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Publications

JOURNAL ARTICLES


Villar JJS, Valdez ARL, Setiadi DH, Fiser B, Viskolcz B, Csizmadia IG, Rágyanszki A. Dimension Reduction in Conformational Analysis: A Two-Rotor Mathematical Model of Amino Acid Diamide Conformational Potential Energy Surface. Canadian Journal of Chemistry 95(8), 2017. 830-836.

Beltran JCB, Montes CA, Villar JJS and Valdez ARL. A Hybrid Method for Detecting Protein Complexes in Weighted Protein-Protein Interaction Networks. Philippine Science Letters, 10(1), 2017. 50-57.

BOOK CHAPTERS


Clemente JB, Adorna HN and Villar JJSWeak Bisimulation between Two Biogeochemical Cycles.In: Nishizaki S-y, Numao M, Caro JD, Suarez MT (Eds.). Theory and Practice of Computation,  World Scientific, 2014.

Villar JJS and Valdez ARL. A Process Algebra Model of Interleukin-2 Trafficking in Hematopoeitic Cells.** In: Nishizaki S-y, Numao M, Caro JD, Suarez MT (Eds.). Theory and Practice of ComputationPICT Vol 7, Springer Japan, 2013.

 Recipient, International Publication Award, Office of the Vice President for Academic Affairs, University of the Philippines System, 2016
** Recipient, International Publication Award, Office of the Vice President for Academic Affairs, University of the Philippines System, 2014


CONFERENCE PROCEEDINGS


Villar JJS, Valdez ARL, Setiadi DH, Fiser B, Viskolcz B, Csizmadia IGRágyanszki A. Computational Modeling and Analysis of Backbone-Sidechain Interactions in Selected Amino Acid Diamide 5D Conformational Potential Energy Surfaces. 
Proceedings of 7th Visegrad Symposium on Structural Systems Biology (VSSSB 2017), 21-24 June 2017, Nove Hrady, Czech Republic

Li Z, Guljas A, Fiser B, Szori M, Ragyanszki A, Viskolcz B, Csizmadia IG, Villar JJS. Computational Modeling and Analysis of 4D Conformational Potential Energy Surface of N-Acetyl-Valine-N-Methylamide. Poster Presentation. Pr
oceedings of 7th Visegrad Symposium on Structural Systems Biology (VSSSB 2017), 21-24 June 2017, Nove Hrady, Czech Republic

Negm L, Guljas A, Fiser B, Szori M, Ragyanszki A, Viskolcz B, Csizmadia IG, Villar JJS. Computational Modeling and Analysis of 5D Conformational Potential Energy Surface of N-Acetyl-Glycylglycine-N-Methylamide. Poster Presentation. Pr
oceedings of 7th Visegrad Symposium on Structural Systems Biology (VSSSB 2017), 21-24 June 2017, Nove Hrady, Czech Republic

Villar JJS, Valdez ARL, Setiadi DH, Fiser B, Viskolcz B, Csizmadia IGRágyanszki ADimension Reduction in Conformational Analysis: Mathematical Modeling of Amino Acid Diamide Conformational Potential Energy Surface
Kemometria és Molekulamodellezés Munkabizottsága-QSAR és Modellezési Szakcsoportja  Szimposia (KeMoMo-QSAR 2017), 1-2 June 2017, Szeged, Hungary

Guljas A, Villar JJS
, Fiser B, 
Rágyanszki A, Jójart B, Viskolcz B, Csizmadia IGComputational Study of TRPV1 Receptor
Kemometria és Molekulamodellezés Munkabizottsága-QSAR és Modellezési Szakcsoportja Szimposia (KeMoMo-QSAR 2017), 1-2 June 2017, Szeged, Hungary

Villar JJS, Rágyanszki A, Setiadi DH, Viskolcz B, Csizmadia IGValdez ARL
A Mathematical Model for Analytical Fitting of Amino 
Acid Diamide Conformational Potential Energy Surfaces
Proceedings of the International Conference on Environmental and Computer Science (VSSSB 2016), 24-26 September 2016, Toronto, Canada

Villar JJS, Rágyanszki A, Valdez ARL, Setiadi DH, Viskolcz B, Csizmadia IG. Mathematical Representation of Relaxed Ramachandran Potential Energy Surfaces of 20 Amino Acid Diamides. Oral Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Cheng SW, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Rágyanszki A, Owen MA. A mathematical representation of side-chain orientation in isoleucine diamide. Conference Poster. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Hung D, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Owen MARágyanszki AA mathematical model and analysis of backbone-sidechain interactions in N-acetyltyrosine N-methylamide with implications in protein foldingPoster Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Liang W, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Owen MARágyanszki AA mathematical representation of side-chain orientation in cysteine diamide.  Poster Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Marceau K, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Rágyanszki A, Owen MA. A mathematical representation of side-chain orientation in asparagine diamide. Poster Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Miao X, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Owen MARágyanszki AConformational analysis of N-acetyl-threonine-N-methylamide to explore possible targets for cancer therapy in MAPK pathway Poster Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Wu Z, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Rágyanszki A, Owen MA. A mathematical representation of side-chain orientation in leucine diamide. Poster Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Xian Z, Villar JJS, Fiser B, Viskolcz B, Csizmadia IG, Owen MARágyanszki AA mathematical representation of side-chain orientation in serine diamide.  Poster Presentation. Proceedings of 6th Visegrad Symposium on Structural Systems Biology (VSSSB 2016), 19-21 June 2016, Warsaw, Poland

Campañano GR, Lopez FJ, Ventura RD, Villar JJ, and Valdez AR. Off-lattice Protein Structure Prediction on 3D Hydrophobic-Polar Side-Chain Model using Parallel Simulated AnnealingProceedings of the Mathematical Society of the Philippines Annual Convention 2016, 30-31 May 2016, Cebu City, Philippines (accepted)

Villar JJRágyanszki A, Valdez AR, Setiadi DH, Viskolcz B and Csizmadia IG. Analysis of Models for Analytical Fitting of Conformational Potential Energy Surfaces. Kemometria és Molekulamodellezés Munkabizottsága-QSAR és Modellezési Szakcsoportja Szimposia (KeMoMo-QSAR 2016), 12-13 May 2016, Miskolc, Hungary

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 Hydrophobic-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.

Villar JJS, Arceo CPP and Mendoza ER. Construction and Structural Stability Analysis of Models of Dopamine D1 Receptor Trafficking in Renal Proximal Tubule Cells. Proceedings of Asian Regional Conference for Systems Biology 2013, Kuala Lumpur, Malaysia,  2013.

Villar JJS, Lubenia PVN, Arceo CPP, Talaue CO, Escaner JML and Mendoza ER. Construction and Structural Stability Analysis of Models of Dopamine Synthesis and D1 Receptor Trafficking in Renal Proximal Tubule Cells.  Poster Presentation. Proceedings of the Frontiers in Systems and Synthetic Biology 2013, Atlanta, GA, USA, 2013.

Villar JJS and Dorado CA. A Regime-Switching Model for Philippine Peso per US Dollar Exchange Spot Rate Volatility Dynamics. Proceedings of the 13th Philippine Computing Science Congress. Ateneo de Manila University, Quezon City, 2013.

Villar JJS, Arceo CPP and Mendoza ER. An ODE Model of Dopamine Receptor Trafficking. International Proceedings of Chemical, Biological and Environmental Engineering, Vol. 45 (presented in the ICLSE 2012, Hong Kong), 2012.

Villar JJS, Arceo CPP and Mendoza ER. A Computational Model of Dopamine D1 Receptor Availability and Intracellular Trafficking in Renal Proximal Tubule Cells. Proceedings of the 2012 Mathematical Society of the Philippines Annual Convention, De La Salle Lipa, Batangas, 2012.


ARTICLES IN PREPARATION


Villar JJSValdez ARL, Setiadi DH, Csizmadia IG, Viskolcz B, Ragyánszki AAn Improved Two-Rotor Function for Conformational Potential Energy Surfaces of 20 Amino Acid Diamides. (Journal Article, Submitted)

Villar JJS, Cheng SW, Hung D, Liang W, Marceau K, Miao X, Wu Z, Xian ZCsizmadia IG, Viskolcz B, Ragyánszki A. Conformational Modeling and Analysis of Backbone-Sidechain Interaction of Amino Acid Diamides.  (Journal Article, In Preparation)

Villar JJSValdez ARL, Setiadi DH, Csizmadia IG, Viskolcz B, Ragyánszki A. Conformational Analysis of 4D Potential Energy Surface of N-acetyl-Valine-N-methylamide.  (Journal Article, In Preparation)

Villar JJS, Lubenia PVN, Mendoza ER and Arceo CPP. Structural Stability Analysis of Models of Dopamine Synthesis and D1 Receptor Trafficking in hRPT Cells using Chemical Reaction Network Theory. (Journal Article, In Preparation)