I have organized the String Algorithms in Bioinformatics Workshop (StringBio), 2018 at UCF Campus (click here for details)
BioSketch: I am currently an Assistant Professor in the department of computer science at University of Central Florida. Before joining UCF, I have worked as a Research Scientist/PostDoc in the School of Computational Science and Engineering, Georgia Institute o f Technology, Atlanta with Prof. Srinivas Aluru and in the Cheriton School of Computer Science, University of Waterloo, Canada with Prof. J. Ian Munro. My Ph.D. is in Computer Science from Louisiana State University (Spring 2014), supervised by Prof. Rahul Shah. My Bachelor degree is in EEE from National Institute of Technology Calicut, India.
Research: I work in the areas of String Algorithms and Bioinformatics, Succinct/Compressed Data Structures and High Performance Computing. My research is supported in part by the US National Science Foundation (NSF) under CCF-1703489 and startup funds from UCF.
Selected Publications: The complete list of my publications can be found in DBLP or Google Scholar.
- Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru: Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. 22nd Annual International Conference in Research in Computational Molecular Biology (RECOMB), 2018 [link].
- Arnab Ganguly, Rahul Shah, and Sharma V. Thankachan: pBWT: Achieving Succinct Data Structures for Parameterized Pattern Matching, and Related Problems. 28th ACM-SIAM Symposium on Discrete Algorithms (SODA), 2017 [pdf].
- Sriram P. Chockalingam, Sharma V. Thankachan, Srinivas Aluru: A parallel algorithm for finding all pairs k-mismatch maximal common substrings. International Conference for High Performance Computing, Networking, Storage and Analysis (Super Computing, SC), 2016 [link].
- Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan: Efficient Alignment Free Sequence Comparison with Bounded Mismatches. 19th Annual International Conference in Research in Computational Molecular Biology (RECOMB), 2015 [link].
- Wing-Kai Hon, Rahul Shah, Sharma V. Thankachan, Jeffrey Scott Vitter: Space-Efficient Frameworks for Top-k String Retrieval. Journal of the ACM (JACM), 61(2), 2014 [pdf].
- COT 5405: Design and Analysis of Algorithms (Spring 2019)
- COP 3503: Computer Science II (Fall 2018)
- COT 6410: Computational Complexity (Spring 2017, Spring 2018)
- The 9th RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-SEQ), 2019.
- The 30th Annual Symposium on Combinatorial Pattern Matching (CPM), 2019.
- IEEE International Workshop on High Performance Computational Biology (HiCOMB), 2018, 2017 and 2016.
- IEEE International Conference on High Performance Computing, Data, and Analytics (HiPC), 2018 and 2017.
- International Symposium on String Processing and Information Retrieval (SPIRE), 2018.
- International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2018 and 2017.
- ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB), 2017.
- IEEE International Workshop on Foundations of Big Data Computing (BigDF), 2016.
- Annual Symposium on Combinatorial Pattern Matching (CPM), 2016.
- Paniz Abedin (PhD Student, Fall 2016 - Present)
- Justin Barry (PhD Student, Fall 2017 - Present)
- Dr. Gireesh Elakkat, MD (PhD Student, Fall 2018 - Present)
- Daniel Gibney (PhD Student, Fall 2018 - Present)
- Sahar Hooshmand (PhD Student, Spring 2017 - Present)
- Jodh Pannu (PhD Student, Spring 2018 - Present)
- Kripalakshmi Babu Venkateswaran (MS Student, Fall 2018 - Present)
- Gary Hoppenworth (Undergraduate Researcher)
- Shauna Hyppolite (Undergraduate Researcher)
- Tiger Sachse (Undergraduate Researcher)