| 2023 | HiPC | Fast Parallel Tensor Times Same Vector for Hypergraphs. | Shruti Shivakumar, Ilya Amburg, Sinan G. Aksoy, Jiajia Li, Stephen J. Young, Srinivas Aluru |
| 2022 | RECOMB | The Complexity of Approximate Pattern Matching on de Bruijn Graphs. | Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru |
| 2022 | WABI | Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. | Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru |
| 2021 | SC | Parallel construction of module networks. | Ankit Srivastava, Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru |
| 2020 | ICLR | GLAD: Learning Sparse Graph Recovery. | Harsh Shrivastava, Xinshi Chen, Binghong Chen, Guanghui Lan, Srinivas Aluru, Han Liu, Le Song |
| 2020 | SC | A parallel framework for constraint-based bayesian network learning via markov blanket discovery. | Ankit Srivastava, Sriram P. Chockalingam, Srinivas Aluru |
| 2019 | RECOMB | On the Complexity of Sequence to Graph Alignment. | Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru |
| 2019 | SC | Distributed enhanced suffix arrays: efficient algorithms for construction and querying. | Patrick Flick, Srinivas Aluru |
| 2019 | WABI | Validating Paired-End Read Alignments in Sequence Graphs. | Chirag Jain, Haowen Zhang, Alexander T. Dilthey, Srinivas Aluru |
| 2018 | RECOMB | Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. | Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru |
| 2018 | SC | Optimizing high performance distributed memory parallel hash tables for DNA | Tony C. Pan, Sanchit Misra, Srinivas Aluru |
| 2017 | HiPC | Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks. | Md. Vasimuddin, Srinivas Aluru |
| 2017 | RECOMB | A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. | Chirag Jain, Alexander T. Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy |
| 2016 | HiPC | Genomes Galore: Big Data Challenges in the Life Sciences. | Srinivas Aluru |
| 2016 | ICPP | Programming Techniques for the Automata Processor. | Indranil Roy, Ankit Srivastava, Srinivas Aluru |
| 2016 | SC | A parallel algorithm for finding all pairs | Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru |
| 2016 | SC | Parallel Interval Stabbing on the Automata Processor. | Indranil Roy, Ankit Srivastava, Matt Grimm, Srinivas Aluru |
| 2016 | SBAC-PAD | Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters. | Yongchao Liu, Tony Pan, Srinivas Aluru |
| 2015 | HiPC | Big data in life sciences and public health. | Srinivas Aluru |
| 2015 | HiPC | Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce. | Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru |
| 2015 | HiPC | Parallel Read Error Correction for Big Genomic Datasets. | Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru |
| 2015 | RECOMB | Efficient Alignment Free Sequence Comparison with Bounded Mismatches. | Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan |
| 2015 | SC | Parallel distributed memory construction of suffix and longest common prefix arrays. | Patrick Flick, Srinivas Aluru |
| 2015 | SC | A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications. | Patrick Flick, Chirag Jain, Tony Pan, Srinivas Aluru |
| 2014 | SC | Parallel Bayesian Network Structure Learning for Genome-Scale Gene Networks. | Sanchit Misra, Md. Vasimuddin, Kiran Pamnany, Sriram P. Chockalingam, Yong Dong, Min Xie, Maneesha R. Aluru, Srinivas Aluru |
| 2012 | SC | Parallel Bayesian network structure learning with application to gene networks. | Olga Nikolova, Srinivas Aluru |
| 2012 | TAMC | An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval. | Xiao Yang, Florian Sikora, Guillaume Blin, Sylvie Hamel, Romeo Rizzi, Srinivas Aluru |
| 2011 | ICPP | Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks. | Olga Nikolova, Srinivas Aluru |
| 2010 | ICPP | A MapReduce Style Framework for Computations on Trees. | William Sarje, Srinivas Aluru |
| 2009 | HiPC | A parallel algorithm for exact Bayesian network inference. | Olga Nikolova, Jaroslaw Zola, Srinivas Aluru |
| 2009 | ICPP | Constructing Gene Regulatory Networks on Clusters of Cell Processors. | Jaroslaw Zola, Abhinav Sarje, Srinivas Aluru |
| 2008 | HiPC | Parallel Information Theory Based Construction of Gene Regulatory Networks. | Jaroslaw Zola, Maneesha Aluru, Srinivas Aluru |
| 2008 | ICPP | Parallel Construction of Bidirected String Graphs for Genome Assembly. | Benjamin G. Jackson, Srinivas Aluru |
| 2008 | ICPP | Tracking Nanostructural Evolution in Alloys: Large-Scale Analysis of Atom Probe Tomography Data on Blue Gene/L. | Sudip Seal, Michael Moody, Anna Ceguerra, Simon P. Ringer, Krishna Rajan, Srinivas Aluru |
| 2007 | COCOON | The Combinatorics of Sequencing the Corn Genome. | Srinivas Aluru |
| 2007 | SC | Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. | Michael Ott, Jaroslaw Zola, Alexandros Stamatakis, Srinivas Aluru |
| 2007 | SPIRE | Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage. | Pang Ko, Srinivas Aluru |
| 2006 | CPM | Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. | Pang Ko, Srinivas Aluru |
| 2006 | ICPP | A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition. | Srikanta Tirthapura, Sudip Seal, Srinivas Aluru |
| 2006 | SC | M11 - High-performance computing methods for computational genomics. | Srinivas Aluru, David A. Bader, Anantharaman Kalyanaraman |
| 2003 | CPM | Space Efficient Linear Time Construction of Suffix Arrays. | Pang Ko, Srinivas Aluru |
| 2003 | ICCCN | Scalable, memory efficient, high-speed lookup and update algorithms for IP routing. | Natsuhiko Futamura, Rama Sangireddy, Srinivas Aluru, Arun K. Somani |
| 2003 | ICPP | Space and Time Optimal Parallel Sequence Alignments. | Stjepan Rajko, Srinivas Aluru |
| 2002 | CLUSTER | Mixed Mode Matrix Multiplication. | Meng-Shiou Wu, Srinivas Aluru, Ricky A. Kendall |
| 2002 | HiPC | Parallel Syntenic Alignments. | Natsuhiko Futamura, Srinivas Aluru, Xiaoqiu Huang |
| 2002 | ICPP | Space and Time Efficient Parallel Algorithms and Software for EST Clustering. | Anantharaman Kalyanaraman, Srinivas Aluru, Suresh C. Kothari |
| 2002 | SC | A scalable parallel fast multipole method for analysis of scattering from perfect electrically conducting surfaces. | Bhanu Hariharan, Srinivas Aluru, Balasubramaniam Shanker |
| 2001 | HiPC | Efficient Parallel Algorithms and Software for Compressed Octrees with Applications to Hierarchical Methods. | Bhanu Hariharan, Srinivas Aluru |
| 1999 | HiPC | A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation. | Srinivas Aluru, Desh Ranjan, Natsuhiko Futamura |
| 1999 | PDPTA | A Practical Parallel Algorithm for Line Segment Visibility. | Srinivas Aluru, Songrit Maneewongvatana |
| 1999 | SC | A Unifying Data Structure for Hierarchical Methods. | Fatih Erdogan Sevilgen, Srinivas Aluru |
| 1997 | HiPC | Parallel domain decomposition and load balancing using space-filling curves. | Srinivas Aluru, Fatih Erdogan Sevilgen |
| 1996 | ICS | Parallel Construction of Multidimensional Binary Search Trees. | Ibraheem Al-Furaih, Srinivas Aluru, Sanjay Goil, Sanjay Ranka |
| 1996 | ICS | Parallel Additive Lagged Fibonacci Random Number Generators. | Srinivas Aluru |
| 1996 | PDPTA | Practical Paralle1 Algorithm for Constructing Line Arrangements. | Srinivas Aluru, Songrit Maneewongvatana |
| 1995 | ICPP | Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators. | Srinivas Aluru |
| 1994 | SC | Truly distribution-independent algorithms for the N-body problem. | Srinivas Aluru, Gurpur M. Prabhu, John L. Gustafson |
| 1993 | ICS | A Massively Parallel Optimizer for Expression Evaluation. | Srinivas Aluru, John L. Gustafson |