate some of the most relevant models of astrocyte metabolism, including genome-scale reconstructions and astrocyte-neuron interactions developed in the last few years. Additionally, we discuss novel strategies from the multi-omics perspective and computational models of other glial cell types that will increase our knowledge in brain metabolism and its association with neurodegenerative diseases.

TERT silencing alters the expression of ARG1, GLUL, VIM, NES genes and hsa-miR-29b-3p in the T98G cell line View Publication

Abstract

The central function of telomerase is maintaining the telomere length. However, several extra-telomeric roles have been identified for this protein complex. In this study, we evaluated the effect of the silencing of the catalytic subunit of telomerase (TERT) on the expression of candidate microRNAs, cell activation markers and glial-related genes in a glioblastoma cell line (T98G). The silencing was performed by a siRNA and the qPCR method was used to analyze the expression of TERT and downstream genes. Flow cytometry was used to quantify the TERT protein, and bioinformatics analysis was carried out to analyze the functions of microRNA target genes. Here, it was observed that after a 50% reduction of the TERT gene, the expression of ARG1 (Arginase 1) was upregulated, whereas NES (Nestin), GLUL (Glutamate-Ammonia Ligase), VIM (Vimentin) and the hsa-miR-29b-3p microRNA were downregulated (P-value <0.05). A bioinformatic analysis showed that target genes of hsa-miR-29b are associated with focal adhesion, the PI3K-Akt signaling pathway, among others. These results are important because they contribute to the knowledge of extratelomeric functions by providing relevant evidence about novel genes modulated by TERT.

The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning
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Abstract

Neurodegenerative diseases (NDs) are characterized by progressive neuronal dysfunction and death of brain cells population. As the early manifestations of NDs are similar, their symptoms are difficult to distinguish, making the timely detection and discrimination of each neurodegenerative disorder a priority. Several investigations have revealed the importance of microRNAs and long non-coding RNAs in neurodevelopment, brain function, maturation, and neuronal activity, as well as its dysregulation involved in many types of neurological diseases. Therefore, the expression pattern of these molecules in the different NDs have gained significant attention to improve the diagnostic and treatment at earlier stages. In this sense, we gather the different microRNAs and long non-coding RNAs that have been reported as dysregulated in each disorder. Since there are a vast number of non-coding RNAs altered in NDs, some sort of synthesis, filtering and organization method should be applied to extract the most relevant information. Hence, machine learning is considered as an important tool for this purpose since it can classify expression profiles of non-coding RNAs between healthy and sick people. Therefore, we deepen in this branch of computer science, its different methods, and its meaningful application in the diagnosis of NDs from the dysregulated non-coding RNAs. In addition, we demonstrate the relevance of machine learning in NDs from the description of different investigations that showed an accuracy between 85% to 95% in the detection of the disease with this tool. All of these denote that artificial intelligence could be an excellent alternative to help the clinical diagnosis and facilitate the identification diseases in early stages based on non-coding RNAs.

Use of a neuron-glia genome-scale metabolic reconstruction to model the metabolic consequences of the Arylsulphatase a deficiency through a systems biology approach
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Abstract

Metachromatic leukodystrophy (MLD) is a human neurodegenerative disorder characterized by progressive damage on the myelin band in the nervous system. MLD is caused by the impaired function of the lysosomal enzyme Arylsulphatase A (ARSA). The physiopathology mechanisms and the biochemical consequences in the brain of ARSA deficiency are not entirely understood. In recent years, the use of genome-scale metabolic (GEM) models has been explored as a tool for the study of the biochemical alterations in MLD. Previously, we modeled the metabolic consequences of different lysosomal storage diseases using single GEMs. In the case of MLD, using a glia GEM, we previously predicted that the metabolism of glycosphingolipids and neurotransmitters was altered. The results also suggested that mitochondrial metabolism and amino acid transport were the main reactions affected. In this study, we extended the modeling of the metabolic consequences of ARSA deficiency through the integration of neuron and glial cell metabolic models. Cell-specific models were generated from Recon2, and these were used to create a neuron-glial bi-cellular model. We propose a workflow for the integration of this type of model and its subsequent study. The results predicted the impairment pathways involved in the transport of amino acids, lipids metabolism, and catabolism of purines and pyrimidines. The use of this neuron-glial GEM metabolic reconstruction allowed to improve the prediction capacity of the metabolic consequences of ARSA deficiency, which might pave the way for the modeling of the biochemical alterations of other inborn errors of metabolism with central nervous system involvement.

Modulation of Small RNA Signatures by Astrocytes on Early Neurodegeneration Stages;Implications for Biomarker Discovery
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Abstract

Diagnosis of neurodegenerative disease (NDD) is complex, therefore simpler, less invasive, more accurate biomarkers are needed. small non-coding RNA (sncRNA) dysregulates in NDDs and sncRNA signatures have been explored for the diagnosis of NDDs, however, the performance of previous biomarkers is still better. Astrocyte dysfunction promotes neurodegeneration and thus derived scnRNA signatures could provide a more precise way to identify of changes related to NDD course and pathogenesis, and it could be useful for the dissection of mechanistic insights operating in NDD. Often sncRNA are transported outside the cell by the action of secreted particles such as extracellular vesicles (EV), which protect sncRNA from degradation. Furthermore, EV associated sncRNA can cross the BBB to be found in easier to obtain peripheral samples, EVs also inherit cell-specific surface markers that can be used for the identification of Astrocyte Derived Extracellular Vesicles (ADEVs) in a peripheral sample. By the study of the sncRNA transported in ADEVs it is possible to identify astrocyte specific sncRNA signatures that could show astrocyte dysfunction in a more simpler manner than previous methods. However, sncRNA signatures in ADEV are not a copy of intracellular transcriptome and methodological aspects such as the yield of sncRNA produced in ADEV or the variable amount of ADEV captured after separation protocols must be considered. Here we review the role as signaling molecules of ADEV derived sncRNA dysregulated in conditions associated with risk of neurodegeneration, providing an explanation of why to choose ADEV for the identification of astrocyte-specific transcriptome. Finally, we discuss possible limitations of this approach and the need to improve the detection limits of sncRNA for the use of ADEV derived sncRNA signatures.

In silico interactions of statins with cell death-inducing DNA fragmentation factor-like effector A (CIDEA)
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Abstract

Statins are the low-density lipoproteins (LDL)-cholesterol-lowering drugs of first choice and are used to prevent the increased risk of cardiovascular and cerebrovascular diseases. Although some of their effects are well known, little is known about their ability to regulate other lipid-related proteins which control apoptotic mechanisms. The aim of this study was to explore whether statins can bind to cell death-inducing DNA fragmentation factor-like effector A (CIDEA), which might be a possible pleiotropic mechanism of action of these drugs on the modulation of apoptosis and lipid metabolism. The structures of statins were subjected to molecular docking and dynamics with the human CIDEA protein to investigate the interaction pattern and identify which residues are important. The docking results indicated that atorvastatin and rosuvastatin showed the best interaction energy (−8.51 and −8.04 kcal/mol, respectively) followed by fluvastatin (−7.39), pitavastatin (−6.5), lovastatin (−6.23), pravastatin (−6.04) and simvastatin (−5.29). Atorvastatin and rosuvastatin were further subjected to molecular dynamics at 50 ns with CIDEA and the results suggested that rosuvastatin-CIDEA complex had lower root-mean square deviation and root-mean square fluctuation when compared with atorvastatin-CIDEA. Since two arginine residues -ARG19 and ARG22-were identified to be common for the interaction with CIDEA, a single-point mutation was induced in these residues to determine whether they are important for binding interaction. Mutation of these two residues seemed to affect mostly the interaction of atorvastatin with CIDEA, suggesting that they are important for the binding and therefore indicate another possible metabolic mechanism of the pleiotropic effects of this statin.

Recent Book Chapters

In Silico Identification of Novel Interactions for FABP5 (Fatty Acid-Binding Protein 5) with Nutraceuticals: Possible Repurposing Approach

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Cabezas, R., Sahebkar, A., Echeverria, V., González, J., Md Ashraf, G., & Barreto, G. E. (2021). In Silico Identification of Novel Interactions for FABP5 (Fatty Acid-Binding Protein 5) with Nutraceuticals: Possible Repurposing Approach. En Barreto, G. E., & Sahebkar, A. (Eds.), Pharmacological Properties of Plant-Derived Natural Products and Implications for Human Health (pp 589-599). Suiza: Springer Nature Switzerland AG.

Neuroprotective Role of Hypothermia in Hypoxic-ischemic Brain Injury: Combined Therapies using Estrogen

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Barreto, G. E., Saraceno, E., Gonzalez, J., Kolliker, R., Castilla, R., & Capani F. (2015). Chapter 8 - Neuroprotection with Estradiol in Experimental Perinatal Asphyxia: A New Approach. En Duncan, K. E. (Ed.), Estrogen Effects on Traumatic Brain Injury (pp. 113-124). United States of America: Elsevier.

Neuroprotection by Exogenous Estrogenic Compounds Following Traumatic Brain Injury

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Lopez-Rodriguez, A. B., Ávila-Rodriguez, M., Vega-Vela, N. E., Capani, F., Gonzalez, J., García-Segura, L. M., & Barreto G. E. (2015). Chapter 6 - Neuroprotection by Exogenous Estrogenic Compounds Following Traumatic Brain Injury. En Duncan, K. E. (Ed.), Estrogen Effects on Traumatic Brain Injury (pp. 73-90). United States of America: Elsevier.

Natural Antioxidants in Dementia: An Overview

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Cabezas, R., Avila, M. F., Torrente, D., Gonzalez, J., Santos El-Bachá, R., Guedes, R., & Barreto, G. E. (2015). Chapter 76 - Natural Antioxidants in Dementia: An Overview. En Martin, C. R., & Preedy, V. R. (Eds.), Diet and Nutrition in Dementia and Cognitive Decline (pp. 827-836). United States of America: Elsevier.

All our publications

1. Barreto, G. E., Gonzalez, J., Reiner, Ž., Jamialahmadi, T., Echeverria, V., Ashraf, G. M., & Sahebkar, A. (2021). In silico interactions of statins with cell death-inducing DNA fragmentation factor-like effector A (CIDEA). Chemico-Biological Interactions, 345, 109528. doi:10.1016/j.cbi.2021.109528
2. Castellanos, D. B., Martín-Jiménez, C. A., Rojas-Rodríguez, F., Barreto, G. E., & González, J. (2021). Brain lipidomics as a rising field in neurodegenerative contexts: Perspectives with machine learning approaches. Frontiers in Neuroendocrinology, 61 doi:10.1016/j.yfrne.2021.100899
3. Echeverri-Peña, O. Y., Salazar-Barreto, D. A., Rodríguez-Lopez, A., González, J., Alméciga-Díaz, C. J., Verano-Guevara, C. H., & Barrera, L. A. (2021). Use of a neuron-glia genome-scale metabolic reconstruction to model the metabolic consequences of the arylsulphatase a deficiency through a systems biology approach. Heliyon, 7(7) doi:10.1016/j.heliyon.2021.e07671
4. García-Fonseca, Á., Martin-Jimenez, C., Barreto, G. E., Pachón, A. F. A., & González, J. (2021). The emerging role of long non-coding rnas and micrornas in neurodegenerative diseases: A perspective of machine learning. Biomolecules, 11(8) doi:10.3390/biom11081132
5. Keikha, M., Barreto, G. E., González, J., & Sahebkar, A. (2021). A bioinformatics study of the involved mechanisms in relapse and drug resistance of tamoxifen-treated breast cancer. Anti-Cancer Agents in Medicinal Chemistry, 21(12), 1594-1601. doi:10.2174/18715206206662010291142
6. Becerra, G. P., Rojas-Rodríguez, F., Ramírez, D., Loaiza, A. E., Tobar-Tosse, F., Mejía, S. M., & González, J. (2020). Structural and functional computational analysis of nicotine analogs as potential neuroprotective compounds in parkinson disease. Computational Biology and Chemistry, 86 doi:10.1016/j.compbiolchem.2020.107266
7. González, J., Pinzón, A., Angarita-Rodríguez, A., Aristizabal, A. F., Barreto, G. E., & Martín-Jiménez, C. (2020). Advances in astrocyte computational models: From metabolic reconstructions to multi-omic approaches. Frontiers in Neuroinformatics, 14 doi:10.3389/fninf.2020.00035
8. Martin-Jiménez, C., González, J., Vesga, D., Aristizabal, A., & Barreto, G. E. (2020). Tibolone ameliorates the lipotoxic effect of palmitic acid in normal human astrocytes. Neurotoxicity Research, 38(3), 585-595. doi:10.1007/s12640-020-00247-4
9. Osorio, D., Pinzón, A., Martín-Jiménez, C., Barreto, G. E., & González, J. (2020). Multiple pathways involved in palmitic acid-induced toxicity: A system biology approach. Frontiers in Neuroscience, 13 doi:10.3389/fnins.2019.01410
10. Rojas-Rodríguez, F., Morantes, C., Pinzón, A., Barreto, G. E., Cabezas, R., Mariño-Ramírez, L., & González, J. (2020). Machine learning neuroprotective strategy reveals a unique set of parkinson therapeutic nicotine analogs. Open Bioinformatics Journal, 13(1), 1-14. doi:10.2174/1874196702008010001
11. Baez-Jurado, E., Guio-Vega, G., Hidalgo-Lanussa, O., González, J., Echeverria, V., Ashraf, G. M., . . . Barreto, G. E. (2019). Mitochondrial neuroglobin is necessary for protection induced by conditioned medium from human adipose-derived mesenchymal stem cells in astrocytic cells subjected to scratch and metabolic injury. Molecular Neurobiology, 56(7), 5167-5187. doi:10.1007/s12035-018-1442-9
12. Jurado-Coronel, J. C., Loaiza, A. E., Díaz, J. E., Cabezas, R., Ashraf, G. M., Sahebkar, A., . . . Barreto, G. E. (2019). (E)-nicotinaldehyde O-cinnamyloxime, a nicotine analog, attenuates neuronal cells death against rotenone-induced neurotoxicity. Molecular Neurobiology, 56(2), 1221-1232. doi:10.1007/s12035-018-1163-0
13. Martin-Jiménez, C., Gaitán-Vaca, D. M., Areiza, N., Echeverria, V., Ashraf, G. M., González, J., . . . Barreto, G. E. (2019). Astrocytes mediate protective actions of estrogenic compounds after traumatic brain injury. Neuroendocrinology, 108(2), 142-160. doi:10.1159/000495078
14. Pinzon, W., Vega, H., Gonzalez, J., & Pinzon, A. (2019). Mathematical framework behind the reconstruction and analysis of genome scale metabolic models. Archives of Computational Methods in Engineering, 26(5), 1593-1606. doi:10.1007/s11831-018-9290-3
15. Cabezas, R., Vega-Vela, N. E., González-Sanmiguel, J., González, J., Esquinas, P., Echeverria, V., & Barreto, G. E. (2018). PDGF-BB preserves mitochondrial morphology, attenuates ROS production, and upregulates neuroglobin in an astrocytic model under rotenone insult. Molecular Neurobiology, 55(4), 3085-3095. doi:10.1007/s12035-017-0567-6
16. Corredor, A. P., González, J., Baquero, L. A., Curtidor, H., Olaya-Galán, N. N., Patarroyo, M. A., & Gutiérrez, M. F. (2018). In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51. PLoS ONE, 13(6) doi:10.1371/journal.pone.0199397
17. Almeciga-Diaz, C. J., Echeverri, O. Y., Salazar-Barreto, D., Rodriguez-Lopez, A., Gonzalez, J., & Barrera, L. A. (2017). Understanding the metabolic consequences of human arylsulfatase A deficiency through a computational systems biology study. Molecular Genetics and Metabolism, 120(1–2), S20. https://doi.org/10.1016/j.ymgme.2016.11.020
18. Alméciga-Díaz, C. J., Tolosa-Díaz, A. D., Pimentel, L. N., Bonilla, Y. A., Rodríguez-López, A., Espejo-Mojica, A. J., . . . Gonzalez-Santos, J. (2017). Anaerobic sulfatase maturase AslB from escherichia coli activates human recombinant iduronate-2-sulfate sulfatase (IDS) and N-acetylgalactosamine-6-sulfate sulfatase (GALNS). Gene, 634, 53-61. doi:10.1016/j.gene.2017.08.043
19. Barreto, G. E., Gómez, R. M., Bustos, R. H., Forero, D. A., Aliev, G., Tarasov, V. V., . . . Gonzalez, J. (2017). Approaches of the transcriptomic analysis in astrocytes: Potential pharmacological targets. Current Pharmaceutical Design, 23(28), 4189-4197. doi:10.2174/1381612823666170406113501
20. Ghotme, K. A., Barreto, G. E., Echeverria, V., Gonzalez, J., Bustos, R. H., Sanchez, M., . . . Aliev, G. (2017). Gliomas: New perspectives in diagnosis, treatment and prognosis. Current Topics in Medicinal Chemistry, 17(12), 1438-1447. doi:10.2174/1568026617666170103162639
21. Martin-Jiménez, C. A., Gaitán-Vaca, D. M., Echeverria, V., González, J., & Barreto, G. E. (2017). Relationship between obesity, Alzheimer’s disease, and Parkinson’s disease: An astrocentric view. Molecular Neurobiology, 54(9), 7096-7115. doi:10.1007/s12035-016-0193-8
22. Martin-Jiménez, C. A., García-Vega, Á., Cabezas, R., Aliev, G., Echeverria, V., González, J., & Barreto, G. E. (2017). Astrocytes and endoplasmic reticulum stress: A bridge between obesity and neurodegenerative diseases. Progress in Neurobiology, 158, 45-68. doi:10.1016/j.pneurobio.2017.08.001
23. Martín-Jiménez, C. A., Salazar-Barreto, D., Barreto, G. E., & González, J. (2017). Genome-scale reconstruction of the human astrocyte metabolic network. Frontiers in Aging Neuroscience, 9(FEB) doi:10.3389/fnagi.2017.00023
24. Niño-Gómez, D. C., Rivera-Hoyos, C. M., Morales-Álvarez, E. D., Gonzalez J., Reyes-Montaño, E. A., Vargas-Alejo, N. E., Ramírez-Casallas, I. Arévalo-Galvis, A. (2017). "In silico" characterization of 3-phytase a and 3-phytase B from aspergillus niger. Enzyme Research, 2017 doi:10.1155/2017/9746191
25. Osorio, D., González, J., & Pinzón, A. (2017). Minval: An R package for minimal validation of stoichiometric reactions. R Journal, 9(1), 114-123. doi:10.32614/rj-2017-031
26. Vega-Vela, N. E., Osorio, D., Avila-Rodriguez, M., Gonzalez, J., García-Segura, L. M., Echeverria, V., & Barreto, G. E. (2017). L-type calcium channels modulation by estradiol. Molecular Neurobiology, 54(7), 4996-5007. doi:10.1007/s12035-016-0045-6
27. Avila-Rodriguez, M., Garcia-Segura, L. M., Hidalgo-lanussa, O., Baez, E., Gonzalez, J., & Barreto, G. E. (2016). Tibolone protects astrocytic cells from glucose deprivation through a mechanism involving estrogen receptor beta and the upregulation of neuroglobin expression. Molecular and Cellular Endocrinology, 433, 35-46. doi:10.1016/j.mce.2016.05.024
28. Barragán-Osorio, L., Giraldo, G., Alméciga-Diaz, C. J., Aliev, G., Barreto, G. E., & Gonzalez, J. (2016). Computational analysis and functional prediction of ubiquitin hypothetical protein: A possible target in parkinson disease. Central Nervous System Agents in Medicinal Chemistry, 16(1), 4-11. doi:10.2174/1871524915666150722120605
29. Cabezas, R., Avila-Rodriguez, M., E., Echeverria, V., González, J., Hidalgo, O. A., Barreto, G. E. (2016). Growth factors and astrocytes metabolism: Possible roles for platelet derived growth factor. Medicinal Chemistry, 12(3), 204-210. doi:10.2174/1573406411666151019120444
30. Garzón, D., Cabezas, R., Vega, N., Ávila-Rodriguez, M., Gonzalez, J., Gómez, R. M., . . . Barreto, G. E. (2016). Novel approaches in astrocyte protection: From experimental methods to computational approaches. Journal of Molecular Neuroscience, 58(4), 483-492. doi:10.1007/s12031-016-0719-6
31. González-Giraldo, Y., Forero, D. A., Echeverria, V., Gonzalez, J., Ávila-Rodriguez, M., Garcia-Segura, L. M., & Barreto, G. E. (2016). Neuroprotective effects of the catalytic subunit of telomerase: A potential therapeutic target in the central nervous system. Ageing Research Reviews, 28, 37-45. doi:10.1016/j.arr.2016.04.004
32. Jurado-Coronel, J. C., Ávila-Rodriguez, M., Capani, F., Gonzalez, J., Morán, V. E., & Barreto, G. E. (2016). Targeting the nicotinic acetylcholine receptors (nAChRs) in astrocytes as a potential therapeutic target in Parkinson’s disease. Current Pharmaceutical Design, 22(10), 1305-1311. doi:10.2174/138161282210160304112133
33. Jurado-Coronel, J. C., Ávila-Rodriguez, M., Echeverria, V., Hidalgo, O. A., Gonzalez, J., Aliev, G., & Barreto, G. E. (2016). Implication of green tea as a possible therapeutic approach for parkinson disease. CNS and Neurological Disorders - Drug Targets, 15(3), 292-300. doi:10.2174/1871527315666160202125519
34. Lanussa, O. H., Ávila-Rodriguez, M., García-Segura, L. M., González, J., Echeverria, V., Aliev, G., & Barreto, G. E. (2016). Microglial dependent protective effects of neuroactive steroids. CNS and Neurological Disorders - Drug Targets, 15(2), 242-249. doi:10.2174/1871527315666160202122032
35. Sáenz-Suárez, H., Poutou-Piñales, R. A., González-Santos, J., Barreto, G. E., Rieto-Navarrera, L. P., Sáenz-Moreno, J. A., . . . Barrera-Avellaneda, L. A. (2016). Prediction of glycation sites: New insights from protein structural analysis. Turkish Journal of Biology, 40(1), 12-25. doi:10.3906/biy-1501-71
36. Salazar, D. A., Rodríguez-López, A., Herreño, A., Barbosa, H., Herrera, J., Ardila, A., . . . Alméciga-Díaz, C. J. (2016). Systems biology study of mucopolysaccharidosis using a human metabolic reconstruction network. Molecular Genetics and Metabolism, 117(2), 129-139. doi:10.1016/j.ymgme.2015.08.001
37. Cabezas, R., Avila, M. F., González, J., El-Bachá, R. S., & Barreto, G. E. (2015). PDGF-BB protects mitochondria from rotenone in T98G cells. Neurotoxicity Research, 27(4), 355-367. doi:10.1007/s12640-014-9509-5
38. Galvis, J., González, J., Uribe, A., & Velasco, H. (2015). Deep genotyping of the IDS gene in colombian patients with hunter syndrome doi:10.1007/8904_2014_376 Retrieved from www.scopus.com
39. González, J., Jurado-Coronel, J. C., Ávila, M. F., Sabogal, A., Capani, F., & Barreto, G. E. (2015). NMDARs in neurological diseases: A potential therapeutic target. International Journal of Neuroscience, 125(5), 315-327. doi:10.3109/00207454.2014.940941
40. Torrente, D., Cabezas, R., Avila, M., Sanchez, Y., Morales, L., Ashraf, G. M., . . . Aliev, G. (2015). Mechanisms of PDGFRalpha promiscuity and PDGFRbeta specificity in association with PDGFB. Frontiers in Bioscience - Elite, 7E(3), 434-446. doi:10.2741/e741
41. Ávila, M. F., Torrente, D., Cabezas, R., Morales, L., García-Segura, L. M., Gonzalez, J., & Barreto, G. E. (2014). Structural insights from GRP78-NF-κB binding interactions: A computational approach to understand a possible neuroprotective pathway in brain injuries. Journal of Theoretical Biology, 345, 43-51. doi:10.1016/j.jtbi.2013.12.010
42. Ávila Rodriguez, M., Garcia-Segura, L. M., Cabezas, R., Torrente, D., Capani, F., Gonzalez, J., & Barreto, G. E. (2014). Tibolone protects T98G cells from glucose deprivation. Journal of Steroid Biochemistry and Molecular Biology, 144(PART B), 294-303. doi:10.1016/j.jsbmb.2014.07.009
43. Cabezas, R., Ávila, M., Gonzalez, J., El-Bachá, R. S., Báez, E., García-Segura, L. M., . . . Barreto, G. E. (2014). Astrocytic modulation of blood brain barrier: Perspectives on parkinson's disease. Frontiers in Cellular Neuroscience, 8(AUG) doi:10.3389/fncel.2014.00211
44. Muñiz, J., Romero, J., Holubiec, M., Barreto, G., González, J., Saint-Martin, M., . . . Capani, F. (2014). Neuroprotective effects of hypothermia on synaptic actin cytoskeletal changes induced by perinatal asphyxia. Brain Research, 1563, 81-90. doi:10.1016/j.brainres.2014.03.023
45. Nocua, P. A., Ramirez, C. A., Barreto, G. E., González, J., Requena, J. M., & Puerta, C. J. (2014). Leishmania braziliensis replication protein A subunit 1: Molecular modelling, protein expression and analysis of its affinity for both DNA and RNA. Parasites and Vectors, 7(1) doi:10.1186/s13071-014-0573-8
46. Pineda, T., Marie, S., Gonzalez, J., García, A. L., Acosta, A., Morales, M., . . . Velasco, H. M. (2014). Genotypic and bioinformatic evaluation of the alpha-L-iduronidase gene and protein in patients with mucopolysaccharidosis type I from colombia, ecuador and peru. Molecular Genetics and Metabolism Reports, 1, 468-473. doi:10.1016/j.ymgmr.2014.10.001
47. Romero, J., Muñiz, J., Tornatore, T. L., Holubiec, M., González, J., Barreto, G. E., Capani, F. (2014). Dual role of astrocytes in perinatal asphyxia injury and neuroprotection. Neuroscience Letters, 565, 42-46. doi:10.1016/j.neulet.2013.10.046
48. Sabogal-Arango, A., Barreto, G. E., Ramírez-Sánchez, D., González-Mendoza, J., Barreto, V., Morales, L., & González, J. (2014). Computational insights of the interaction among sea anemones neurotoxins and Kv1.3 channel. Bioinformatics and Biology Insights, 8, 73-81. doi:10.4137/BBi.s13403
49. Torrente, D., Avila, M. F., Cabezas, R., Morales, L., Gonzalez, J., Samudio, I., & Barreto, G. E. (2014). Paracrine factors of human mesenchymal stem cells increase wound closure and reduce reactive oxygen species production in a traumatic brain injury in vitro model. Human and Experimental Toxicology, 33(7), 673-684. doi:10.1177/0960327113509659
50. Torrente, D., Mendes-da-Silva, R. F., Lopes, A. A. C., González, J., Barreto, G. E., & Guedes, R. C. A. (2014). Increased calcium influx triggers and accelerates cortical spreading depression in vivo in male adult rats. Neuroscience Letters, 558, 87-90. doi:10.1016/j.neulet.2013.11.004
51. Zárate-Bonilla, L. J., del Portillo, P., Sáenz-Suárez, H., González, J., Barreto-Sampaio, G. E., Poutou-Piñales, R. A., Rey, A. F., & Rey, J. G. (2014). Computational modeling and preliminary iro N, fep A, and cir A gene expression in Salmonella Enteritidis under iron-deficiency-induced conditions. Poultry Science, 93(1), 221–230. https://doi.org/10.3382/ps.2012-02993
52. Ávila, M. F., Cabezas, R., Torrente, D., Gonzalez, J., Morales, L., Alvarez, L., . . . Barreto, G. E. (2013). Novel interactions of GRP78: UPR and estrogen responses in the brain. Cell Biology International, 37(6), 521-532. doi:10.1002/cbin.10058
53. Dos Santos, A. B., Campos, S. L., Ribeiro, S., Morales, L., González, J., Dos Santos Trindade, J., & Barreto, G. E. (2013). Relationship between quality of sleep and cognitive function in patients with parkinson's disease. [Relação entre qualidade do sono e funções cognitivas em pacientes com doença de parkinson] Universitas Scientiarum, 18(3), 269-281. doi:10.11144/Javeriana.SC18-3.rqsf
54. González, J., Gálvez, A., Morales, L., Barreto, G. E., Capani, F., Sierra, O., & Torres, Y. (2013). Integrative approach for computationally inferring interactions between the alpha and beta subunits of the calcium-activated potassium channel (BK): A docking study. Bioinformatics and Biology Insights, 7, 73-82. doi:10.4137/BBI.S10077
55. Gonzalez, J., & Barreto, G. E. (2013). In Silico Insights of L-Glutamate: Structural Features in Vacuum and in Complex with Its Receptor. Journal of Amino Acids, 2013, 1–6. https://doi.org/10.1155/2013/872058
56. Albarracin, S. L., Stab, B., Casas, Z., Sutachan, J. J., Samudio, I., Gonzalez, J., Barreto, G. E. (2012). Effects of natural antioxidants in neurodegenerative disease. Nutritional Neuroscience, 15(1), 1-9. doi:10.1179/1476830511Y.0000000028}
57. Barreto, L. V., Barreto, G. E., Morales, L., Acevedo, O. E., & González, J. (2012). Proteína LIC10494 de Leptospira interrogans serovar Copenhageni: modelo estructural y regiones funcionales asociadas. Universitas Scientiarum, 17(1), 16–27.
58. Barreto, G. E., Gonzalez, J., Capani, F., & Morales, L. (2012). Neuroprotective agents in brain injury: A partial failure? International Journal of Neuroscience, 122(5), 223-226. doi:10.3109/00207454.2011.648292
59. Cabezas, R., El-Bachá, R. S., González, J., & Barreto, G. E. (2012). Mitochondrial functions in astrocytes: Neuroprotective implications from oxidative damage by rotenone. Neuroscience Research, 74(2), 80-90. doi:10.1016/j.neures.2012.07.008
60. Grimaldi, M., Romer, I., González de Apodaca, M. T., Iturbe, L., Catania, I. D., González, J., Capani, F. (2012). Early changes in the synapses of the neostriatum induced by perinatal asphyxia. Nutritional Neuroscience, 15(3), 103-110. doi:10.1179/1476830511Y.0000000026
61. Saraceno, G. E., Castilla, R., Barreto, G. E., Gonzalez, J., Klliker-Frers, R. A., & Capani, F. (2012). Hippocampal dendritic spines modifications induced by perinatal asphyxia. Neural Plasticity, 2012 doi:10.1155/2012/873532
62. Sierra Bello, O., Gonzalez, J., Capani, F., & Barreto, G. E. (2012). In silico docking reveals possible riluzole binding sites on Nav1.6 sodium channel: Implications for amyotrophic lateral sclerosis therapy. Journal of Theoretical Biology, 315, 53-63. doi:10.1016/j.jtbi.2012.09.004
63. Sutachan, J. J., Casas, Z., Albarracin, S. L., Stab II, B. R., Samudio, I., Gonzalez, J., Barreto, G. E. (2012). Cellular and molecular mechanisms of antioxidants in parkinson's disease. Nutritional Neuroscience, 15(3), 120-126. doi:10.1179/1476830511Y.0000000033
64. Barreto, G. E., Gonzalez, J., Torres, Y., & Morales, L. (2011). Astrocytic-neuronal crosstalk: Implications for neuroprotection from brain injury. Neuroscience Research, 71(2), 107-113. doi:10.1016/j.neures.2011.06.004
65. González, J., Corredor, C. F., & Lareo, L. R. (2009). Theoretical Studies of Glutamate Enantiomers at Different pH Conditions. Bioastronomy, 420, 203–208.
66. Lareo, L. R., & González, J. (2008). Intramolecular excited energy transfer pathways in proteins. Journal of Theoretical and Computational Chemistry, 7(1), 91-102. doi:10.1142/S0219633608003629
67. González, J., Novoa, F., Acevedo, O. E., & Lareo, L. (2005). Identificación de criterios para la selección natural de RNA mensajeros. Universitas Scientiarum, 10(2), 57–69.

Books and Book Chapters

Cabezas, R., Sahebkar, A., Echeverria, V., González, J., Md Ashraf, G., & Barreto, G. E. (2021). In Silico Identification of Novel Interactions for FABP5 (Fatty Acid-Binding Protein 5) with Nutraceuticals: Possible Repurposing Approach. En Barreto, G. E., & Sahebkar, A. (Eds.), Pharmacological Properties of Plant-Derived Natural Products and Implications for Human Health (pp 589-599). Suiza: Springer Nature Switzerland AG.
Shakour, N., Cabezas, R., González, J., Barreto, G. E., Jamialahmadi, T., Hadizadeh, F., & Sahebkar, A. (2021). Curcumin Can Bind and Interact with CRP: An in silico Study. En Barreto, G. E., & Sahebkar, A. (Eds.), Pharmacological Properties of Plant-Derived Natural Products and Implications for Human Health (pp 91-100). Suiza: Springer Nature Switzerland AG.
Barreto, G. E., Saraceno, E., Gonzalez, J., Kolliker, R., Castilla, R., & Capani F. (2015). Chapter 8 - Neuroprotection with Estradiol in Experimental Perinatal Asphyxia: A New Approach. En Duncan, K. E. (Ed.), Estrogen Effects on Traumatic Brain Injury (pp. 113-124). United States of America: Elsevier.
Cabezas, R., Avila, M. F., Torrente, D., Gonzalez, J., Santos El-Bachá, R., Guedes, R., & Barreto, G. E. (2015). Chapter 76 - Natural Antioxidants in Dementia: An Overview. En Martin, C. R., & Preedy, V. R. (Eds.), Diet and Nutrition in Dementia and Cognitive Decline (pp. 827-836). United States of America: Elsevier.
Lopez-Rodriguez, A. B., Ávila-Rodriguez, M., Vega-Vela, N. E., Capani, F., Gonzalez, J., García-Segura, L. M., & Barreto G. E. (2015). Chapter 6 - Neuroprotection by Exogenous Estrogenic Compounds Following Traumatic Brain Injury. En Duncan, K. E. (Ed.), Estrogen Effects on Traumatic Brain Injury (pp. 73-90). United States of America: Elsevier.
Cabezas, R., Torrente, D., Avila, M. F., González, J., & Barreto G. E. (2014). Analysis of Binding Residues between PDGF-BB and Epidermal Growth Factor Receptor: A Computational Docking Study. En Castillo, L. F., Cristancho, M., Isaza, G., Pinzón, A., & Corchado Rodríguez, J. M. (Eds.), Advances in Computational Biology. Advances in Intelligent Systems and Computing, vol 232 (pp. 29-39). Cham, Suiza: Springer International Publishing Switzerland.
Díaz, D. A., Barreto, G. E., & González, J. (2014). Structural and Functional Prediction of the Hypothetical Protein Pa2481 in Pseudomonas Aeruginosa Pao1. En Castillo, L. F., Cristancho, M., Isaza, G., Pinzón, A., & Corchado Rodríguez, J. M. (Eds.), Advances in Computational Biology. Advances in Intelligent Systems and Computing, vol 232 (pp. 47-55). Cham, Suiza: Springer International Publishing Switzerland.
Galvis, J., González, J., Torrente, D., Velasco, H., Barreto, G. E. (2014). In silico Analysis of Iduronate 2 Sulfatase Mutations in Colombian Patients with Hunter Syndrome (MPSII). En Castillo, L. F., Cristancho, M., Isaza, G., Pinzón, A., & Corchado Rodríguez, J. M. (Eds.), Advances in Computational Biology. Advances in Intelligent Systems and Computing, vol 232 (pp. 205-212). Cham, Suiza: Springer International Publishing Switzerland.
Cabezas, R., Avila, M. F., Torrente, D., Santos El-Bachá, R., Morales, L., Gonzalez, J., & Barreto, G. E. (2013). Astrocytes Role in Parkinson: A Double-Edged Sword. En Kishore, U. (Ed.), Neurodegenerative Diseases (pp- 491-517). Rijeka , Croacia: InTech.
George E. Barreto, Janneth González, Francisco Capani, Ludis Morales. Role of astrocytes in Neurodegenerative diseases. In “Neurodegenerative Diseases”. ISBN 979-953-307-041-3, InTech, 2011.
David Diaz, George E. Barreto, Janneth González. Structural and functional prediction of the hypothetical protein PA2481. In: 2nd Colombian Congress on Computational Biology and Bioinformatics (CCBCOL). Advances in Computational Biology. 1ed: Springer, 2013, v1, p. 47-55.
Ricardo Cabezas, Daniel Torrente, Marcos Avila, Janneth Gonzalez, George E. Barreto. Analysis of Binding Residues between PDGF-BB and Epidermal Growth Factor Receptor: A Computational Docking Study. In: 2nd Colombian Congress on Computational Biology and Bioinformatics (CCBCOL). Advances in Computational Biology. 1ed: Springer, 2013, v1, p. 29-39.
Ricardo Cabezas, Marco Fidel Avila, Daniel Torrente, Janneth Gonzalez, Ramon Santos El-Bacha, Rubem Guedes, George E. Barreto. Natural antioxidants in dementia: an overview. In “Diet and Nutrition in Dementia and cognitive decline series book”. Academic Press (Elsevier), 2014.
Ana Belen Lopez-Rodriguez, Marco Ávila-Rodrigueza, Francisco Capani, Janneth Gonzalez, Luis Miguel García-Segura, George E. Barreto. Neuroprotection by exogenous estrogenic compounds following traumatic brain injury. In “Estrogen Effects on Traumatic Brain Injury”. Elsevier, 2014.
George Barreto, Ezequiel Saraceno, Janneth González, Rodolfo Kolliker, Rocío Castilla, Francisco Capani. Neuroprotection with estradiol in experimental perinatal asphyxia: a new approach. In “Estrogen Effects on Traumatic Brain Injury”. Elsevier, 2014.

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