Maestría en Biociencias (tesis)
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Publicación Biotechnological Advances in Plant-Based Nutrition : From Metabolomic Characterization to Gene Editing(Universidad EAFIT, 2025) Rivera Patiño, Paola Irene; Villanueva Mejía, Diego FernandoPublicación Detection of carbapenem resistance in Klebsiella pneumoniae using convolutional vision transformers and MALDI-TOF proteomic profiles.(Universidad EAFIT, 2025) Salazar Marín, Valentina; Fernández García, Geysson Javier; Bravo Ortíz, Mario AlejandroAntimicrobial resistance is a growing global health problem, significantly increasing morbidity, mortality and healthcare costs. Traditionally, the identification of antibiotic resistance is based on phenotypic methods such as agar diffusion or automated systems such as VITEK, which require 24-72 hours to yield definitive results, delaying appropriate patient management. In this context, the need for faster and more accurate diagnostic aid strategies arises. This study explores the integration of artificial intelligence (AI) and mass spectrometry techniques for the classification of carbapenem-resistant Klebsiella pneumoniae strains. Specifically, matrix-assisted laser desorption/ionization-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) data were used to generate proteomic profiles potentially associated with resistance mechanisms. However, the complexity and high volume of these data make the use of AI tools capable of identifying robust patterns indispensable. A convolutional vision transformer (CVT) model was implemented to classify carbapenem-resistant Klebsiella pneumoniae strains from a set of 180 proteomic spectra collected by Synlab Colombia. The CVT model outperformed traditional convolutional neural networks and other automated learning approaches, achieving higher accuracy and stability. Grad-CAM visualization improved model interpretability by identifying key spectral regions associated with resistance. The results highlight the potential of Vision Transformers in microbiological diagnostics by significantly reducing resistance detection time and contributing to a timelier clinical response. Future studies should explore the applicability of this methodology on other resistant pathogens to improve global surveillance efforts against antimicrobial resistance.Publicación Caracterización de la microbiota intestinal de pacientes colombianos con diagnósticos psiquiátricos : serie de casos(Universidad EAFIT, 2025) Vélez Pardo, Pedro; Sierra Zapata, LauraPublicación Biogas production from organic solid waste through anaerobic digestion : a meta-analysis(Universidad EAFIT, 2024) Triviño Pineda, Jairo Smith; Sánchez Rodríguez, Aminael; Pinel Peláez, Nicolás; Los autores extienden su más sincero agradecimiento a Coedugar de la Escuela Cooperativa Presentación de Garzón por la ayuda financiera y también a la Universidad EAFIT por sus invaluables y constructivos conocimientos. Su asociación y aportes han sido vitales para mejorar y reforzar la amplitud y excelencia de este estudio.Publicación Evaluation of a Landfill Leachate Bioremediation System Using Spirulina sp.(Universidad EAFIT, 2025) González López, Federico; Rendón Castrillón, Leidy Johanna; Ramírez Carmona, Margarita Enid; Ocampo López, Carlos; Rendón Castrillón, Leidy JohannaPublicación In Silico Identification of Alternative Molecular Targets from Probiotic Strains for Potential Therapeutic Repositioning in Gut Microbiome-Associated Diseases(Universidad EAFIT, 2025) Buitrago Roldán, Nicolás; García Zea, Jerson Alexander; Sierra Zapata, LauraHuman gut hosts over 100 trillion symbiotic bacteria, far exceeding the number of host cells. These microorganisms collectively form what is known as the gut microbiota. This microbiota performs a wide range of functions crucial for the human body, including protection against pathogens, nutrient extraction, metabolism, and immunity, which, under healthy conditions, result in stability, resilience, and beneficial symbiotic interactions. A probiotic microorganism is defined as a live microorganism that confers a health benefit to the host when administered in adequate amounts. Consequently, in recent years, the number of studies linking probiotic strains to prevent and treat several diseases, such as autoimmune diseases, atopy, metabolic syndrome, metabolic disorders, cancer, and certain behavioral disorders, has increased significantly. Similarly, more research is emerging that employs omics sciences, which involves obtaining comprehensive data that includes genomic, proteomic, metabolic, and other omics information, aiming to assess this data before and after probiotic treatment administration. In this context, and thanks to open access data and cooperative Omics bioinformatic tools, this project proposes an in-silico approach to analyze the effects of probiotic strains on human cells, focusing on differentially expressed genes and their protein-protein interactions. The results highlight the ability of probiotics, such as Propionibacterium freudenreichii ITG P9 and Bacillus subtilis CW14, to modulate human cellular responses, particularly in pathways related to immunity and the cell cycle. This study emphasizes the role of probiotics in regulating genes associated with metabolic, neurological, and autoimmune diseases, revealing potential neuroprotective and antitumoral properties.Publicación Analysis of gene expression regulation of colon adenocarcinoma genes treated with three probiotic species(Universidad EAFIT, 2024) Vélez García, Alejandra; García Zea, Jerson Alexander; Sierra Zapata, LauraPublicación First genetic assessment of Colombian bunching onion Germplasm bank accessions : unexpected variation and global context(Universidad EAFIT, 2024) Florian Cruz, Andrés Felipe; Correa Álvarez, Javier; Correa Álvarez, Javier; Sistema General de Regalias(BPIN: 2020000100413)Publicación Microbiología predictiva mediante aprendizaje automatizado para la optimización de procesos productivos : Metanálisis(Universidad EAFIT, 2024) Yepes Medina, Verónica; Pinel Peláez, Nicolás; NingunoUnsafe food containing harmful bacteria, viruses, parasites or chemicals can cause more than 200 different illnesses, from diarrhea to cancer. Worldwide, an estimated 600 million (nearly 1 in 10 people) fall ill each year after eating contaminated food, resulting in 420.000 deaths and the loss of 33 million years of healthy life. Therefore, it is necessary to detect and respond to public health threats associated with unsafe food with enabling technologies or tools. Predictive microbiology is concerned with preventing, controlling or limiting the existence of microorganisms by mapping their potential responses to particular environmental conditions, such as temperature, pH, nutrients (protein and fat), water activity (aw) and others. And machine learning as a branch or artificial intelligence learns from these data, identifying patterns for decision making. Recent studies are based in the use of supervised machine learning models to predict the presence of a foodborne pathogenic microorganism at any stage of the production chain, the most commonly used models include Random Forest and support vector machine with rating metrics for accuracy and sensitivity >80%. The main evaluation metrics of the algorithms are: accuracy, F1 score, confusion matrix, sensitivity, specificity and area under the curve (ROC-AUC, Receiver-Operating-Characteristic). Studies have shown that Random Forest was the best model, exhibiting an accuracy of 95% and a F1 score of 98%. Here were evaluated twenty five (25) articles with library metafor of Rstudio version 4.2.1 and this information provides new opportunities to explore non-destructive models for rapid detection of microorganisms in the production chain.Publicación The random forest machine learning model performs better in predicting drug repositioning using networks : systematic review and meta-analysis(Universidad EAFIT, 2024) García Marín, Darlyn Juranny; García Zea, Jerson Alexander; García Zea, Jerson AlexanderPublicación Identification of non-model mammal species using the MinION DNA sequences from Oxford Nanopore(Universidad EAFIT, 2023) Velásquez-Restrepo, Sara; Díaz-Nieto, Juan Fernando; Díaz Nieto, Juan Fernando; Fundación Alejandro Angel Escobar - Beca Colombia BiodiversaPublicación Coalescent-delimitation framework and ecogeographic patterns disentangle the species boundaries within the Neotropical mouse-opossums subgenus Marmosops(Universidad EAFIT, 2022) Carillo Restrepo, Jhan Carlos; Díaz Nieto, Juan FernandoThe Neotropics encompasses a wide range of biomes and habitat types that place it as one of the most important Earth's regions for understanding the prevalence of cryptic and unknown diversity. However, it has been shown that this region is one of the least represented in genetic data in the tree of life. Therefore, advancing intra and interspecific genetic revisions in this region represents a major scientific priority to reduce our ignorance of the planet's biodiversity. American marsupials of Marmosops subgenus are distributed in a wide variety of Neotropical habitats, so it is an attractive group to undertake studies on Neotropical diversification processes, but such research is hindered by the fact that we do not yet fully understand the species limits of some groups within the subgenus. Herein, we evaluate the evolutionary independence of 13 morphologically-cryptic mtDNA haplogroups within Marmosops that were identified by our previous single-locus species delimitation analyses. For this purpose, we analyzed a multi-locus dataset (12 unlinked nuclear loci and one mtDNA locus) in a Bayesian Multi-Species Coalescent framework implemented in BPP, combined with heuristic criterion (gdi) that incorporated the speciation-continuum process into species delimitation analyses, to further understand the genetic boundaries within this Neotropical mouse opossum’s clade. Our BPP analyses recovered each of the 13 haplogroups as independent evolutionary lineages. However, heuristic gdi showed that the tested lineages are across the entire spectrum of the speciation continuum, and that only seven lineages recognized by BPP correspond to “true” species. Three of these seven lineages are currently recognized as valid species, demonstrating the effectiveness of our study; while ecogeographic patterns information revealed that the remaining four lineages have promising information to be recognized as possible new species for science.Publicación Bacillus spp. antibacterial activity induced by triphenyl tetrazolium chloride : metabolome changes and oxidative stress response(Universidad EAFIT, 2023) González Marín, Carolina; Villegas Escobar, ValeskaPublicación Microbial and Chemical Diversity of the Gut Microbiota in a cohort of pregnant and lactating women from Antioquia-Colombia(Universidad EAFIT, 2023) Londoño Osorio, Sara; Sierra Zapata, Laura; MincienciasPublicación Analysis of bioenergetic function alterations as part of the antifungal effect of cyclic lipopeptides and cinnamon extract against Fusarium spp. and Colletotrichum spp.(Universidad EAFIT, 2023) Ramírez Mejía, Julieta María; Gómez Ramírez, Luis Alejandro; Villegas Escobar, Valeska; MincienciasPublicación Multi-omics characterization of the microbial and chemical ecology of a water Kefir fermentation(Universidad EAFIT, 2023) Arrieta Echeverri, Maria Clara; Sierra Zapata, Laura; Fernández García, Geysson Javier; Iluma AlliancePublicación Silenciamiento del gen ácido graso desaturasa 2 (FAD2) en Ricinus communis (Malpighiales: Euphorbiaceae) mediante edición genética basada en el uso de la tecnología CRISPR/Cas9(Universidad EAFIT, 2022) Susunaga Gómez, Danna Melissa; Villanueva Mejía, Diego Fernando; Universidad EAFITPublicación Culturable Gut Microbiota of Pregnant and Breastfeeding Women Involved in The Metabolism of a Dietary Source Rich in Choline : Biological Diversity and Biochemical Characterization of a Pilot Cohort in Colombia(Universidad EAFIT, 2022) Gómez Mesa, Laura; Sierra Zapata, Laura; Universidad EAFITPublicación Estudio del efecto del selenio en diferentes microalgas con propósitos de producción de biomasa enriquecida(Universidad EAFIT, 2022) Hoyos Gutiérrez, Brenda Seleny; Sáez Vega, Álex Armando; Villanueva Mejía, Diego Fernando; Miranda Parra, Alejandra María; Universidad EAFIT; ARGOS S.A.S.; Illuma AlliancePublicación Molecular elements underlying Bacillus tequilensis unrestrained loss of social traits(Universidad EAFIT, 2022) García-Botero, Camilo Alejandro; Villegas Escobar, Valeska; Cuellar Gaviria, Tatiana Zazini