Heuristic parallelizable algorithm for similarity based biosystems comparison. - Mathialakan Thavappiragasam; Carol M. Lushbough; Etienne Z. Gnimpieba (BCB, 2014)

Automatic biosystems comparison using semantic and name similarity. - Mathialakan Thavappiragasam; Carol M. Lushbough; Etienne Z. Gnimpieba (BCB, 2014)

SBMLDock: Docker Driven Systems Biology Tool Development and Usage. - Etienne Z. Gnimpieba; Mathialakan Thavappiragasam; Abalo Chango; Bill Conn; Carol M. Lushbough (CMSB, 2015)

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. - Scott LeGrand; Aaron Scheinberg; Andreas F. Tillack; Mathialakan Thavappiragasam; Josh Vincent Vermaas; Rupesh Agarwal; Jeff Larkin; Duncan Poole; Diogo Santos-Martins; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; et al. (BCB, 2020)

Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms. - Mathialakan Thavappiragasam; Aaron Scheinberg; Wael R. Elwasif; Oscar R. Hernandez; Ada Sedova (P3HPC@SC, 2020)

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. - Atanu Acharya; Rupesh Agarwal; Matthew B. Baker; Jérôme Baudry; Debsindhu Bhowmik; Swen Böhm; Kendall G. Byler; Sam Yen-Chi Chen; Leighton Coates; Connor J. Cooper; Omar Demerdash; Isabella Daidone; et al. (J. Chem. Inf. Model., 2020)

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement. - Russell B. Davidson; Mathialakan Thavappiragasam; T. Chad Effler; Jess Woods; Dwayne A. Elias; Jerry M. Parks; Ada Sedova (BCB, 2021)

Addressing Load Imbalance in Bioinformatics and Biomedical Applications: Efficient Scheduling across Multiple GPUs. - Mathialakan Thavappiragasam; Vivek Kale; Oscar R. Hernandez; Ada Sedova (BIBM, 2021)

High-throughput virtual laboratory for drug discovery using massive datasets. - Jens Glaser; Josh Vincent Vermaas; David M. Rogers 001; Jeff Larkin; Scott LeGrand; Swen Boehm; Matthew B. Baker; Aaron Scheinberg; Andreas F. Tillack; Mathialakan Thavappiragasam; Ada Sedova; Oscar R. Hernandez (Int. J. High Perform. Comput. Appl., 2021)

Parallel Algorithms for Successive Convolution. - Andrew J. Christlieb; Pierson T. Guthrey; William A. Sands; Mathialakan Thavappiragasam (J. Sci. Comput., 2021)

Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms? - Mathialakan Thavappiragasam; Wael R. Elwasif; Ada Sedova (CCGRID, 2022)

OpenMP's Asynchronous Offloading for All-pairs Shortest Path Graph Algorithms on GPUs. - Mathialakan Thavappiragasam; Vivek Kale (HiPar@SC, 2022)

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. - Russell B. Davidson; Jess Woods; T. Chad Effler; Mathialakan Thavappiragasam; Julie C. Mitchell; Jerry M. Parks; Ada Sedova (Bioinform., 2022)

CPU-GPU Tuning for Modern Scientific Applications using Node-Level Heterogeneity. - Mathialakan Thavappiragasam; Vivek Kale (HiPC, 2023)

Performance Porting the ExaStar Multi-Physics App Thornado On Heterogeneous Systems - A Fortran-OpenMP Code-Base Evaluation. - Mathialakan Thavappiragasam; James Austin Harris; Eirik Endeve; Brice Videau (IWOMP, 2024)

AI and HPC Applications on Leadership Computing Platforms: Performance and Scalability Studies. - JaeHyuk Kwack; Colleen Bertoni; Umesh Unnikrishnan; Riccardo Balin; Khalid Hossain; Yasaman Ghadar; Timothy J. Williams; Abhishek Bagusetty; Mathialakan Thavappiragasam; Väinö Hatanpää; Archit Vasan; John R. Tramm; et al. (IPDPS, 2025)