Research Projects
My name is highlighted in bold in the research papers that I am the corresponding author.
Error Control Codes for DNA-Based Data Storage (2019-Present)
Advances in synthesis and sequencing technologies have made DNA macromolecules an attractive medium for digital information storage. Scientists have been storing digital data in DNA since 2012. Deletion, insertion, and substitution have been found as the common errors that happen during DNA synthesis and sequencing. Recent experiments demonstrated the need of error-correcting codes (capable of correcting errors whenever they occur) and constrained codes (avoiding sequences that are more prone to errors) for DNA storage. We aim to design coding techniques that merge error-correcting codes and constrained codes to achieve high-rate codes with a low complexity of encoding/decoding algorithms.
Selected published papers:
T. T. Nguyen, K. Cai, and K. A. S. Immink, "Efficient DNA Synthesis Codes with Error Correction and Runlength Limited Constraint", to appear, 2024 IEEE International Symposium on Information Theory (IEEE ISIT 2024), 7-13 July, Athens, Greece, paper accepted on 10 April 2024.
T. T. Nguyen, K. Cai, H. M. Kiah, D. T. Dao, and K. A. S. Immink, "On the Design of Codes for DNA Computing: Secondary Structure Avoidance Codes", 2023 IEEE International Symposium on Information Theory (IEEE ISIT 2023), 25-30 June, Taipei, Taiwan.
K. Cai, Y. M. Chee, R. Gabrys, H. M. Kiah, and T. T. Nguyen, “Correcting a Single Indel / Edit for DNA-Based Data Storage: Linear-Time Encoders and Order-Optimality”, IEEE Transactions on Information Theory, publication in the special issue of the IEEE Transactions on Information Theory 2020, which is devoted to the memory of Vladimir I. Levenshtein, Nov 2020.
K. Cai, X. He, H. M. Kiah, and T. T. Nguyen, "Efficient Constrained Encoders Correcting a Single Nucleotide Edit in DNA Storage", in the 45th International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2020), invited paper, Barcelona, Spain.
Y. M. Chee, J. Chrisnata, H. M. Kiah, and T. T. Nguyen, "Linear-time encoding/decoding of irreducible words for codes correcting tandem duplications," in NVMW 2019- Proceedings of the 10th Annual Non-Volatile Memories Workshop, accepted January 2019. Memorable Paper Award Finalist.
Research updates are available at: My Research Gate or My Google Scholar
Brief introduction on storing information in DNA by Twist Bioscience, available on youtube at
A short introduction of our recent results on error-correction codes for DNA data storage in NVMW2021.
Energy-Harvesting Codes for Simultaneous Energy and Information Transfer (2019-Present)
We study properties and constructions of constrained binary codes that enable simultaneous energy and information transfer. In the binary channel, when on-off keying is employed, bit 1 (bit 0) denotes the presence (absence) of a high energy signal. As such, sufficient energy is achieved theoretically by using relatively high weight codes. The first class of codes, known as subblock energy-constrained codes, whose codewords are partitioned into subblocks of same length and the weight of all subblocks are required to be at least e, for some e>0. The second class of codes, known as sliding-window energy-constrained codes, imposes a strong constraint that requires the weight over every window to be at least e. In this work, we study properties and propose efficient methods to construct such codes with low redundancy and linear-time complexity.
Selected published papers:
T. T. Nguyen, K. Cai and K. A. Schouhamer Immink, "Efficient Design of Subblock Energy-Constrained Codes and Sliding Window-Constrained Codes," in IEEE Transactions on Information Theory, vol. 67, no. 12, pp. 7914-7924, Dec. 2021, doi: 10.1109/TIT.2021.3119568.
K. Cai, H. M. Kiah, M. Motani, and T. T. Nguyen, "Coding for Segmented Edits with Local Weight Constraints", in IEEE ISIT 2021- Proceedings of the 2021 IEEE International Symposium on Information Theory, 2021.
T. T. Nguyen, K. Cai, and K. A. S. Immink, "Subblock Energy-Constrained Codes: Knuth's Balancing and Sequence Replacement Techniques", in IEEE ISIT 2020- Proceedings of the 2020 IEEE International Symposium on Information Theory, 2021.
Research updates are available at: My Research Gate or My Google Scholar
Burst-Error-Correcting Codes in Permutations and Multi-permutations (2017-2019)
Permutation codes and multi-permutation codes are widely studied due to various applications in information theory. Recently, they have attracted attention due to their emerging applications in storage systems, such as flash memories. Flash memories store information in arrays of memory cells, and each cell can store one or more bits of information. In this project, we study the related problem of burst deletions in rank modulated flash memories, that is, a series of deletions that occur in consecutive cells. The motivation behind considering burst deletions is that as flash memory scales, the parasitic capacitance of adjacent cells increases, which can cause corruptions in a cell to bleed to adjacent cells, through capacitative coupling. Our recent results included bounds on the size of optimal codes, code constructions, and efficient decoding algorithms.
Selected published papers :
Y. M. Chee, S. Ling, T. T. Nguyen, V. K. Vu, H. Wei, and X. Zhang, "Burst deletion-correcting codes for permutations and multipermutations", IEEE Transactions on Information Theory, Aug 2019.
Y. M. Chee, S. Ling, T. T. Nguyen, V. K. Vu, and H. Wei, “Permutation codes correcting a single burst deletion II: stable deletions", in IEEE ISIT 2017-Proceedings of the 2017 IEEE International Symposium on Information Theory, Aachen, pp. 2688-2692.
Research updates are available at: My Research Gate or My Google Scholar