Genomics research

Head of group: Gonzalo Riadi

Participants

  • Gonzalo Riadi (PhD)
  • Braulio Valdebenito
  • Daniela Araya
  • Camilo Fuentes
  • Bairon Hernández
  • Matias Fuentes
  • Cristopher Fierro
  • Poliana Venegas

Research lines

  • Genomic Mobile Elements.
  • Molecular Evolution.
  • Exploratory analysis.

Informatics Research

We focus on the development of Machine Learning and Artificial Intelligence methods for modeling problems in different areas of application such as bioinformatics, structural biology, biomedical sciences, smart agriculture, and others.

www.thinkagro.cl

Participants

  • José Antonio Reyes (Ph.D.)
  • Patricia Möller (Ph.D.)
  • Carolina Urzúa (MBA)
  • María Alejandra Bravo (Bioinformatics Engineer)
  • Silvia Möller (Agronomic Engineer)
  • Eduardo Poblete (Informatic Engineer)
  • Susana Arredondo (Agronomic Engineer)
  • Luís Cáceres (Civil Industrial Engineer)
  • Alex Rojas (Civil Informatic Engineer)
  • Felipe Ojeda (Bioinformatics Engineer)
  • Sebastián Ortega (Informatic Engineer)
  • Felipe Medina (Automation Engineering)
  • Magna Espinoza (Financial Officer)
  • Ivonne Chamorro (Administrative)
  • Yetzabel Gonzalez (undergraduate student)

Research lines

  • Prediction of molecular interactions based on structural and physicochemical features.
  • Modeling of extreme weather conditions that affects agriculture.
  • Predictive models for plant diseases and conditions based on climatic and phenological features.
  • Prediction of annual harvest yield and quality in fruticulture based on climatic conditions and phenological features.

Funding

  • “THINKAGRO – Center for Technological Extensions in Intelligent Industries: Digitalization and Automation of the Chilean Agroindustrial Sector”. Funded by CORFO. (2018-2020). www.thinkagro.cl
  • “Early warning and sectorized system of frost episodes: a tool to increase the competitiveness of agriculture in the Maule Region”. Funded by Maule Government (2017-2019).
  • “Early prediction system for bull eye root disease in apples of the Cripps Pink variety”. Funded by Fondef (2017-2019)
  • “Early warning system of frost episodes”. Funded by FIA (2015-2016).
  • “Design of an apiculture mapping at Maule Region”. Funded  by Maule Government (2013-2015)
  • “Development of a mobile system for heat mapping generation for the optimization of agricultural irrigation”. Funded by FONDEF. 2013-2015.

Collaborations

  • Dr. Mauricio Arenas, Department of Bioinformatics – Universidad de Talca
  • Dr. Felipe Besoaín, Department of Bioinformatics – Universidad de Talca
  • MSc. Alejandro Valdés, Department of Bioinformatics – Universidad de Talca
  • Dr. Claudio Tenreiro, Faculty of Engineering – Universidad de Talca
  • Dr. José Antonio Yuri, Director of Centro de Pomaceas – Universidad de Talca
  • Dr. Mauricio Lolas, Director of Phytopathology Laboratory – Universidad de Talca
  • Dr. Samuel Ortega, Director of CITRA – Universidad de Talca

Publications

  • Renzo Angles, Mauricio Arenas, Roberto García, Jose Antonio Reyes-Suarez and Ehmke Pohl. GSP4PDB: A web tool to visualize, search and explore protein-ligand structural patterns. On press BMC Bioinformatics.
  • Patricia Möller-Acuña, Roberto Ahumada-García, and José Reyes-Suárez. Machine Learning for Prediction of Frost Episodes in the Maule Region of Chile. UCAmI 2017, LNCS 10586, 2017.
  • Roberto Ahumada-García, Patricia Möller-Acuña, and José Antonio Reyes-Suárez. An expert system for handling Phytosanitary Products in Chilean export fruit. IEEE Explorer, Octubre 2017.
  • Patricia Möller-Acuña, Alejandro Valdés-Jimenéz, Roberto Ahumada-García, and José Antonio Reyes-Suárez. An information system for preventive alerting of frost episodes in the Central Region of Chile. IEEE Explorer, Octubre 2017.
  • Patricia Möller-Acuña, Roberto Ahumada-García, and José Antonio Reyes-Suárez. An Information System for online Quality Control of Export Fruits. IEEE Explorer, Octubre 2017.
  • Yetzabel González, Roberto Ahumada-García, Patricia Möller-Acuña, and José Antonio Reyes-Suárez. A system for online quality analysis for cherry harvest process inside the orchard. IEEE Explorer, Octubre 2017.
  • B. Valdebenito-Maturana, J, Antonio Reyes-Suarez, J. Henriquez, D. S. Holmes, R. Quatrini, E. Pohl, M. Arenas-Salinas. “Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins J. Comput. Chem. 2017, 38, 467–474
  • P. Moller, R. Ahumada-García & J. Reyes-Suárez. “Prediction of frost episodes based in agrometeorological information and machine learning techniques”. IEEE International Conference on Automatica (ICA-ACCA) 2016.
  • R. Ahumada-García, F. Besoain, C. Poblete-Echeverria & J. Reyes-Suárez. “Inference of foliar temperature profile of a vineyard using integrated sensors into a motorized vehicle”. IEEE International Conference on Automatica (ICA-ACCA) 2016.
  • N. Grandón, R. Ahumada-Garciía, J. Reyes-Suárez & F. Besoaín. “Information system for improving local productivity and decision making in organic beekeeping”. IEEE International Conference on Automatica (ICA-ACCA) 2016.
  • Besoain, Felipe and Perez-Navarro, Antoni and Ojeda, Felipe and Reyes-Suarez, Jose Antonio. “Promoting Healthy Nutrition Behavior Using Mobile Devices and Ubiquitous Computing”. Lecture Notes in Computer Science, 9455, 89-100 2015. Springer International Publishing.
  • S.H. Park, J. Reyes, D.R. Gilbert, J.W. Kim, and S. Kim, “Prediction of protein-protein interaction types using association rule based classification.,” BMC Bioinformatics, vol. 10, Jan. 2009, p. 36.
  • J. Reyes and D. Gilbert, “Combining One-Class Classification Models Based on Diverse Biological Data for Prediction of Protein-Protein Interactions,” Lecture Notes in Computer Science, vol. 5109, 2008, pp. 177-191.
  • J. Reyes and D. Gilbert, “Prediction of protein-protein interactions using one-class classification methods and integrating diverse biological data,” Journal of Integrative Bioinformatics, vol. 4, 2007.
  • Reyes J. A., Gilbert D., Girolami M. “Implementation of the Alternating Decision Trees Classification Algorithm in WEKA, for prediction of genetic regulatory response”. Personal Communication in the European Conference on Computational Biology (ECCB), 2005.

Head of the group: Gabriel Núñez-Vivanco

Participants

  • Dr. Gabriel Núñez-Vivanco (Bioinformatics Engineer, PhD. in Biotechnology): Group leader
  • Mg. Fabio Durán (Informatics Engineer, Mg. in Free Software): Researcher
  • Mg Alejandro Valdés (Informatics Engineer, Mg. in Free Software): Researcher
  • Iñaki Hojas: Undergraduate thesis student
  • Fabián Ramírez: Undergraduate thesis student
  • Christofer Núñez: Undergraduate thesis student

Research lines

  • Software development
  • Structural bioinformatics
  • Polypharmacology
  • Structured-based drug design

Funding

  • Fondecyt Research Regular Grant Nº 1170662. MULTISTERIC DRUGS: DESIGN OF POLYPHARMACOLOGICAL AGENTS THAT SIMULTANEOUSLY INTERACT WITH MONOAMINERGIC PROTEINS AND NICOTINIC RECEPTORS, BASED ON SIMILARITIES BETWEEN THEIR MULTIPLE BINDING SITES. Co-investigator.

Collaborations

  • Dr. Pablo Moya, Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Valparaiso, Chile.
  • Dr. Miguel Reyes-Parada, Facultad de Medicina, Universidad de Santiago de Chile, Santiago Chile.
  • Dr. Dayan Lozano, Universidad Simón Bolivar, Barranquilla, Colombia.
  • PhD Gonzalo Torres, Center for Addiction Research and Education, University of Florida, Gainesville, USA
  • PhD Josep-L Larriba-Pey, DAMA-UPC, Universitat Politécnica de Catalunya BarcelonaTech, Spain

Computational Physical Chemistry research

Head of the group: Jans Alzate-Morales

Participants

  • Ing. en Bioinformática Jocelyn Solorza Márquez, Research Assistant
  • M.Sc. Rodrigo Recabarren Hurtado, PhD Student
  • Rubén Fritz Fritz, PhD Student
  • Q.F. Jefferson Romero Marulanda, PhD Student
  • Dra. Camila Muñoz Gutiérrez, PostDoctoral Researcher

Research Lines

  • Computer Assisted Drug Design, protein engineering, enzyme catalysis

Funding

  • PI FONDECYT Regular No. 1181253, “Estimating residence time in protein-ligand complexes: New computational protocols for understanding binding kinetics of drugs.”
  • Sponsoring Researcher, FONDECYT Postdoctoral No. 3180321, “EVALUATION OF THE MOLECULAR STABILITY OF CYLINDRIN-LIKE STRUCTURES VIA MICROSECOND MOLECULAR DYNAMICS SIMULATIONS”.
  • Co-researcher, FONDECYT Regular No. 1150615 “DESIGNING CHEMICAL POLY-BULLETS FOR NICOTINIC ACETYLCHOLINE RECEPTORS AND MONOAMINE TRANSPORTERS (SERT, NET AND DAT). A POLY-PHARMACOLOGY APPROACH TO UNDERSTAND THE NICOTINE ADDICTION AND WITHDRAWAL SYNDROME MEDIATED BY MULTIPLE RECEPT”.
  • Co-researcher, FONDECYT Regular No. 1170662 “Multisteric drugs: Design of polypharmacological agents that simultaneously interact with monoaminergic proteins and nicotinic receptors, based on similarities between their multiple binding sites”.

Head of the group: Horacio Poblete

Participants

  • Horacio Poblete Vilches (PI)
  • Matias Zuñiga-Bustos (Post-Doc)
  • Constanza Galaz Araya (Undergraduate)
  • Roberto Rosales Rojas (Undergraduate)

Research Lines

  • Theoretical and Computational Biophysics: Predicting the adsorption of proteins onto nano-surfaces, using molecular dynamics and Free-energy calculation for inorganic/biological systems. Design of new bio-nanomaterials for bio-medicine applications.

Funding

  • Fondecyt Regular 2017, PI “New Insights into conformational equilibria of proteins absorbed to nanometal surfaces using molecular dynamics simulations: structural effects and protein camouflage applicable to nanomedicine.” Universidad de Talca. 2017 – 2021
  • Fondecyt Regular 2018, Co-Investigator: Horacio Poblete, PI: Jans Alzate-Morales “Estimating residence time in protein-ligand complexes: New computational tools for understanding the in-vivo pharmacological effects of drugs.” Universidad de Talca. 2018 – 2021
  • Millennium Nucleus 2017, Young Investigator “Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD).” Universidad de Talca. 2017 – 2021
  • Talca University Research support “Desarrollo Nucleo Cientifico Multidiciplinario” 2017-2020

Research Interests

  • Free-energy methods
  • Biophysics
  • Nanotechnology
  • Metal surfaces
  • Membrane dynamics
  • Ion channels
  • Transmembrane transporting.

Head of the group: Julio Caballero

Participants

  • Julio Caballero (Ph.D.)
  • Francisco Adasme (Ph.D.)
  • Erix Wiliam Hernández (Ph.D.)
  • José Luis Velázquez-Libera
  • Luis Prent Peñaloza
  • Sergio Alfaro

Research lines

  • Protein-ligand interactions using protocols including docking, molecular dynamics (MD), QSAR, hybrid calculation methods, pharmacophore modeling, de novo design, virtual screening.
  • Ligand-based molecular modeling (QSAR, pharmacophore modeling, chemoinformatics). Applications to the study of the potency of synthetic bioactive compounds and natural products.
  • Modeling of enzyme–inhibitor systems such as protein kinase inhibitors, angiotensin converting enzyme inhibitors, acetylcholinesterase inhibitors, etc.
  • Structural features of target proteins, such as potassium channels, the sigma1 receptor, the TRPV-1 channel, etc.
  • Methods of computational biochemistry, pharmaceutical modeling, protein structure and function, enzyme reactivity and selectivity, and contributions to medicinal chemistry topics.

Funding

  • FONDECYT Regular # 1170718 ‘Design and synthesis of angiotensin-converting enzyme inhibitors using molecular modeling and multicomponent reactions’ 2017-2021.
  • FONDECYT postdoctorade project Francisco Adasme Carreño. #  3180193 ” Derivation of amino acid structural propensities from theoretical potentials for protein structure prediction”, 2018-2021, (Sponsor)
  • FONDECYT postdoctorade project Alexander Fernández de la Torre. #  3170003 ” Diseño, síntesis y evaluación biológica de una nueva librería de compuestos fosfono-peptidomiméticos como inhibidores de la enzima Pseudomona elastasa (LasB)”, 2017-2020, (Sponsor)
  • FONDECYT postdoctorade project Erix Wiliam Hernández Rodríguez. #  3170107 ” Modelación computacional de capacidades para la producción fotosensibilizada de oxígeno singlete en rodopsinas mutantes asociadas a degeneración retiniana”, 2017-2020, (Sponsor)
  • FONDECYT postdoctorade project Fabián Andrés Ávila Salas. #  3170909 “Diseño racional, síntesis y evaluación de nuevas nanoformulaciones basadas en polímeros para liberación controlada de feromonas sexuales de Lobesia botrana a través de una estrategia híbrida in-silico/experimental”, 2017-2020, (Sponsor)

Structural Biology research

Head of the group: Ingo Dreyer

Participants

  • Ingo Dreyer (PhD)
  • Maria Rubio Melendez (PhD)
  • Carlos Navarro Retamal (PhD)
  • Naomí Hernández (Undergraduate student)
  • Luisa Willmann (Guest student)

Research lines

  • Computational plant cell biology
  • Electrical signaling in plants

Postdocs

  • Dr. Carlos Navarro Retamal; Fondecyt Postdoc; Structural determinants of the permeation through two-pore channels (TPC) from plants and animals
  • Dr. Maria Rubio Melendz; Fondecyt Postdoc; Canales “Gap Junction” en el pulgón verde del duraznero (Myzus persicae): Potencial uso para el control de áfidos

Head of the group: Ariela Vergara-Jaque

Dr. Vergara-Jaque’s group uses sophisticated computational methodologies to study membrane proteins that function as channels and transporters. Our goal is to understand how membrane proteins rearrange their internal structure to allow or block the passage of specific substances to either side of the membrane. Moreover, we are interested in revealing the structural basis of protein−protein interactions regulating the function of membrane proteins.

Participants

  • Dr. Ariela Vergara-Jaque (Bioinformatics Engineer, PhD. in Applied Sciences): Group leader
  • Héctor Montecino (Bioinformatics Engineer): Research assistant
  • Ivana Orellana: Undergraduate thesis student
  • Genoveva Rojas: Undergraduate thesis student

Research lines

  • Sequence and structural bioinformatics.
  • Molecular modeling.
  • Protein-protein docking simulations.
  • Molecular dynamics.
  • Free-energy calculations.

Funding

  • Fondecyt Research Initiation Grant Nº 11170223. Exploring the structural basis of membrane transporter dysfunction associated with neural and endocrine diseases. Principal Investigator.
  • Fondecyt Postdoctorate Nº 3180484. Heteroaryl-acrylonitrile derivatives as inhibitors of NADPH Oxidases in an isoform-specific manner. Sponsoring Researcher.
  • Millennium Nucleus of Ion Channels−Associated Diseases (MiNICAD). Young Investigator.

Collaborations

  • Dr. Miguel Holmgren. National Institute of Neurological Disorders and Stroke. National Institutes of Health, Maryland, USA.
  • Dr. Peying Fong. Department of Anatomy and Physiology, Kansas State University, College of Veterinary Medicine, Kansas, USA.
  • Dr. Tomas Lagace. Atherosclerosis, Genetics and Cell Biology Research Group, University of Ottawa Heart Institute, Ottawa, Canada.

URL: http://www.protechlab.cl

Head of the group: Mauricio Arenas Salinas

Participants:

  • Mauricio Arenas Salinas
  • Yerko Argandoña
  • Claudia Gonzalez
  • Francisco Imas
  • Patricia Obando
  • Andrea Olivos
  • Angela Astudillo

Research lines:

  • Protein design and production for the food industry
  • Protein characterization through structural bioinformatic and structural biology

Funding:

  • Fondecyt Research Initiation Grant Nº 11180665. “Identification and characterization of the regulatory iron binding site from the Acidithiobacillus ferrooxidans transcription factor“. (2018-2020).
  • FIC–R Maule 2017 No. BIP Nº40.001.111-0. “Nuevo servicio biotecnológico para la industria alimentaria basado en el diseño y producción de enzimas“. (2018-2020).

Collaborations:

  • Dr. Jose Antonio Reyes (UTALCA)
  • Dr. Felipe Besoain (UTALCA)
  • Dr. Renzo Angles (UTALCA)
  • Dr. Jorge Villaseñor (UTALCA)
  • Dr. Felipe Arenas (USACH)
  • Dr. Carlos Vera (USACH)
[/fussion_toggle]

Head of the group: Janin Riedelsberger

Participants

  • Catalina Acuña González (Undergraduate)
  • Lilibeth Diaz Pacheco (Undergraduate)

Research lines

  • Transport systems in biological membranes
  • Structure and function relation of plant ion channels and ion transporters
  • Combination of experimental (molecular biology and electrophysiology among others) and computational (homology modeling and molecular dynamics simulation) approaches

Funding

  • Convocatoria Nacional Subvención A La Instalación En La Academia, (#PAI77170035), Elucidación del mecanismo de conducción iónica de los canales K+/Na+ HKT de plantas mediante estudios computacionales y experimentales, 2017-2020, Principle Investigator
  • Fondecyt Postdoctorado (#3150173), Investigation of the selectivity and ion conduction mechanism of HKT Na+/K+ transporters, 2014-2017, Principle Investigator

Collaborations

  • Dr. Christina Kühn, Faculty of Life Sciences Institute of Biology, Plant Physiology, Humboldt University, Berlin, Germany
  • Dr. Miguel Piñeros, Robert W. Holley Center for Agriculture and Health (USDA-ARS), Cornell University, Ithaca, NY, USA
  • Dr. Maria Pertusa, Biology Department, Faculty of Chemistry and Biology, University of Santiago de Chile

Head of the group: Wendy González

Participants

  • Wendy González (Ph.D.)
  • Subramanian Boopathi (Ph.D.)
  • Trinidad Mariqueo (Ph.D.)
  • Mauricio Bedoya
  • Daniel Bustos
  • Javiera Baeza

Research lines

  • Biophysics of ion channels
  • Ion channels-drugs interactions
  • Molecular Modeling
  •  
  • Bioinformatics

Funding

Grant title

Funded by

Role

From-Until

“Structural insights into the mechanism of multi-channel blockers of atrial ion channels”. Fondecyt Regular 1191133 Main Researcher 2019-2023
Proyecto de postdoctorado “Identification of small molecules to inhibit the aggregation of Amyloid β peptides of Alzheimer’s Disease”. Fondos de atracción de postdoctorandos, Universidad de Talca Advisor 2018-2020
Proyecto Redes 180117. “Combining computational and experimental approaches to enhance and perfect research on membrane transport proteins”. Conicyt Main Researcher 2018-2019
MODULATION OF GLYCINE RECEPTORS BY β AUXILIARY SUBUNIT: A CRITICAL TARGET FOR CENTRAL PAIN SENSITIZATION.

Fondecyt Postdoctorado

Advisor 2016-2019
Núcleo Milenio MINICAD (Enfermedades asociadas a canales iónicos). Ministerio de Economía y Fomento Co-researcher 2017-2020
Renovación del Clúster de Cómputo del Centro de Bioinformática y Simulación Molecular (CBSM) de la Universidad de Talca. Fondequip Coordinator 2016-2018