| 2018 | ICSE | A parallel framework for ab initio transcript-clustering. | Dhananjai Madhava Rao |
| 2018 | PADS | Performance comparison of Cross Memory Attach capable MPI vs. Multithreaded Optimistic Parallel Simulations. | Dhananjai Madhava Rao |
| 2017 | FIE | Music maker: Using music to introduce coding and concurrency to young learners. | Dhananjai Madhava Rao |
| 2017 | PADS | Multi-tier Priority Queues and 2-tier Ladder Queue for Managing Pending Events in Sequential and Optimistic Parallel Simulations. | Julius Higiro, Meseret Gebre, Dhananjai Madhava Rao |
| 2014 | PADS | Accelerating parallel agent-based epidemiological simulations. | Dhananjai Madhava Rao |
| 2008 | WSC | Parallel simulation of the global epidemiology of Avian Influenza. | Dhananjai Madhava Rao, Alexander Chernyakhovsky |
| 2006 | PADS | Predicting Performance of Resolution Changes in Parallel Simulations. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 2006 | WSC | Applying parallel, dynamic-resolution simulations to accelerate VLSI power estimation. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 2002 | WSC | Web-based simulation 2: performance prediction of dynamic component substitutions. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 2001 | MASCOTS | Multi-Resolution Network Simulations Using Dynamic Component Substitution. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 2000 | MASCOTS | Parallel Co-Simulation of Conventional and Active Networks. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 2000 | WSC | Dynamic component substitution in web-based simulation. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 1999 | MASCOTS | Simulation of Ultra-Large Communication Networks. | Dhananjai Madhava Rao, Philip A. Wilsey |
| 1998 | WSC | Unsynchronized Parallel Discrete Event Simulation. | Dhananjai Madhava Rao, Narayanan V. Thondugulam, Radharamanan Radhakrishnan, Philip A. Wilsey |