Information-theoretic foundations of DNA data storage

I Shomorony, R Heckel - Foundations and Trends® in …, 2022 - nowpublishers.com
Due to its longevity and enormous information density, DNA is an attractive medium for
archival data storage. Natural DNA more than 700.000 years old has been recovered, and …

Survey for a Decade of Coding for DNA Storage

O Sabary, HM Kiah, PH Siegel… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Advancements in DNA synthesis and sequencing technologies have enabled the storage of
data on synthetic DNA strands. However, realizing its potential relies on the design of …

Optimal systematic t-deletion correcting codes

J Sima, R Gabrys, J Bruck - 2020 IEEE International …, 2020 - ieeexplore.ieee.org
Systematic deletion correcting codes play an important role in applications of document
exchange. Yet despite a series of recent advances made in deletion correcting codes, most …

Explicit two-deletion codes with redundancy matching the existential bound

V Guruswami, J Håstad - IEEE Transactions on Information …, 2021 - ieeexplore.ieee.org
We give an explicit construction of length-n binary codes capable of correcting the deletion
of two bits that have size 2 n/n 4+ o (1). This matches up to lower order terms the existential …

Beyond single-deletion correcting codes: Substitutions and transpositions

R Gabrys, V Guruswami, J Ribeiro… - IEEE Transactions on …, 2022 - ieeexplore.ieee.org
We consider the problem of designing low-redundancy codes in settings where one must
correct deletions in conjunction with substitutions or adjacent transpositions; a combination …

Systematic codes correcting multiple-deletion and multiple-substitution errors

W Song, N Polyanskii, K Cai… - IEEE Transactions on …, 2022 - ieeexplore.ieee.org
We consider construction of deletion and substitution correcting codes with low redundancy
and efficient encoding/decoding. First, by simplifying the method of Sima et al.(ISIT 2020) …

Correcting deletions with multiple reads

J Chrisnata, HM Kiah, E Yaakobi - IEEE Transactions on …, 2022 - ieeexplore.ieee.org
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a
communication scenario where the sender transmits a codeword from some codebook and …

Sequence reconstruction under single-burst-insertion/deletion/edit channel

Y Sun, Y Xi, G Ge - IEEE Transactions on Information Theory, 2023 - ieeexplore.ieee.org
Motivated by applications in modern storage devices such as DNA storage and racetrack
memories, we study the sequence reconstruction problem which involves two important …

Optimal codes for the q-ary deletion channel

J Sima, R Gabrys, J Bruck - 2020 IEEE International …, 2020 - ieeexplore.ieee.org
The problem of constructing optimal multiple deletion correcting codes has long been open
until recent break-through for binary cases. Yet comparatively less progress was made in the …

Efficient linear and affine codes for correcting insertions/deletions

K Cheng, V Guruswami, B Haeupler, X Li - SIAM Journal on Discrete …, 2023 - SIAM
This paper studies linear and affine error-correcting codes for correcting synchronization
errors such as insertions and deletions. We call such codes linear/affine insdel codes …