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Bioinformatics and Systems Biology



Welcome to the SCL Bioinformatics and Systems Biology Research Interest Group Page!



Overview



This is a special research interest group under SCL that aims to understand the properties and behavior of complex biological systems, in terms of its individual (molecular) components and how they interact at different levels of the organization. Specifically, we are interested in the study of efficient extraction, storage, analysis and integration of important biological information from these systems through utilization of different computational approaches, such as modeling, data mining, machine learning and visualization, to give meaningful insights from these biological data, and for us to provide answers to pressing bioinformatics problems.


Research Projects

Currently, there are active research projects being tackled by the group, which include the following:


1. Construction and Analysis of Potential Energy Hypersurfaces for Protein Structure Prediction through Quantum Chemical Calculations

John Justine Villar, M.Sc., Adrian Roy Valdez, Ph.D., in collaboration with David Setiadi, Ph.D. (University of Toronto, Canada),  Amador Muriel, Ph.D. (The City University of New York, USA) and Imre Csizmadia, Ph.D. (University of Miskolc, Hungary)
This study aims to combine potential energy surfaces of different amino acids through ab initio calculations and bosonic-fermionic statistics to provide insights on the potential energy hypersurface given an amino acid sequence. We intend to compare our results to results from other computational techniques, as well as traditional methods, such as X-ray crystallography, NMR, infrared spectroscopy. Results from databases like the PDB will also be explored.


Jerome Cary Beltran, Catalina Montes, John Justine Villar, M.Sc. and Adrian Roy Valdez, Ph.D.
This research aims to incorporate biological information into purely graph-based clustering methods to more precisely predict relevant protein complexes from protein-protein interaction networks (PPIN). The resulting algorithm will be compared to existing PPIN frameworks, in terms of the number of complexes correctly predicted from gold standard datasets, and other performance metrics.

*Second Prize, 2015 UP College of Engineering Undergraduate Project Competition


Gerald Roy Campañano, Francis Jonathan Lopez, Rowel Ventura, John Justine Villar, M.Sc. and Adrian Roy Valdez, Ph.D.
This project aims to predict the final conformation of a protein by sampling possible conformations through an off-lattice model. This also provides a parallel implementation of the simulated annealing algorithm for conformational energy minimization. The results were applied to several proteins from Protein Data Bank, where minimum energy values and number of hydrogen bonds were compared.



Selected Research Publications


Villar JJ, Rágyanszki AR, Valdez AR, Setiadi D, Viskolcz B and Csizmadia IG. Mathematical Representation of 20 Amino Acid Diamide Relaxed Conformational Potential Energy Surfaces. Proc. 6th Visegrad Symposium on Structural Systems Biology 2016, Warsaw, Poland, 2016.

Campañano GR, Lopez FJ, Ventura R, Villar, JJ and Valdez AR. Off-lattice Protein Structure Prediction on 3D Hydrophobic-Polar Side-Chain Model using Parallel Simulated Annealing. Proceedings of the Mathematical Society of the Philippines Annual Convention 2016, Cebu City, Philippines, 2016.

Villar JJ, Rágyanszki AR, Valdez AR, Setiadi D, Viskolcz B and Csizmadia IG. Analysis of Models for Analytical Fitting of Conformational Potential Energy Surfaces. Proc. Kemometria és Molekulamodellezés Munkabizottsága-QSAR és Modellezési Szakcsoportja Szimposia (KeMoMo-QSAR 2016), Miskolc, Hungary, 2016.

Beltran JC, Montes C, Villar JJ, Soriano J and Valdez AR. On Incorporating Core-Attachment Scheme for Protein Complex Detection on Weighted Protein-Protein Interaction Networks. Proceedings of the 2015 Mathematical Society of the Philippines Annual Convention, Laoag City, Philippines, 2015.

Gozum RP, Mendoza KM, Villar JJ, Soriano J and Valdez AR. On Protein Structure Prediction using the Hydrophoic-Polar Model on a Tetrahedral Lattice. Proceedings of the 2015 Mathematical Society of the Philippines Annual Convention, Laoag City, Philippines, 2015.

Beltran JC, Montes C, Villar JJ, Soriano J and Valdez AR. A Hybrid Method for Detecting Protein Complexes in Weighted Protein-Protein Interaction Networks. Proceedings of the 8th Research Workshop on Modeling, Simulation and Scientific Computing in the Philippines (MODEL 2015), Manila, Philippines, 2015.

Gozum RP, Mendoza KM, Villar JJ, Soriano J and Valdez AR. A Branch-and-Bound Method for the 3D HP Protein Folding Model over a Tetrahedral Lattice. Proceedings of the 8th Research Workshop on Modeling, Simulation and Scientific Computing in the Philippines (MODEL 2015), Manila, Philippines, 2015.

Soriano J, Valdez AR and Fontanilla IK. Discrimination of Class Aves Families Using Codon Counts From Unaligned COI Sequences. Proceedings of the 8th Research Workshop on Modeling, Simulation and Scientific Computing in the Philippines (MODEL 2015), Manila, Philippines, 2015.

Soriano J, Sapasap R, Chua T, Santi N, Fontanilla I and Valdez AR. DNA Barcoding of Class Aves Species Using Codon Counts with Artificial Neural NetworkInternational Conference of Artificial Intelligence in Computer Science. Langkawi, Malaysia, 2013.

Soriano J, Rondon R, Meneses A, Cardenas M, Lim-Yap S and Valdez AR. Creating Functional Groups for Palanan Forest Dynamics Plot using Linear Discriminant AnalysisInternational Conference of Artificial Intelligence in Computer Science. Langkawi, Malaysia, 2013.

* Villar JJS and Valdez ARL. A Process Algebra Model of Interleukin-2 Trafficking in Hematopoeitic CellsTheory and Practice of ComputationPICT Vol 7, Springer Japan, 2013.
    


*Recipient, 2013 International Publication Award (Book Chapter), Office of the Vice President for Academic Affairs, University of the Philippines System

Members


Faculty
Jaymar Soriano, M.Sc.

Graduate Student
John Justine Villar, M.Sc.

Undergraduate Students
Gerald Roy Campañano
Francis Jonathan Lopez
Rowel Ventura