RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, co-expression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci
Anish M.S. Shrestha, Mark Edward M. Gonzales, Phoebe Clare L. Ong, Pierre Larmande, Hyun-Sook Lee, Ji-Ung Jeung, Ajay Kohli, Dmytro Chebotarov, Ramil P. Mauleon, Jae-Sung Lee, Kenneth L. McNally
GigaScience, in press

Protein embeddings improve phage-host interaction prediction
Mark Edward M. Gonzales, Jennifer C. Ureta, Anish M.S. Shrestha
PLOS ONE 18(7), e0289030

A Reconfigurable FeFET Content Addressable Memory for Multi-State Hamming Distance
Liu Liu, Ann Franchesca Laguna, Ramin Rajaei, Mohammad Mehdi Sharifi, Arman Kazemi, Xunzhao Yin, Michael Niemier, Xiaobo Sharon Hu
IEEE Transactions on Circuits and Systems I: Regular Papers, 70(6), pp. 2356–2369

DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms
Kyle Christian L. Santiago, Anish M.S. Shrestha
GIW XXXI/ISCB-Asia V, Tainan, Taiwan, Dec. 12–14, 2022 (To appear in BMC Bioinformatics Supplement)

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment
Anish M.S. Shrestha, Joyce Emlyn B. Guiao, Kyle Christian L. Santiago
BMC Genomics 23, 97

Complementary Preparation for Frame Alignment Algorithms Using PYNQ-Z2 FPGA
Aaron Eldrich Wong, Carlos Louis Ting, Stanley Vincent Lim, Steven Edward Lim, Roger Luis Uy, Rayner Alfred, Zamhar Iswandono
Proceeedings of the 9th International Conference on Computational Science and Technology, Johor Bahru, Malaysia, Aug. 27–28, 2022, pp. 317–326

SIMD Implementation of Modified Zhang’s Three-Frame Alignment Algorithm
Stanley Vincent Lim, Steven Edward Lim, Carlos Louis Ting, Aaron Eldrich Wong, Roger Luis Uy
2021 IEEE 13th International Conference on Humanoid, Nanotechnology, Information Technology, Communication and Control, Environment, and Management (HNICEM), Manila, Philippines, Nov. 28–30, 2021, pp. 1–6

Identifying drug-resistant tuberculosis from chest X-ray images using a simple convolutional neural network
Jennifer Ureta, Anish M.S. Shrestha
Journal of Physics: Conference Series, 2071; 2021 International Conference on Biomedical Engineering (ICoBE), Malaysia, Sept. 14–15, 2021

Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites
Anish M.S. Shrestha, Crissa Ann I. Lilagan, Joyce Emlyn B. Guiao, Maria Rowena R. Romana-Eguia, Ma. Carmen Ablan Lagman
BMC Genomics 22, 580

Multiprocessing Implementation for Building a DNA q-gram Index Hash Table
Candace Claire Mercado, Aaron Russell Fajardo, Saira Kaye Manalili, Raphael Zapanta, Roger Luis Uy
Computational Science and Technology, Lecture Notes in Electrical Engineering, 724, pp. 179–191

Multiprocessing Implementation of Pigeonhole-based Filter for DNA Read Mapping
Roger Luis Uy, Candace Claire Mercado, Aaron Russell Fajardo, Raphael Zapanta, Saira Kaye Manalili
2021 DLSU Research Congress, Manila, Philippines, July 7–9, 2021

Wide-and-shallow vs. narrow-and-deep: comparing two transcriptome assemblies of S. serrata
Anish M.S. Shrestha, Crissa Ann I. Lilagan, Ma. Carmen A. Lagman
2020 DLSU Research Congress, Manila, Philippines, June 17–19, 2020

On the Complexity of Reducing Storage for DNA q-gram Index Hash Table
Candace Claire Mercado, Saira Kaye Manalili, Aaron Russell Fajardo, Raphael Zapanta, Roger Luis Uy
20th Philippine Computing Science Congress (PCSC), Baguio, Philippines, March 19–21, 2020, pp. 118–124

Implementation of hyyrö’s bit-vector algorithm using advanced vector extensions 2
Kyle Matthew Chan Chua, Janz Aeinstein Fauni Villamayor, Lorenzo Campos Bautista, Roger Luis Uy
International Journal of Advances in Intelligent Informatics, 5(3), pp. 230–242

Grouped-alignment of RNA-seq reads for accurate prediction of splice sites
Anish M.S. Shrestha
6th International Conference on Molecular Systems Biology (ICMSB), Manila, Philippines, Oct. 28–30, 2019

Challenges in Sequence Analysis in the Era of Big Biological Data
Anish M.S. Shrestha
19th Philippine Computing Science Congress (PCSC), Manila, Philippines, March 28–30, 2019

Biological sequence analysis in the era of high-throughput sequencers
Anish M.S. Shrestha
Bioinformatics Symposium, Philippine Genome Center, Manila, Philippines