Director, Computational Genomics and Systems Biology Program, Philippine Genome Center
Chair and Assistant Professor, Department of Computer Science, University of the Philippines Diliman
Mantaring-Gervasio Professorial Chair
PhD, University of the Philippines Diliman

Research Areas: Computational (Systems) Biology, Rice Genomics, Bioinformatics, Data Structures and Algorithmics, Data Analysis and Visualization

Jan has been delving into the field of bioinformatics and systems biology for more than a decade now, beginning with his stint as research assistant under the International Rice Research Institute. It was also there where his specific interest in rice science began. During his time there, he was involved in a large scale software development project that gave rise to the Generation Challenge Programme platform, a software suite for collection, warehousing, and (genetic) analysis of crop genetic and genomic data.

During his Ph.D. work, he became acquainted with systems genetics and integrative genomics, which involved data integration and analyses of heterogeneous biological datasets. His dissertation tweaked and applied a particular framework meant for analysis of human traits to handle rice data, specifically to analyze genetic mechanisms of rice salt tolerance.

He currently serves as Assistant Professor under the UP Diliman Department of Computer Science. He is affiliated with the Algorithms and Complexity Laboratory (ACLab), and heads both research groups on Computation for Biology with Relevant Algorithmics (CoBRA) and Representation, Analysis, Visualization, and Extraction of Information (RAVEn) under the aforementioned lab.

Relevant Publications

  • Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M, Simon R, Balaji J, Akintunde A, Mauleon R, Wanchana S, Shah T, Anacleto M, Portugal A, Ulat VJ, Thongjuea S, Braak K, Ritter S, Dereeper A, Skofic M, Rojas E, Martins N, Pappas G, Alamban R, Almodiel R, Barboza LH, Detras J, Manansala K, Mendoza MJ, Morales J, Peralta B, Valerio R, Zhang Y, Gregorio S, Hermocilla J, Echavez M, Yap JM, Farmer A, Schiltz G, Lee J, Casstevens T, Jaiswal P, Meintjes A, Wilkinson M, Good B, Wagner J, Morris J, Marshall D, Collins A, Kikuchi S, Metz T, McLaren G, van Hintum T. The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science. Int J Plant Genomics. 2008; vol. 2008: [6 pages]. doi:10.1155/2008/369601.
  • Yap, JM. A Pi-Calculus Model of the CD95 Receptor Mediated Pathway of Apoptosis. Electronic Proceedings of the 8th Philippine Computing Science Congress. 2008: 189-201.
  • Bernabe JFK, Ilano AKMC, Clemente JB, Yap JMC. Quantitative Trait Loci Mapping Using A Least Squares-Based Method. Electronic Proceedings of the 10th Philippine Computing Science Congress. 2010: 91-94.
  • Yap JM, Adorna H, Mauleon R, Mendoza E. Correctness and Algorithmic Efficiency of a Method for Systems Genetics. Philippine Computing Journal. 2013; 8(2): 12-18.
  • Yap JM, Mauleon R, Mendoza E, Adorna H. A partial regression coefficient analysis framework to infer candidate genes causal to traits in recombinant inbred lines. Phil Sci Lett. 2014; 7(1): 245-274.