At Work

Research

I am interested in the field of computational biology, specifically in the use of parallel computing to construct cellular and gene regulatory networks from gene expression data. I am also interested in developing parallel algorithms in the analysis of high-throughput sequencing reads such as error correction and clustering.

Software

  1. ALFRED is a Alignment Free Distance Estimator software for Phylogenetic Inference. It is based on the metric of average common substring.
  2. PSbEC is a parallel spectrum based error correction software for reads from high-throughput sequencing machines.

Publications

  1. Sriram P. Chockalingam, Sharma V. Thankachan, and Srinivas Aluru. 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), p. 67., 2016.
  2. Sharma V. Thankachan, Sriram P. Chockalingam, and Srinivas Aluru. 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., 2016.
  3. Sriram Chockalingam, Maneesha Aluru, and Srinivas Aluru. Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories. Microarrays. Vol. 5, No. 3 (2016): p. 23.
  4. Sriram P. Chockalingam, Maneesha Aluru and Srinivas Aluru. 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., 2015.
  5. Nagakishore Jammula, Sriram Chockalingam, and Srinivas Aluru. Parallel Read Error Correction for Big Genomic Datasets. In Proceedings of the 22nd IEEE International Conference on High Performance Computing (HiPC), pp. 446-455., 2015.
  6. Sharma V. Thankachan, Sriram Chockalingam, Yongchao Liu, Ambujam Krishnan and Srinivas Aluru. A greedy alignment-free distance estimator for phylogenetic inference. In Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2015.
  7. Inna Rytsareva, David S Campo, Yueli Zheng, Seth Sims, Cansu Tetik, Jain Chirag, Sriram Chockalingam, Sharma Thankachan, Amanda Sue, Srinivas Aluru and Yury Khudyakov. 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), 2015.
  8. Sudip Misra, Md Vasimuddin, Kiran Pamnany, Sriram Chockalingam, Yong Dong, Min Xie, Maneesha Aluru, and Srinivas Aluru. 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), 2014.
  9. Ankit R. Shah, Sriram P. Chockalingam, and Srinivas Aluru. A Parallel Algorithm for Spectrum-based Short Read Error Correction. In Proceedings of the 26th IEEE International Symposium on Parallel and Distributed Processing (IPDPS), 2012.
  10. Xiao Yang, Chockalingam, Sriram P. Chockalingam, and Srinivas Aluru. A survey of error-correction methods for next-generation sequencing. Briefings in Bioinformatics. April 2012. doi: 10.1093/bib/bbs015

Past Life

Prior to being a Ph.D student, I used to work as a software engineer in an IT consultancy company. I have over eight years of experience as a software engineer, four of which I was also as a project leader. My work involved in developing software to manage multiple versions of product engineering designs, all throughout the product's life cycle. A summary of my past work is here.