News Paper Boy

Publications

Research papers that I co-authored published either as Journal Articles (or) in Conference Proceedings. DOI links to the papers are also given below. If you any trouble accessing the papers, please feel free to contact me.

Journal Articles

  1. Bhattaram, Swethasree, Sriram Chockalingam, Maneesha Aluru and Srinivas Aluru (2026). ‘scSAGA: Single-cell Sampled Gromov Wasserstein Alignment for Scalable and Memory-efficient Integration of Multi-modal Single Cell Data’. In: bioRxiv. DOI: 10.64898/2026.03.26.714573.
  2. Chockalingam, Sriram P, Maneesha Aluru and Srinivas Aluru (2025). ‘SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data’. In: Bioinformatics 41.2, btaf057. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btaf057.
  3. Connolly, Erin, Tony Pan, Maneesha Aluru, Sriram Chockalingam, Vishal Dhere and Greg Gibson (2024). ‘Loss of immune cell identity with age inferred from large atlases of single cell transcriptomes’. In: Aging Cell 23.12. e14306 ACE-24-0600.R1, e14306. DOI: 10.1111/acel.14306.
  4. Connolly, Erin, Maneesha Aluru, Sriram Chockalingam, Vishal Dhere, Greg Gibson and Tony Pan (2023). ‘Acceleration of Large-Scale Single Cell Differential Gene Expression Analysis with FastDE’. In: bioRxiv, pp. 2023–06. DOI: 10.1101/2023.06.15.545003.
  5. Pan, Tony C, Sriram P Chockalingam, Maneesha Aluru and Srinivas Aluru (2023). ‘MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework’. In: Bioinformatics 39.6, pp. 1–8. DOI : 10.1093/bioinformatics/btad373.
  6. Srivastava, Ankit, Sriram P Chockalingam and Srinivas Aluru (2023). ‘A parallel framework for constraint-based Bayesian network learning via Markov blanket discovery’. In: IEEE Transactions on Parallel and Distributed Systems. DOI : 10.1109/TPDS.2023.3244135.
  7. Aluru, Maneesha, Harsh Shrivastava, Sriram P Chockalingam, Shruti Shivakumar and Srinivas Aluru (2022). ‘EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks’. In: Bioinformatics 38.5, pp. 1312–1319. DOI: 10.1093/bioinformatics/btab829.
  8. Chockalingam, Sriram P, Jodh Pannu, Sahar Hooshmand, Sharma V Thankachan and Srinivas Aluru (2020). ‘An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction’. In: BMC bioinformatics 21.6, pp. 1–12. DOI: 10.1186/s12859-020-03738-5.
  9. Chockalingam, Sriram P, Sharma V Thankachan and Srinivas Aluru (2020). ‘Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings’. In: Journal of Parallel and Distributed Computing 144, pp. 68–79. DOI: 10.1016/j.jpdc.2020.05.018
  10. Rytsareva, Inna, David S Campo, Yueli Zheng, Seth Sims, Sharma V Thankachan, Cansu Tetik, Jain Chirag, Sriram P Chockalingam, Amanda Sue, Srinivas Aluru et al. (2017). ‘Efficient detection of viral transmissions with next-generation sequencing data’. In: BMC Genomics 18.4, p. 372. DOI: 10.1186/s12864-017-3732-4
  11. Thankachan, Sharma V, Sriram P Chockalingam, Yongchao Liu, Ambujam Krishnan and Srinivas Aluru (2017). ‘A greedy alignment-free distance estimator for phylogenetic inference’. In: BMC Bioinformatics 18.8, p. 238. DOI: 10.1186/s12859-017-1658-0
  12. Chockalingam, Sriram, Maneesha Aluru and Srinivas Aluru (2016). ‘Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories’. In: Microarrays 5.3, p. 23. DOI: 10.3390/microarrays5030023
  13. Thankachan, Sharma V, Sriram P Chockalingam, Yongchao Liu, Alberto Apostolico and Srinivas Aluru (2016). ‘ALFRED: a practical method for alignment-free distance computation’. In: Journal of Computational Biology 23.6, pp. 452–460. DOI: 10.1089/cmb.2015.0217
  14. Yang, Xiao, Sriram P Chockalingam and Srinivas Aluru (2012). ‘A survey of error-correction methods for next-generation sequencing’. In: Briefings in Bioinformatics 14.1, pp. 56–66. DOI: 10.1093/bib/bbs015

Conference Proceedings

  1. Srivastava, Ankit, Sriram P Chockalingam, Maneesha Aluru and Srinivas Aluru (2021). ‘Parallel construction of module networks’. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC’21), pp. 1–14. DOI: 10.1145/3458817.3476207
  2. Srivastava, Ankit, Sriram Chockalingam and Srinivas Aluru (2020). ‘A parallel framework for constraint-based bayesian network learning via markov blanket discovery’. In: 2020 SC20: International Conference for High Performance Computing, Networking, Storage and Analysis (SC’20). IEEE Computer Society, pp. 74–88. DOI: 10.5555/3433701.3433710
  3. Pannu, Jodh, Sahar Hooshmand, Sriram P. Chockalingam, Sharma V. Thankachan and Srinivas Aluru (2019). ‘An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction’. In: Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA). DOI: 10.1145/3233547.3233648
  4. Pannu, Jodh, Sriram P. Chockalingam, Sharma V. Thankachan and Srinivas Aluru (2018). ‘An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction’. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 540–540. DOI: 10.1145/3233547.3233648
  5. Thankachan, Sharma V, Chaitanya Aluru, Sriram P Chockalingam and Srinivas Aluru (2018). ‘Algorithmic framework for approximate matching under bounded edits with applications to sequence analysis’. In: Proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB), pp. 211–224. DOI: 10.1007/978-3-319-89929-9_14
  6. Vasimuddin, Md, Sriram P Chockalingam and Srinivas Aluru (2018). ‘A parallel algorithm for Bayesian network inference using arithmetic circuits’. In: Proceedings of the 32nd IEEE International Parallel & Distributed Processing Symposium (IPDPS), pp. 60–70. DOI: 10.1109/IPDPS.2018.00014
  7. Chockalingam, Sriram P, Maneesha Aluru, Hongqing Guo, Yanhai Yin and Srinivas Aluru (2017). ‘Reverse engineering gene networks: A comparative study at genome-scale’. In: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 480–490. DOI: 10.1145/3107411.3107428
  8. Jammula, Nagakishore, Sriram P Chockalingam and Srinivas Aluru (2017). ‘Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses’. In: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 417–424. DOI: 10.1145/3107411.3107491
  9. Nihalani, Rahul, Sriram P Chockalingam, Shaowei Zhu, Vijay Vazirani and Srinivas Aluru (2017). ‘Probabilistic estimation of overlap graphs for large sequence datasets’. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 247–252. DOI: 10.1109/BIBM.2017.8217657
  10. Chockalingam, Sriram P, Sharma V Thankachan and Srinivas Aluru (2016). ‘A parallel algorithm for finding all pairs k-mismatch maximal common substrings’. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC’16), p. 67. DOI: 10.1109/SC.2016.66.
  11. Thankachan, Sharma V, Sriram P Chockalingam and Srinivas Aluru (2016). ‘An efficient algorithm for finding all pairs k-mismatch maximal common substrings’. In: Proceedings of the International Symposium on Bioinformatics Research and Applications (ISBRA), pp. 3–14. DOI: 10.1007/978-3-319-38782-6_1
  12. Chockalingam, Sriram P, Maneesha Aluru and Srinivas Aluru (2015). ‘Information theory based genome-scale gene networks construction using MapReduce’. In: Proceedings of the 22nd IEEE International Conference on High Performance Computing (HiPC), pp. 464–473. DOI: 10.1109/HiPC.2015.29
  13. Jammula, Nagakishore, Sriram Chockalingam and Srinivas Aluru (2015). ‘Parallel read error correction for big genomic datasets’. In: Proceedings of the 22nd IEEE International Conference on High Performance Computing (HiPC), pp. 446–455. DOI: 10.1109/HiPC.2015.47.
  14. Rytsareva, Inna, David S Campo, Yueli Zheng, Seth Sims, Cansu Tetik, Jain Chirag, Siram P Chockalingam, Sharma V Thankachan, Amanda Sue, Srinivas Aluru et al. (2015). ‘Efficient detection of viral transmission with threshold-based methods’. In: Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), pp. 1–6. DOI: 10.1109/ICCABS.2015.7344723.
  15. Misra, Sanchit, Md Vasimuddin, Kiran Pamnany, Sriram P Chockalingam, Yong Dong, Min Xie, Maneesha R Aluru and Srinivas Aluru (2014). ‘Parallel bayesian network structure learning for genome-scale gene networks’. In: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC’14), pp. 461–472. DOI: 10.1109/SC.2014.43.
  16. Shah, Ankit R, Sriram Chockalingam and Srinivas Aluru (2012). ‘A parallel algorithm for spectrum-based short read error correction’. In: Proceedings of the 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS), pp. 60–70. DOI: 10.1109/IPDPS.2012.16