Publications and conference presentations

2023
  • Mark Edward M. Gonzales, Jennifer C. Ureta, Anish M.S. Shrestha: Protein embeddings improve phage-host interaction prediction, Preprint.
2022
  • Kyle Christian L. Santiago and Anish M.S. Shrestha: DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms, GIW XXXI/ISCB-Asia V, Dec 12 – 14, 2022, Tainan, Taiwan. Link
  • Anish M.S. Shrestha, Joyce Emlyn B. Guiao, Kyle Christian L. Santiago: Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment, BMC Genomics 23, 97 (2022). Link
2021
  • Stanley Vincent Lim, Steven Edward Lim, Carlos Louis Ting, Aaron Eldrich Wong, and Roger Luis Uy: SIMD Implementation of Modified Zhang’s Three-Frame Alignment Algorithm, 2021 IEEE 13th International Conference on Humanoid, Nanotechnology, Information Technology, Communication and Control, Environment, and Management (HNICEM), 2021, pp. 1-6, Link
  • Jennifer Ureta and Anish M.S. Shrestha: Identifying drug-resistant tuberculosis from chest X-ray images using a simple convolutional neural network, Journal of Physics, Conference Series, Vol 2071, International Conference on Biomedical Engineering (ICoBE) 2021. Link
  • Anish M.S. Shrestha, Crissa Ann I. Lilagan, Joyce Emlyn B. Guiao, Maria Rowena R. Romana-Eguia, Ma. Carmen Ablan Lagman: Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites, BMC Genomics 22, 580 (2021). Link
  • Mercado C.C., Fajardo A.R., Manalili S.K., Zapanta R., Uy R.L. (2021) Multiprocessing Implementation for Building a DNA q-gram Index Hash Table. In: Alfred R., Iida H., Haviluddin H., Anthony P. (eds) Computational Science and Technology. Lecture Notes in Electrical Engineering, vol 724. Springer. Link
  • Uy, R.L., Mercado, C.C., Fajardo, A.R., Zapanta, R. and Manalili, S.K., , “Multiprocessing Implementation of Pigeonhole-based Filter for DNA Read Mapping,” In Proceedings of the DLSU Research Congress 2021, Manila, Philippines, 2021

2020

  • Anish M.S. Shrestha, Crissa Ann I. Lilagan, Ma. Carmen A. Lagman : Wide-and-shallow vs. narrow-and-deep: comparing two transcriptome assemblies of S. serrata, DLSU Research Congress 2020.
  • A. R. Fajardo, S. K. Manalili, C. C. Mercado, R. Zapanta and R. L. Uy, “Multiprocess Implementation of DNA Pre-alignment Filtering using the Bit Matrix Algorithm,” 2020 IEEE 12th International Conference on Humanoid, Nanotechnology, Information Technology, Communication and Control, Environment, and Management (HNICEM), 2020, pp. 1-6. Link
  • Mercado, C.C., Manalili, S.K., Fajardo, A.R., Zapanta, R. and R.L. Uy, “On the Complexity of Reducing Storage for DNA q-gram Index Hash Table,” In Proceedings of the 2020 Philippine Computing Science Congress (PCSC 2020), Baguio, Philippines, 2020, pp. 118-124.
2019
  • K. M. C. Chua, J. A. F. Villamayor, L. C. Bautista, and R. L. Uy, “Implementation of hyyrö’s bit-vector algorithm using advanced vector extensions 2,” International Journal of Advances in Intelligent Informatics, vol. 5, no. 3, pp. 230–242, Oct. 2019, doi: 10.26555/ijain.v5i3.362.
  • Anish M.S. Shrestha: Grouped-alignment of RNA-seq reads for accurate prediction of splice sites, 16th International Conference on Molecular Systems Biology ICMSB 2019, Manila.
  • Anish M.S. Shrestha: Challenges in Sequence Analysis in the Era of Big Biological Data, Invited Talk, Philippine Computing Science Congress, Manila 2019
  • Anish M.S. Shrestha: Biological sequence analysis in the era of high-throughput sequencers, Bioinformatics Symposium, Philippine Genome Center, Manila 2019