A Parallel Algorithm for Spectrum-based Short Read Error Correction. - Ankit Shah; Sriram P. Chockalingam; Srinivas Aluru (IPDPS, 2012)

A survey of error-correction methods for next-generation sequencing. - Xiao Yang; Sriram P. Chockalingam; Srinivas Aluru (Briefings Bioinform., 2013)

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 (SC, 2014)

Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce. - Sriram P. Chockalingam; Maneesha Aluru; Srinivas Aluru (HiPC, 2015)

Parallel Read Error Correction for Big Genomic Datasets. - Nagakishore Jammula; Sriram P. Chockalingam; Srinivas Aluru (HiPC, 2015)

Efficient detection of viral transmission with threshold-based methods. - Inna Rytsareva; Seth Sims; Sriram P. Chockalingam; Srinivas Aluru; David S. Campo; Cansu Tetik; Sharma V. Thankachan; Yury Khudyakov; Yueli Zheng; Chirag Jain; Amanda Sue (ICCABS, 2015)

A greedy alignment-free distance estimator for phylogenetic inference (extended abstract). - Sharma V. Thankachan; Sriram P. Chockalingam; Yongchao Liu; Ambujam Krishnan; Srinivas Aluru (ICCABS, 2015)

An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. - Sharma V. Thankachan; Sriram P. Chockalingam; Srinivas Aluru (ISBRA, 2016)

A parallel algorithm for finding all pairs k-mismatch maximal common substrings. - Sriram P. Chockalingam; Sharma V. Thankachan; Srinivas Aluru (SC, 2016)

ALFRED: A Practical Method for Alignment-Free Distance Computation. - Sharma V. Thankachan; Sriram P. Chockalingam; Yongchao Liu; Alberto Apostolico; Srinivas Aluru (J. Comput. Biol., 2016)

Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. - Sriram P. Chockalingam; Maneesha Aluru; Hongqing Guo; Yanhai Yin; Srinivas Aluru (BCB, 2017)

Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses. - Nagakishore Jammula; Sriram P. Chockalingam; Srinivas Aluru (BCB, 2017)

Probabilistic estimation of overlap graphs for large sequence datasets. - Rahul Nihalani; Sriram P. Chockalingam; Shaowei Zhu 001; Vijay V. Vazirani; Srinivas Aluru (BIBM, 2017)

A greedy alignment-free distance estimator for phylogenetic inference. - Sharma V. Thankachan; Sriram P. Chockalingam; Yongchao Liu; Ambujam Krishnan; Srinivas Aluru (BMC Bioinform., 2017)

An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction. - Jodh Pannu; Sriram P. Chockalingam; Sharma V. Thankachan; Srinivas Aluru (BCB, 2018)

A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits. - Md. Vasimuddin; Sriram P. Chockalingam; Srinivas Aluru (IPDPS, 2018)

Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. - Sharma V. Thankachan; Chaitanya Aluru; Sriram P. Chockalingam; Srinivas Aluru (RECOMB, 2018)

An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction. - Sriram P. Chockalingam; Jodh Pannu; Sahar Hooshmand; Sharma V. Thankachan; Srinivas Aluru (BMC Bioinform., 2020)

Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings. - Sriram P. Chockalingam; Sharma V. Thankachan; Srinivas Aluru (J. Parallel Distributed Comput., 2020)

Parallel construction of module networks. - Ankit Srivastava; Sriram P. Chockalingam; Maneesha Aluru; Srinivas Aluru (SC, 2021)

EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks. - Maneesha Aluru; Harsh Shrivastava 001; Sriram P. Chockalingam; Shruti Shivakumar; Srinivas Aluru (Bioinform., 2022)

A Parallel Framework for Constraint-Based Bayesian Network Learning via Markov Blanket Discovery. - Ankit Srivastava; Sriram P. Chockalingam; Srinivas Aluru (IEEE Trans. Parallel Distributed Syst., 2023)

Datasets for evaluating SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data. - Sriram P. Chockalingam; Maneesha Aluru; Srinivas Aluru (Zenodo, 2024)