| BioPerf: A benchmark suite to evaluate high-performance computer architecture on bioinformatics applications DA Bader, Y Li, T Li, V Sachdeva IEEE International. 2005 Proceedings of the IEEE Workload Characterization …, 2005 | 118 | 2005 |
| Exploring the viability of the Cell Broadband Engine for bioinformatics applications V Sachdeva, M Kistler, E Speight, THK Tzeng Parallel Computing 34 (11), 616-626, 2008 | 98 | 2008 |
| Enabling high-performance computing as a service M AbdelBaky, M Parashar, H Kim, KE Jordan, V Sachdeva, J Sexton, ... Computer 45 (10), 72-80, 2012 | 97 | 2012 |
| A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic. DA Bader, V Sachdeva PDCS, 41-48, 2005 | 87 | 2005 |
| OpenRBC: A fast simulator of red blood cells at protein resolution YH Tang, L Lu, H Li, C Evangelinos, L Grinberg, V Sachdeva, ... Biophysical journal 112 (10), 2030-2037, 2017 | 74 | 2017 |
| Fully integrated FPGA molecular dynamics simulations C Yang, T Geng, T Wang, R Patel, Q Xiong, A Sanaullah, C Wu, J Sheng, ... Proceedings of the International Conference for High Performance Computing …, 2019 | 60 | 2019 |
| Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Nature communications 13 (1), 5884, 2022 | 37 | 2022 |
| OpenCL for HPC with FPGAs: Case study in molecular electrostatics C Yang, J Sheng, R Patel, A Sanaullah, V Sachdeva, MC Herbordt 2017 IEEE High Performance Extreme Computing Conference (HPEC), 1-8, 2017 | 37 | 2017 |
| K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity CS Kim, MD Winn, V Sachdeva, KE Jordan BMC bioinformatics 18, 1-15, 2017 | 25 | 2017 |
| Molecular dynamics range-limited force evaluation optimized for FPGAs C Yang, T Geng, T Wang, C Lin, J Sheng, V Sachdeva, W Sherman, ... 2019 IEEE 30th International Conference on Application-specific Systems …, 2019 | 23 | 2019 |
| Mesh interface resolution and ghost exchange in a parallel mesh representation TJ Tautges, JA Kraftcheck, N Bertram, V Sachdeva, J Magerlein 2012 IEEE 26th International Parallel and Distributed Processing Symposium …, 2012 | 18 | 2012 |
| Upgrade of fpga range-limited molecular dynamics to handle hundreds of processors C Wu, T Geng, S Bandara, C Yang, V Sachdeva, W Sherman, M Herbordt 2021 IEEE 29th Annual International Symposium on Field-Programmable Custom …, 2021 | 14 | 2021 |
| Evaluating the jaccard-tanimoto index on multi-core architectures V Sachdeva, DM Freimuth, C Mueller Computational Science–ICCS 2009: 9th International Conference Baton Rouge …, 2009 | 14 | 2009 |
| A Communication-Efficient Multi-Chip Design for Range-Limited Molecular Dynamics C Wu, T Geng, C Yang, V Sachdeva, W Sherman, M Herbordt 2020 IEEE High Performance extreme Computing Conference (HPEC), 1-8, 2020 | 13 | 2020 |
| Atomic-resolution prediction of degrader-mediated ternary complex structures by combining molecular simulations with hydrogen deuterium exchange T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Biorxiv, 2021.09. 26.461830, 2021 | 12 | 2021 |
| System-level modeling of GPU/FPGA clusters for molecular dynamics simulations C Wu, S Bandara, T Geng, V Sachdeva, W Sherman, M Herbordt 2021 IEEE high performance extreme computing conference (HPEC), 1-8, 2021 | 12 | 2021 |
| Execution of complete molecular dynamics simulations on multiple FPGAs C Pascoe, L Stewart, BW Sherman, V Sachdeva, MW Herbordt 2020 IEEE High Performance Extreme Computing Conference (HPEC), 1-2, 2020 | 12 | 2020 |
| SimBSP: Enabling RTL Simulation for Intel FPGA OpenCL Kernels A Sanaullah, C Yang, D Crawley, M Herbordt Proc. Heterogeneous High Performance Reconfigurable Computing, 2018 | 10 | 2018 |
| BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation performance computer systems DA Bader, V Sachdeva, V Agarwal, G Goel, AN Singh University of New Mexico, Tech. Rep, 2005 | 9 | 2005 |
| Particle mesh ewald for molecular dynamics in opencl on an fpga cluster LC Stewart, C Pascoe, BW Sherman, M Herbordt, V Sachdeva arXiv preprint arXiv:2009.12617, 2020 | 8 | 2020 |
