BioSketch: I am an Assistant Professor in the Department of Computer Science at University of Central Florida since 2017. 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 mentored by Prof. Srinivas Aluru and in the Cheriton School of Computer Science, University of Waterloo, Canada mentored by 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.

Fully funded PhD positions available. 

Research Areas: Algorithms on Strings/Graphs with Applications to Computational Biology; Compressed/Succinct Data Structures; High Performance Computing.

Selected Publications: The complete list of my publications can be found in DBLP or Google Scholar.

1. Daniel Gibney, Sharma V. Thankachan and Srinivas Aluru:  The Complexity of Approximate Pattern Matching on De Bruijn Graphs. The 26th International Conference on Research in Computational Molecular Biology (RECOMB), 2022 [link].
2. Chirag Jain, Daniel Gibney and Sharma V. Thankachan:  Co-linear chaining with overlaps and gap costs. The 26th International Conference on Research in Computational Molecular Biology (RECOMB), 2022 [link].
3. Arnab Ganguly, Dhrumil Patel , Rahul Shah , and Sharma V. Thankachan:  LF Successor: Compact Space Indexing for Order-Isomorphic Pattern Matching. The 48th International Colloquium on Automata, Languages, and Programming (ICALP), 2021  [link].
4. Daniel Gibney, Gary Hoppenworth, and Sharma V. Thankachan:  Simple Reductions from Formula-SAT to Pattern Matching on Labeled Graphs and Subtree Isomorphism. SIAM Symposium on Simplicity in Algorithms (SOSA), 2021  [link].
5. Daniel Gibney and Sharma V. Thankachan:  Finding an Optimal Alphabet Ordering for Lyndon Factorization is Hard. International Symposium on Theoretical Aspects of Computer Science (STACS), 2021  [link].
6. Gary Hoppenworth, Jason Bentley, Daniel Gibney and Sharma V. Thankachan:  Fine-grained Complexity of the Median and Center String Problems under Edits. 28th Annual European Symposium on Algorithms (ESA), 2020 [link].
7. Jason Bentley, Daniel Gibney and Sharma V. Thankachan:  On the Complexity of BWT-runs Minimization via Alphabet Reordering. 28th Annual European Symposium on Algorithms (ESA), 2020 [link].
8. Daniel Gibney and Sharma V. Thankachan:  On the Hardness and Inapproximability of Recognizing Wheeler Graphs. 27th Annual European Symposium on Algorithms (ESA), 2019 [link].
9. Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam and 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].
10. 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].
11. Sriram P. Chockalingam, Sharma V. Thankachan and 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].
12. Srinivas Aluru, Alberto Apostolico and Sharma V. Thankachan: Efficient Alignment Free Sequence Comparison with Bounded Mismatches. 19th Annual International Conference in Research in Computational Molecular Biology (RECOMB), 2015 [link].
13. Wing-Kai Hon, Rahul Shah and Sharma V. Thankachan, Jeffrey Scott Vitter: Space-Efficient Frameworks for Top-k String Retrieval. Journal of the ACM (JACM), 61(2), 2014 [pdf].

Teaching

• COT 5405: Design and Analysis of Algorithms (Fall 2019, Spring 2019, Fall 2020, Spring 2021, fall 2021, Spring 2022)
• COT 4400: Tools for Algorithm Analysis (Fall 2019)
• COP 3503: Computer Science II (Fall 2018)
• COT 6410: Computational Complexity (Spring 2017, Spring 2018)

Program Committee

• The RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-SEQ), 2022, 2021, 2020 and 2019. 
• Conference on algorithms in bioinformatics (WABI), 2021 and 2020. 
• ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB), 2021 and 2017.
• The 27th International Computing and Combinatorics Conference (COCOON), 2021.
• International Symposium on String Processing and Information Retrieval (SPIRE), 2020 [Co-Chair] and 2018. 
• Annual Symposium on Combinatorial Pattern Matching (CPM), 2020, 2019 and 2016. 
• [Co-Chair] The 18th International Workshop on Data Mining in Bioinformatics (BIOKDD), 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 Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2021, 2019, 2018 and 2017.
• IEEE International Workshop on Foundations of Big Data Computing (BigDF), 2016. 

Current and Former PhD Students 

• Ms. Paniz Abedin (Fall 2017 - Present)
• Mr. Elakkat Dharmaraj Gireesh (Fall 2018 - Present)
• Dr. Daniel Gibney (Fall 2018 - Spring 2021: Now Postdoc at the Georgia Institute of Technology, Atlanta)
• Dr. Sahar Hooshmand (Spring 2017 - Fall 2020: Now Assistant Professor at the California State University Dominguez Hills)