**Journal Articles**

- Mengran Fan, Jian Wang, Huaipan Jiang, Yilin Feng, Mehrdad Mahdavi, Kamesh Madduri, Mahmut T Kandemir and Nikolay V Dokholyan, 2021, "GPU-Accelerated Flexible Molecular Docking", The Journal of Physical Chemistry B,
**125**, (4), pp. 1049-1060

- George M Slota, Cameron Root, Karen Devine, Kamesh Madduri and Sivasankaran Rajamanickam, 2020, "Scalable, Multi-Constraint, Complex-Objective Graph Partitioning", IEEE Transactions on Parallel and Distributed Systems,
**31**, (12), pp. 13

- Bei Wang, Stephane Ethier, William Tang, Khaled Z. Ibrahim, Kamesh Madduri, Samuel Williams and Leonid Oliker, 2019, "Modern Gyrokinetic Particle-In-Cell Simulation of Fusion Plasmas on Top Supercomputers", SAGE International Journal of High Performance Computing Applications (IJHPCA),
**33**, (1), pp. 20

- H. Zhan, G. Gomes, X. S. Li, Kamesh Madduri, A. Sim and K. Wu, 2018, "Consensus Ensemble System for Traffic Flow Prediction", IEEE Transactions on Intelligent Transportation Systems,
**19**, (12), pp. 3903-3914

- Lorne Leonard, Alan Maceachren and Kamesh Madduri, 2017, "Graph-based visual analysis for large-scale hydrological modeling", SAGE Information Visualization,
**16**, (3), pp. 205-216

- George M Slota, Kamesh Madduri and Sivasankaran Rajamanickam, 2016, "Complex Network Partitioning using Label Propagation", SIAM Journal on Scientific Computing,
**38**, (5), pp. S620–S645

- Lorne Leonard, Kamesh Madduri and Christopher J Duffy, 2016, "Tuning Heterogeneous Computing Platforms for Large-scale Hydrology Data Management", IEEE Transactions on Parallel and Distributed Systems,
**27**, (9), pp. 2753-2765

- George M. Slota and Kamesh Madduri, 2015, "Parallel color-coding", Parallel Computing,
**47**, pp. 51–69

- Khaled Z Ibrahim, Kamesh Madduri, Samuel Williams, Bei Wang, Stéphane Ethier and Leonid Oliker, 2013, "Analysis and optimization of gyrokinetic toroidal simulations on homogenous and heterogenous platforms", International Journal of High Performance Computing Applications,
**27**, (4), pp. 454–473

- Kamesh Madduri, Jimmy Su, Samuel Williams, Leonid Oliker, Stéphane Ethier and Katherine A. Yelick, 2012, "Optimization of Parallel Particle-to-Grid Interpolation on Leading Multicore Platforms", IEEE Transactions on Parallel and Distributed Systems,
**23**, (10), pp. 1915–1922

- Kamesh Madduri, Eun-Jin Im, Khaled Z. Ibrahim, Samuel Williams, Stéphane Ethier and Leonid Oliker, 2011, "Gyrokinetic particle-in-cell optimization on emerging multi- and manycore platforms", Parallel Computing,
**37**, (9), pp. 501–520

- K. Subramani and Kamesh Madduri, 2010, "Two-level heaps: a new priority queue structure with applications to the single source shortest path problem", Computing,
**90**, (3-4), pp. 113–130

- James B. Orlin, Kamesh Madduri, K. Subramani and Matthew D. Williamson, 2010, "A faster algorithm for the single source shortest path problem with few distinct positive lengths", Journal of Discrete Algorithms,
**8**, (2), pp. 189–198

- K. Subramani, C. Tauras and Kamesh Madduri, 2010, "Space-time tradeoffs in negative cycle detection - an empirical analysis of the Stressing Algorithm", Applied Mathematics and Computation,
**215**, (10), pp. 3563–3575

- David A. Bader and Kamesh Madduri, 2008, "A graph-theoretic analysis of the human protein-interaction network using multicore parallel algorithms", Parallel Computing,
**34**, (11), pp. 627–639

- K. Subramani and Kamesh Madduri, 2008, "A Randomized Queueless Algorithm for Breadth-First Search", International Journal of Computers and Their Applications,
**15**, (3), pp. 177–186

- David A. Bader, Virat Agarwal, Kamesh Madduri and Seunghwa Kang, 2007, "High performance combinatorial algorithm design on the cell broadband engine processor", Parallel Computing,
**33**, (10-11), pp. 720–740

**Conference Proceedings**

- Michael S Gilbert, Seher Acer, Erik G Boman, Kamesh Madduri and Sivasankaran Rajamanickam, 2021, "Fast Spectral Graph Layout on Multicore Platforms", pp. 213-222

- Ashirbad Mishra, Shad Kirmani and Kamesh Madduri, 2020, "Fast Spectral Graph Layout on Multicore Platforms", pp. 11

- V. Rengasamy, Mahmut T Kandemir, Paul Medvedev and Kamesh Madduri, 2018, "Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data"

- H. Zhan, G. Gomes, X. S. Li, Kamesh Madduri and K. Wu, 2018, "Efficient Online Hyperparameter Learning for Traffic Flow Prediction"

- S. Kirmani and Kamesh Madduri, 2018, "Spectral Graph Drawing: Building Blocks and Performance Analysis"

- Humayun Kabir and Kamesh Madduri, 2017, "Shared-memory Graph Truss Decomposition",
*Proceedings of the 24th IEEE International Conference on High Performance Computing, Data, and Analytics (HiPC), Jaipur, India*, pp. 13-22

- Vasudevan Rengasamy, Tao-Yang Fu, Wang Lee and Kamesh Madduri, 2017, "Optimizing Word2Vec Performance on Multicore Systems",
*Proceedings of the 7th Workshop on Irregular Applications: Architectures and Algorithms (IA3), Denver, CO*, pp. 1-9

- Jagadish B Kotra, Seongbeom Kim, Kamesh Madduri and Mahmut T Kandemir, 2017, "Congestion-Aware Memory Management on NUMA Platforms: A VMware ESXi case study",
*Proceedings of the 13th IEEE International Symposium on Workload Characterization (IISWC), Seattle, WA*, pp. 146-155

- Humayun Kabir and Kamesh Madduri, 2017, "Parallel k-truss Decomposition on Multicore Systems",
*Proceedings of the 21st IEEE High Performance Extreme Computing (HPEC) Conference, Waltham, MA*, pp. 1-7

- Humayun Kabir and Kamesh Madduri, 2017, "Parallel k-core Decomposition on Multicore Platforms",
*Proceedings of the Second IEEE Workshop on Parallel and Distributed Processing for Computational Social Systems (ParSocial), Orlando, FL*, pp. 1482-1491

- Ramachandran K. Narayanan and Kamesh Madduri, 2017, "Parallel Particle-in-Cell Performance Optimization: A Case Study of Electrospray Simulation",
*Proceedings of the 18th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC), Orlando, FL*, pp. 1158-1167

- Hongyuan Zhan and Kamesh Madduri, 2017, "Analyzing Community Structure in Networks",
*Proceedings of the First IEEE Workshop on the Intersection of Graph Algorithms and Machine Learning (GraML), Orlando, FL*, pp. 1540-1547

- Sindhuja Parimalarangan, George M. Slota and Kamesh Madduri, 2017, "Fast Parallel Graph Triad Census and Triangle Counting on Shared-memory Platforms",
*Proceedings of the Second IEEE Workshop on Parallel and Distributed Processing for Computational Social Systems (ParSocial), Orlando, FL*, pp. 1500-1509

- George M. Slota, Sivasankaran Rajamanickam, Karen Devine and Kamesh Madduri, 2017, "Partitioning Trillion-Edge Graphs in Minutes",
*Proceedings of the 31st IEEE International Parallel and Distributed Processing Symposium (IPDPS), Orlando, FL*, pp. 646-655

- George M. Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2017, "Order or Shuffle: Empirically Evaluating Vertex Order Impact on Parallel Graph Computations",
*Proceedings of the 4th IEEE Workshop on Graph Algorithms Building Blocks (GABB), Orlando, FL*, pp. 588-597

- Vasudevan Rengasamy, Paul Medvedev and Kamesh Madduri, 2017, "Parallel and Memory-efficient Preprocessing for Metagenome Assembly",
*Proceedings of the 16th IEEE International Workshop on High Performance Computational Biology (HiCOMB), Orlando, FL*, pp. 283-292

- William Tang, Bei Wang, Stephane Ethier, Grzegorz Kwasniewski, Torsten Hoefler, Khaled Z Ibrahim, Kamesh Madduri, Samuel Williams, Leonid Oliker, Carlos Rosales-Fernandez and Tim Williams, 2016, "Extreme Scale Plasma Turbulence Simulations on Top Supercomputers Worldwide",
*Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2016), Salt Lake City, UT*

- George Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2016, "HPCGraph: Benchmarking Massive Graph Analytics on Supercomputers", pp. 2

- Vasudevan Rengasamy and Kamesh Madduri, 2016, "SPRITE: A Fast Parallel SNP Detection Pipeline", pp. 159-177

- George M Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2016, "A Case Study of Complex Graph Analysis in Distributed Memory: Implementation and Optimization", pp. 293-302

- Hongyuan Zhan and Kamesh Madduri, 2016, "Graph Sparsification as a Knapsack Problem Formulation", pp. 8

- Lorne Leonard, Kamesh Madduri and Christopher J Duffy, 2015, "Graph-based Analysis for Large-scale Hydrological Modelling", pp. 4

- Kamesh Madduri, Vasudevan Rengasamy and Paul Medvedev, 2015, "SPRITE: A fast parallel SNP detection pipeline (poster)", pp. 1

- George M. Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2015, "High-Performance Graph Analytics on Manycore Processors", pp. 17–27

- George M Slota and Kamesh Madduri, 2014, "Simple Parallel Biconnectivity Algorithms for Multicore Platforms", pp. 10

- George M Slota and Kamesh Madduri, 2014, "Parallel complex network partitioning (poster)", pp. 1

- George M Slota, Kamesh Madduri and Sivasankaran Rajamanickam, 2014, "PuLP: Scalable multi-objective multi-constraint partitioning for small-world networks", pp. 481-490

- Thap Panitanarak and Kamesh Madduri, 2014, "Performance analysis of single-source shortest path algorithms on distributed-memory systems", pp. 60-63

- George M Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2014, "BFS and coloring-based parallel algorithms for strongly connected components and related problems", pp. 550–559

- George M Slota and Kamesh Madduri, 2014, "Complex network analysis using parallel approximate motif counting", pp. 405–414

- Jee Choi, Aparna Chandramowlishwaran, Kamesh Madduri and Richard Vuduc, 2014, "A CPU: GPU hybrid implementation and model-driven scheduling of the fast multipole method", pp. 8

- Bei Wang, Stéphane Ethier, William M. Tang, Timothy J. Williams, Khaled Z. Ibrahim, Kamesh Madduri, Samuel Williams and Leonid Oliker, 2013, "Kinetic turbulence simulations at extreme scale on leadership-class systems", pp. 12

- George M Slota and Kamesh Madduri, 2013, "Fast Approximate Subgraph Counting and Enumeration", pp. 210–219

- George Slota and Kamesh Madduri, 2013, "FASCIA: Fast Approximate Subgraph Counting and Enumeration (poster)", pp. 1

- David Hadka, Kamesh Madduri and Patrick M Reed, 2013, "Scalability Analysis of the Asynchronous, Master-Slave Borg Multiobjective Evolutionary Algorithm", pp. 425–434

- Michael R. Frasca, Kamesh Madduri and Padma Raghavan, 2012, "NUMA-aware graph mining techniques for performance and energy efficiency", pp. 11

- Bei Wang, Stéphane Either, William M. Tang, Khaled Z. Ibrahim, Kamesh Madduri, Samuel W. Williams, Leonid Oliker and Timothy J. Williams, 2012, "Advances in Gyrokinetic Particle in Cell Simulation for Fusion Plasmas to Extreme Scale (poster)", pp. 1439–1440

- Aparna Chandramowlishwaran, JeeWhan Choi, Kamesh Madduri and Richard W. Vuduc, 2012, "Brief announcement: towards a communication optimal fast multipole method and its implications at exascale", pp. 182–184

- Aydin Buluc and Kamesh Madduri, 2012, "Graph partitioning for scalable distributed graph computations", pp. 16

- Aydin Buluc and Kamesh Madduri, 2011, "Parallel breadth-first search on distributed memory systems", pp. 12

- Kamesh Madduri, Khaled Z. Ibrahim, Samuel Williams, Eun-Jin Im, Stéphane Ethier, John Shalf and Leonid Oliker, 2011, "Gyrokinetic toroidal simulations on leading multi- and manycore HPC systems", pp. 12

- Kamesh Madduri and Kesheng Wu, 2011, "Massive-Scale RDF Processing Using Compressed Bitmap Indexes", pp. 470–479

- Rajesh Sudarsan, Julian Borrill, Christopher Cantalupo, Theodore Kisner, Kamesh Madduri, Leonid Oliker, Yili Zheng and Horst Simon, 2011, "Cosmic microwave background map-making at the petascale and beyond", pp. 305–316

- Aparna Chandramowlishwaran, Kamesh Madduri and Richard W. Vuduc, 2010, "Diagnosis, Tuning, and Redesign for Multicore Performance: A Case Study of the Fast Multipole Method", pp. 12

- E. Strohmaier, S. Williams, A. Kaiser, Kamesh Madduri, K. Ibrahim, D. Bailey and J. Demmel, 2010, "A Kernel Testbed for Parallel Architecture, Language, and Performance Research", pp. 1297-1300

- Kesheng Wu, Kamesh Madduri and Shane Canon, 2010, "Multi-level bitmap indexes for flash memory storage", pp. 114–116

- A. Kaiser, S. Williams, Kamesh Madduri, K. Ibrahim, D. Bailey, J. Demmel and E. Strohmaier, 2010, "A Principled Kernel Testbed for Hardware/Software Co-Design Research", pp. 7

- Kamesh Madduri and Kesheng Wu, 2009, "Efficient joins with compressed bitmap indexes", pp. 1017–1026

- Kamesh Madduri, Samuel Williams, Stéphane Ethier, Leonid Oliker, John Shalf, Erich Strohmaier and Katherine A. Yelick, 2009, "Memory-efficient optimization of Gyrokinetic particle-to-grid interpolation for multicore processors", pp. 12

- K. Subramani and Kamesh Madduri, 2009, "Two-Level Heaps: A New Priority Queue Structure with Applications to the Single Source Shortest Path Problem", pp. 186–196

- Xiaofeng Gu, Kamesh Madduri, K. Subramani and Hong-Jian Lai, 2009, "Improved Algorithms for Detecting Negative Cost Cycles in Undirected Graphs", pp. 40–50

- Kamesh Madduri, David Ediger, Karl Jiang, David A. Bader and Daniel G. Chavarría-Miranda, 2009, "A faster parallel algorithm and efficient multithreaded implementations for evaluating betweenness centrality on massive datasets", pp. 8

- Kamesh Madduri and David A. Bader, 2009, "Compact graph representations and parallel connectivity algorithms for massive dynamic network analysis", pp. 11

- David A. Bader and Kamesh Madduri, 2008, "SNAP: Small-world Network Analysis and Partitioning: An open-source parallel graph framework for the exploration of large-scale networks", pp. 12

- K. Subramani and Kamesh Madduri, 2007, "Accomplishing Approximate FCFS Fairness Without Queues", pp. 540–551

- David A. Bader, Shiva Kintali, Kamesh Madduri and Milena Mihail, 2007, "Approximating Betweenness Centrality", pp. 124–137

- David A. Bader and Kamesh Madduri, 2007, "A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multicore Parallel Algorithms", pp. 8

- David A. Bader, Virat Agarwal and Kamesh Madduri, 2007, "On the Design and Analysis of Irregular Algorithms on the Cell Processor: A Case Study of List Ranking", pp. 10

- David A. Bader, Varun Kanade and Kamesh Madduri, 2007, "SWARM: A Parallel Programming Framework for Multicore Processors", pp. 8

- Joseph R. Crobak, Jonathan W. Berry, Kamesh Madduri and David A. Bader, 2007, "Advanced Shortest Paths Algorithms on a Massively-Multithreaded Architecture", pp. 8

- Kamesh Madduri, David A. Bader, Jonathan W. Berry and Joseph R. Crobak, 2007, "An Experimental Study of a Parallel Shortest Path Algorithm for Solving Large-Scale Graph Instances"

- Kamesh Madduri, D. Bader, J. Berry and J. Crobak, 2006, "Parallel Shortest Path Algorithms for Solving Large-scale Instances", pp. 40

- David A. Bader and Kamesh Madduri, 2006, "Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2", pp. 523–530

- David A. Bader and Kamesh Madduri, 2006, "Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks", pp. 539–550

- David A. Bader and Kamesh Madduri, 2005, "Design and Implementation of the HPCS Graph Analysis Benchmark onSymmetric Multiprocessors", pp. 465–476

- David A. Bader and Kamesh Madduri, 2004, "A Parallel State Assignment Algorithm for Finite State Machines", pp. 297–308

- Kamesh Madduri, K. H. Aparna and V. S. Chakravarthy, 2004, "PATRAM: A handwritten word processor for Indian languages", pp. 557–562

**Other**

- S. Kirmani and Kamesh Madduri, 2018, "A Fast and Simple Multilevel Spectral Graph Drawing Algorithm"

- Hongyuan Zhan and Kamesh Madduri, 2016, "A Combinatorially-Interpretable Matrix Factorization for Network Community Structure Evaluation", pp. 37

- George M Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2015, "PuLP: Complex objective partitioning of small-world networks using label propagation", pp. 28

- George Slota, Kamesh Madduri and Sivasankaran Rajamanickam, 2014, "BFS and Coloring-based Parallel Algorithms for Strongly Connected Components and Related Problems"

- George M Slota and Kamesh Madduri, 2014, "Complex Network Analysis using Parallel Approximate Motif Counting"

- George M Slota and Kamesh Madduri, 2014, "Characterizing biological networks using subgraph counting and enumeration", pp. 31

- George M Slota, Sivasankaran Rajamanickam and Kamesh Madduri, 2014, "Parallel strongly connected components in shared memory architectures", pp. 51

- Kamesh Madduri, 2013, "Parallel analysis of large graph-structured data in genomics and proteomics", pp. 1

- Kamesh Madduri, 2012, "High-performance Metagenomic Data Clustering and Assembly", pp. 28

- Kamesh Madduri, 2012, "Scalable SPARQL Querying with Compressed Bitmap Indexes", pp. 17

- Kamesh Madduri, 2011, "Optimizing Short-read Genome Assembly Algorithms for Emerging Multicore Platforms", pp. 37

- Kamesh Madduri, 2010, "Hybrid Parallel Programming for Massive Graph Analysis", pp. 26

- Kamesh Madduri, 2009, "Scaling Up Graph Algorithms on Emerging Multicore Systems", pp. 22

- Kamesh Madduri, 2008, "High Performance Combinatorial Techniques for Processing Dynamic Interaction Networks", pp. 29

- David A Bader and Kamesh Madduri, 2007, "High Performance Combinatorial Techniques for Analyzing Massive Dynamic Interaction Networks"

- David A Bader and Kamesh Madduri, 2006, "Efficient Shared-memory Algorithms and Implementations for Solving Large-scale Graph Algorithms", pp. 28