RESEARCH INTERESTS: Mathematical Modeling of Complex Biological and Social Systems; Theoretical Science and Mathematical Philosophy; Technology-mediated InstructionPublished in Refereed Journals (2013-present)Rabajante, J.F., Tubay, J.M., Ito, H., Uehara, T., Kakishima, S., Morita, S., Yoshimura, J. and Ebert, D. 2016. "Host-parasite Red Queen dynamics with phase-locked rare genotypes". Science Advances, 2(3): e1501548. DOI: 10.1126/sciadv.1501548. American Association for the Advancement of Science (AAAS) Editors: Shahid Naeem (Columbia University) and Cedric Tan (Oxford University). This is another result of my PhD dissertation. Jatulan, E.O., Rabajante, J.F., Banaay, C.G.B., Fajardo, A.C. Jr. and Jose, E.C. 2015. "A mathematical model of intra-colony spread of American Foulbrood in European honeybees ( Apis mellifera L.)". PLoS ONE, 10(12): e0143805.DOI: 10.1371/journal.pone.0143805. Impact Factor at the time of submission/publication: 3.234 Tubay, J.M., Suzuki, K., Uehara, T., Kakishima, S., Ito, H., Ishida, A., Yoshida, K., Mori, S., Rabajante, J.F., Morita, S., Yokozawa, M. and Yoshimura, J. 2015. Microhabitat locality allows multi-species coexistence in terrestrial plant communities. Scientific Reports, 5: 15376. DOI: 10.1038/srep15376. Nature Publishing Group. Impact Factor at the time of submission/publication: 5.578 Rabajante, J.F. and Gavina, M.K.A. 2015. Producing oscillatory decisions. Neuroscience Communications, 2: e859. DOI: 10.14800/nc.859. Rabajante, J.F., Tubay, J.M., Uehara, T., Morita, S., Ebert, D. and Yoshimura, J. 2015. Red Queen dynamics in multi-host and multi-parasite interaction system. Scientific Reports, 5: 10004. DOI: 10.1038/srep10004. Nature Publishing Group. Editor: Elisa Thebault, CNRS IEES-Paris. Impact Factor at the time of submission/publication: 5.078 This is a result of my PhD dissertation. Rabajante, J.F., Babierra, A.L., Tubay, J.M. and Jose, E.C. 2015. Mathematical modeling of cell-fate specification: From simple to complex epigenetics. Stem Cell Epigenetics, 2: e752. DOI: 10.14800/sce.752. Rabajante, J.F. and Talaue, C.O. 2015. Equilibrium switching and mathematical properties of nonlinear interaction networks with concurrent antagonism and self-stimulation. Chaos, Solitons and Fractals: the interdisciplinary journal of Nonlinear Science, and Nonequilibrium and Complex Phenomena, 73: 166-182. DOI: 10.1016/j.chaos.2015.01.018. Elsevier. Editor: Maurice Courbage, Université Denis Diderot - Paris 7. Impact Factor at the time of submission/publication: 1.503 This is a result of my MSc thesis. Rabajante, J.F. and Babierra, A.L. 2015. Branching and oscillations in the epigenetic landscape of cell-fate determination. Progress in Biophysics and Molecular Biology, 117: 240-249. DOI: 10.1016/j.pbiomolbio.2015.01.006. Elsevier. Editor: Tom Blundell, University of Cambridge. Impact Factor at the time of submission/publication: 3.377 Gavina, M.K.A., Rabajante, J.F. and Cervancia, C.R. 2014. Mathematical Programming Models for Determining the Optimal Location of Beehives. Bulletin of Mathematical Biology, 76(5): 997-1016. DOI: 10.1007/s11538-014-9943-9. Springer. Editor: Philip Maini, Mathematical Institute, Oxford University. Impact Factor at the time of submission/publication: 2.023 Talabis, D.A.SJ., Manay, E.J.V, Babierra, A.L., Flores, J.J.M and Rabajante J.F. 2013. A Numerical Model of Philippine Population Growth: Child Policy, Quantitative Insights and Challenges. IAMURE International Journal of Social Sciences, 8: 45-71, DOI: 10.7718/ijss.v8i1.667. Published in Refereed Journals (2009-2012)Bosaing, A.A.D., Rabajante, J.F. and De Lara, M.L.D. 2012. Assignment Problems with Weighted and Nonweighted Neighborhood Constraints in 3^6, 4^4 and 6^3 Tilings. Southeast Asian Journal of Sciences, 1(1): 55-75. Rabajante, J.F. 2012. Investigating the Propagation and Death of Information in Human Subpopulation Networks. International Journal of Applied Mathematical Research, 1(4): 433-451. DOI: 10.14419/ijamr.v1i4.336. Umali, R.E.DC. and Rabajante, J.F. 2011. A Mathematical Model of Rumor Propagation for Disaster Management. Journal of Nature Studies, 10(2): 61-70. Tambaoan, R.S., Rabajante, J.F., Esteves, R.J.P. and Villadelrey, M.C. 2011. Prediction of migration path of a colony of bounded-rational species foraging on patchily distributed resources. Advanced Studies in Biology, 3(7): 333-345. Castilan, M.G.D., Naanod, G.R.K., Otsuka, Y.T. and Rabajante, J.F. 2011. From Numbers to Nature. Journal of Nature Studies, 9(2)/10(1): 35-39. Esteves, R.J.P., Villadelrey, M.C. and Rabajante, J.F. 2010. Determining the optimal distribution of bee colony locations to avoid overpopulation using mixed integer programming. Journal of Nature Studies, 9(1): 79-82. Rabajante, J.F., Figueroa, R.B. Jr. and Jacildo, A.J. 2009. Modeling the area restrict searching strategy of stingless bees, Trigona biroi, as a quasi-random walk process. Journal of Nature Studies, 8(2): 15-21. Published in Conference ProceedingsWalican, J.P.J., Leyeza, M.B.E.L., Jose, E.C., Rabajante, J.F. and Fajardo, A.C. Jr. 2015. Varroa destructor: Spatial Distribution Over A Modified Cellular Automaton. Proceedings of the 11th Taiwan-Philippines Symposium on Analysis. Nazareno, A.L. and Rabajante, J.F. When the customer writes his own story: A segmentation scheme for the life insurance market. 4th International Conference of the Asian Academy of Applied Business (AAAB) 2009. Asian Institute of Management Conference Center, Manila. December 17-18, 2009. (ISBN 978-983-2868-01-9) Figueroa, R.B. Jr., Jacildo, A.J and Rabajante, J.F. Simulating the foraging behavior of Trigona biroi using Multi-Agent Systems. 10th Philippine Computing Science Congress. Davao City, Philippines. March 5-6, 2010. (ISSN 1908-1146) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Paper Presentation in Conferences2008-2013:Optimal Deployment of Community Police Force. 1st UPLB-CAS Student-Faculty Research Conference. University of the Philippines Los Baños, Philippines. December 8, 2008. Oral presentation. This is a result of my BSc research. An Analogy of Chaotic System and Organizational Sociogram. International Conference of Management Education and Practice (ICMEP). Saint Mary’s University Nueva Vizcaya, Philippines. February 20-22, 2009. Oral presentation. Simulation of bee foraging behavior using Biroi Preference Algorithm. 15th BEENET Conference and Techno-fora. Hotel Agripino, Salagdoong, Maria, Siquijor, Philippines. July 23-25, 2009. Oral presentation. (co-authors: R.B. Figueroa, Jr. and A.J. Jacildo) On training Trigona biroi: Behavioral complexity and apparent patterns. 15th BEENET Conference and Techno-fora. Hotel Agripino, Salagdoong, Maria, Siquijor, Philippines. July 23-25, 2009. Oral presentation. (co-author: A.C. Fajardo, Jr.) Prediction of a math class’ exam performance using the Passing Rate Simulator. MATHTED 2009: An International Conference in Mathematics Education (The 7th Biennial Conference of the Philippine Council of Mathematics Teacher Educators (MATHTED), Inc.). Palawan State University, Puerto Princesa City, Palawan, Philippines. October 23-24, 2009. Oral presentation. Modeling the area restrict searching strategy of stingless bees, Trigona biroi, as a quasi-random walk process. 9th Annual National Convention, Philippine Society for the Study of Nature. MSU-IIT Iligan City, Mindanao, Philippines. November 12-15, 2009. Oral presentation; finalist, best research paper – life science category. (co-authors: R.B. Figueroa, Jr. and A.J. Jacildo)Determining the optimal distribution of bee colony locations to avoid overpopulation using mixed integer programming. 9th Annual National Convention, Philippine Society for the Study of Nature. MSU-IIT Iligan City, Mindanao, Philippines. November 12-15, 2009. Oral presentation; 3rd place, best research paper – life science category. (co-authors: M.C. Villadelrey and R.J. Esteves). Analysis of foraging behavior of Trigona biroi Friese: Distance, Directionality and Height. 9th Annual National Convention, Philippine Society for the Study of Nature. MSU-IIT Iligan City, Mindanao, Philippines. November 12-15, 2009. Oral presentation. (co-authors: R.R. Ciar, L.S. Bonto, MH.P. Bayer and S.P. Lubag). Fractals in the 2006 Philippines Family Annual Income Distribution Data. 2nd UPLB-CAS Student-Faculty Research Conference. University of the Philippines Los Baños, Philippines. December 14, 2009. Poster presentation. (co-authors: M.U. Herrera and A.L. Elumbre) Fractals in Age-Sex Population Distribution of the Philippines using Post-Second World War Census Data. 2nd UPLB-CAS Student-Faculty Research Conference. University of the Philippines Los Baños, Philippines. December 14, 2009. Poster presentation. (co-authors: M.U. Herrera, H.R.E. Forio and C.Z. Gocatek) Counting Stingless Bees, Trigona biroi, Using Image Analysis. 10th Philippine Computing Science Congress. Davao City, Philippines. March 5-6, 2010. Poster presentation. (co-authors: M.L. Saldua, A.J. Jacildo, V.Y. Mariano, M.C.S. Paterno and A.C. Fajardo, Jr.) Optimal migration strategy of species foraging on patchily distributed food sources. Mathematical Society of the Philippines Annual Convention. Cebu City, Philippines. May 20-21, 2010. Oral presentation. (co-authors: M.C. Villadelrey and R.J. Esteves). Strategy Analysis for the Control of Epidemics. 16th Annual BEENET Conference and Technofora. University of Southern Philippines, Davao City. August 18-22, 2010. Oral presentation. (co-author: A.L. Nazareno). Modeling the Dynamics of Disease Contagion. 16th Annual BEENET Conference and Technofora. University of Southern Philippines, Davao City. August 18-22, 2010. Oral presentation. (co-author: M.J.V. Cortez). Population assignments in grids with neighborhood constraint. 2010 International Industrial Engineering Conference: Research, Applications and Best Practices. Cebu Parklane International Hotel, Cebu City. August 24-27, 2010. Oral presentation. (co-author: M.L.D. de Lara). Event study on the effect of severe weather conditions in Manila on the Philippine Stock Price Index (PSEI) from January 1998 to September 2010. 10th Annual National Convention of the Philippine Society for the Study of Nature. University of the Philippines Baguio. October 20-24, 2010. Oral presentation. (co-authors: R.J.P. Esteves, S.M. Reyes and M.C. Villadelrey). From Numbers to Nature. 10th Annual National Convention of the Philippine Society for the Study of Nature. University of the Philippines Baguio. October 20-24, 2010. Oral presentation; 2nd place, best research paper – physical sciences category. (co-authors: M.G.D. Castilan, G.R.K. Naanod and Y.T. Otsuka).A model of information propagation in social networks. 8th National Conference on Information Technology Education (NCITE), Boracay, Aklan. October 20-23, 2010. Oral presentation. (co-author: Y.T. Otsuka). Strategic management of corporate grapevine. 4th National Conference of the Operations Research Society of the Philippines. Eastwood Richmonde Hotel, Quezon City. November 05, 2010. Oral presentation. Money Circulation in an Artificial Community (oral presentation); Digitized Signatures using Bézier Curves (oral presentation); Simulation of a Virtual Stock Market (oral presentation); A Simulation on the Levels of Motivation of Workers in an Organization (oral presentation); P-Noymial Interpolation (poster presentation). 3rd CAS Student-Faculty Research Conference (SFRC 2010). University of the Philippines Los Baños. November 22, 2010. (co-authors: Math 174-Numerical Analysis I undergraduate students). Automated Counting and Tracking of Stingless Bees, Trigona biroi, Friese, Using Image Processing and Video Analysis. 10th Asian Apicultural Association Conference and Api Expo. Busan, South Korea. November 04-07, 2010. Oral presentation. (co-authors: A.J. Jacildo, M.L. Saldua, J.C. Manalastas, V.Y. Mariano, M.C.S. Paterno and A.C. Fajardo). Simulation of Bee Foraging Behavior Using Biroi Preference Algorithm and Assimilation of Data from Wet Lab Experiments. 10th Asian Apicultural Association Conference and Api Expo. Busan, South Korea. November 04-07, 2010. Oral presentation; awarded with excellent scientific contribution to Asian Apiculture. (co-authors: R.B. Figueroa, Jr., A.J. Jacildo, R.R. Ciar, L.S. Bonto, M.P. Bayer and C.R. Cervancia).Parameter variability and state stochasticity in information evolution modeling. Mathematical Society of the Philippines CALABARZON First Annual Regional Convention. De Lasalle Lipa, Lipa City. May 4, 2011. Oral Presentation. (co-authors: M.A.P. Soriano and Y.T. Otsuka). Mathematical Models of Rumor Propagation for Disaster Management. 11th Philippine Society for the Study of Nature National Annual Scientific Convention. UP Open University and UPLB, Philippines. May 24-28, 2011. Oral Presentation; best research paper – environmental science category. (co-authors: Y.T. Otsuka and R.E.DC. Umali).Pollen Shape Analysis using Bézier Curves. 17th BEENET Conference and Techno-fora. Development Academy of the Philippines, Tagaytay City, Cavite. August 18-20, 2011. Oral Presentation. An ODE Approach to Decision Making Involving Pairwise Comparison of Choices. 4th UPLB-CAS Student-Faculty Conference. UPLB. December 12, 2011. Oral Presentation. (co-author: Y.T. Otsuka). Assignment Problems with Weighted and Nonweighted Neighborhood Constraints in 3^6, 4^4 and 6^3 Tilings. International Conference in Mathematics and Applications. University of Economics and Law, Ho Chi Minh City, Vietnam. December 20-22, 2011. Oral Presentation. (co-authors: A.A.D. Bosaing and M.L.D.De Lara). The Flow of the Cinquin-Demongeot Model of Cellular Differentiation. 2012 Mathematical Society of the Philippines Annual Convention. De La Salle Lipa, Lipa, Batangas. May 18-19, 2012. Oral Presentation. (co-authors: C.O.Talaue and B.D. Aguda). Bézier Curves: Integrating Math, Arts and Technology. 2012 Annual Convention of the Mathematics Teachers Association of the Philippines (MTAP) - Tertiary Level. University of the Philippines Visayas, Iloilo City Campus. August 16-17,2012. Oral Presentation. Mathematical strategies for determining the best location of beehives to minimize resource competition. 11th Asian Apicultural Association Conference, ApiExpo and Workshop. Kuala Terengganu, Malaysia. September 28 - October 2, 2012. Oral Presentation. (co-authors: A.C. Fajardo and C.R. Cervancia). Exogenous stimulus can induce transdifferentiation and can assure unipotency towards the desired cell lineage. 5th UPLB-CAS Student-Faculty Research Conference. UPLB. December 14, 2012. Oral Presentation. A Numerical Study on the effect of imposing an n-child policy: The Philippine Case. 5th UPLB-CAS Student-Faculty Research Conference. UPLB. December 14, 2012. Oral Presentation. (co-authors: D.A.SJ. Talabis and E.J.V. Manay) Probabilistic and Fuzzy Model for Determining the Best Location of Beehives to Minimize Intercolony Resource Competition. 2013 Mathematical Society of the Philippines (MSP) Annual Convention. Puerto Princesa, Palawan. May 17-18, 2013. Poster Presentation. (co-author: M.K.A. Gavina) Population Dynamics of the Philippines: A Quantitative Study. 2013 Mathematical Society of the Philippines (MSP) Annual Convention. Puerto Princesa, Palawan. May 17-18, 2013. Poster Presentation. (co-authors: D.A.SJ. Talabis and E.J.V. Manay) Spatial Distribution Over a Modified Hexagonal Cellular Automaton. 2013 Mathematical Society of the Philippines (MSP) Annual Convention. Puerto Princesa, Palawan. May 17-18, 2013. Oral Presentation. (co-authors: J.P.J. Walican, M.B.E.L. Leyeza, A.C. Fajardo, Jr. and E.C. Jose) --- similar papers are presented in Ukraine and Taiwan (c/o EC Jose and JPJ Walican) 2014-present:Branching and Oscillations in Cell-Fate Determination. 2014 Hands-on Research in Complex Systems School. ICTP, Trieste, Italy. June 30 - July 11, 2014. Poster presentation; Jury's Choice Poster award. (co-authors: A.L. Babierra and C.O. Talaue)Mathematical analysis of a multistable switch model of cell differentiation. 2014 International Congress of Mathematicians. Seoul, South Korea. August 13-21, 2014. Poster presentation (Mathematics in Science and Technology). (co-authors: C.O. Talaue and B.D. Aguda)
The Uninsurable Social Class? A Marketing Stance is cited in
http://parenthoodphils.wordpress.com/2009/09/21/working-abroad-may-affect-your-family-if-not-planned-properly/ Also visit http://www.scribd.com/jfr_jomar and http://www.scribd.com/jrabajante |

MSc THESIS ABSTRACT

Mathematical Strategies for Programming Biological Cells

by Jomar F. Rabajante

Advisers: Cherryl O. Talaue, Ph.D. and Baltazar D. Aguda, Ph.D.

In this thesis, we study a phenomenological gene regulatory network (GRN) of a mesenchymal cell differentiation system. The GRN is composed of four nodes consisting of pluripotency and differentiation modules. The differentiation module represents a circuit of transcription factors (TFs) that activate osteogenesis, chondrogenesis, and adipogenesis.

We investigate the dynamics of the GRN using Ordinary Differential Equations (ODE). The ODE model is based on a non-binary simultaneous decision model with autocatalysis and mutual inhibition. The simultaneous decision model can represent a cellular differentiation process that involves more than two possible cell lineages. We prove some mathematical properties of the ODE model such as positive invariance and existence-uniqueness of solutions. We employ geometric techniques to analyze the qualitative behavior of the ODE model.

We determine the location and the maximum number of equilibrium points given a set of parameter values. The solutions to the ODE model always converge to a stable equilibrium point. Under some conditions, the solution may converge to the zero state. We are able to show that the system can induce multistability that may give rise to co-expression or to domination by some TFs.

We illustrate cases showing how the behavior of the system changes when we vary some of the parameter values. Varying the values of some parameters, such as the degradation rate and the amount of exogenous stimulus, can decrease the size of the basin of attraction of an undesirable equilibrium point as well as increase the size of the basin of attraction of a desirable equilibrium point. A sufficient change in some parameter values can make a trajectory of the ODE model escape an inactive or a dominated state.

Sufficient amounts of exogenous stimuli affect the potency of cells. The introduction of an exogenous stimulus is a possible strategy for controlling cell fate. A dominated TF can exceed a dominating TF by adding a corresponding exogenous stimulus. Moreover, increasing the amount of exogenous stimulus can shutdown multistability of the system such that only one stable equilibrium point remains.

We observe the case where a random noise is present in our system. We add a Gaussian white noise term to our ODE model making the model a system of stochastic DEs. Simulations reveal that it is possible for cells to switch lineages when the system is multistable. We are able to show that a sole attractor can regulate the effect of moderate stochastic noise in gene expression.

## http://www.scribd.com/doc/89272178/JFRabajante-MS-Applied-Math-Thesis

CORRIGENDUM AND NOTES:

1) Typographical error in page 18: The parameters beta, c and g represent the relative speed of transcription (or strength of the unrepressed TF expression relative to

the first-order degradation), cooperativity and "leak", respectively.

2) Cobweb diagram is used in discrete models. However, similar results can be derived if cobweb diagram is used in our model.

3) Page 31: Matrix 4.7 is already corrected in the online version of this thesis.

4) Theorem 6.7 is not necessarily if and only if.

5) See this file for updated write-up: http://jfrabajante.weebly.com/uploads/1/1/5/5/11551779/rabajante_et_al_main_text.pdf and https://peerj.com/preprints/382

6) Always converging to equilibrium point is not true. Example of oscillation:

d/dt (x) = (x^2)/(1+x^2+y^2)-.1*x+.1

d/dt (y) = (y^2)/(1+y^2+z^2)-.1*y+.1

d/dt (z) = (z^2)/(1+z^2+x^2)-.1*z+.1

init x = .1

init y = .2

init z = .3

See this file: https://peerj.com/preprints/382

1) Typographical error in page 18: The parameters beta, c and g represent the relative speed of transcription (or strength of the unrepressed TF expression relative to

the first-order degradation), cooperativity and "leak", respectively.

2) Cobweb diagram is used in discrete models. However, similar results can be derived if cobweb diagram is used in our model.

3) Page 31: Matrix 4.7 is already corrected in the online version of this thesis.

4) Theorem 6.7 is not necessarily if and only if.

5) See this file for updated write-up: http://jfrabajante.weebly.com/uploads/1/1/5/5/11551779/rabajante_et_al_main_text.pdf and https://peerj.com/preprints/382

6) Always converging to equilibrium point is not true. Example of oscillation:

d/dt (x) = (x^2)/(1+x^2+y^2)-.1*x+.1

d/dt (y) = (y^2)/(1+y^2+z^2)-.1*y+.1

d/dt (z) = (z^2)/(1+z^2+x^2)-.1*z+.1

init x = .1

init y = .2

init z = .3

See this file: https://peerj.com/preprints/382