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Entropy
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Coding and Algorithms for DNA-Based Data Storage Systems
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Coding and Algorithms for DNA-Based Data Storage Systems

A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Information Theory, Probability and Statistics".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 3290

Special Issue Editors

Prof. Dr. Olgiça Milenković

E-Mail Website
Guest Editor
Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
Interests: bioinformatics and computational biology; graph and hypergraph neural networks; coding theory and applications; molecular storage and computing
Dr. Jin Sima

E-Mail Website
Guest Editor
Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
Interests: information and coding theory and applications; privacy-preserving learning; bio-inspired computational models

Special Issue Information

Dear Colleagues,

Molecular storage, and DNA-based data storage in particular, has emerged as a viable alternative to classical optical and magnetic recorders due to its ultra-high storage density, durability and ease of data replication. Still, practical advances in the field are hampered by the lack of low-cost and parallel synthesis platforms, and the size and time-delays of the read-write connectome and sequencing platforms. To mitigate some of these problems and ensure high levels of data integrity, specialized new coding and machine learning solutions have been proposed for random data access, data sequencing and retrieval. The goal of the Special Issue is to showcase new results in the field of coding theory and computational and learning algorithm design that strengthen the case for archival DNA-based data storage.

Prof. Dr. Olgiça Milenković
Dr. Jin Sima
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Entropy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • coding theory
  • computational biology
  • DNA-based data storage
  • DNA synthesis and sequencing

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Published Papers (4 papers)

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Research

20 pages, 342 KiB  
Article
Generalized Orthogonal de Bruijn and Kautz Sequences
by Yuan-Pon Chen, Jin Sima and Olgica Milenkovic
Entropy 2025, 27(4), 366; https://doi.org/10.3390/e27040366 - 30 Mar 2025
Viewed by 232
Abstract
A de Bruijn sequence of order k over a finite alphabet is a cyclic sequence with the property that it contains every possible k-sequence as a substring exactly once. Orthogonal de Bruijn sequences are the collections of de Bruijn sequences of the [...] Read more.
A de Bruijn sequence of order k over a finite alphabet is a cyclic sequence with the property that it contains every possible k-sequence as a substring exactly once. Orthogonal de Bruijn sequences are the collections of de Bruijn sequences of the same order, k, that satisfy the joint constraint that every (k+1)-sequence appears as a substring in, at most, one of the sequences in the collection. Both de Bruijn and orthogonal de Bruijn sequences have found numerous applications in synthetic biology, although the latter remain largely unexplored in the coding theory literature. Here, we study three relevant practical generalizations of orthogonal de Bruijn sequences, where we relax either the constraint that every (k+1)-sequence appears exactly once or the sequences themselves are de Bruijn rather than balanced de Bruijn sequences. We also provide lower and upper bounds on the number of fixed-weight orthogonal de Bruijn sequences. The paper concludes with parallel results for orthogonal nonbinary Kautz sequences, which satisfy similar constraints as de Bruijn sequences, except for being only required to cover all subsequences of length k whose maximum run length equals one. Full article
(This article belongs to the Special Issue Coding and Algorithms for DNA-Based Data Storage Systems)
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31 pages, 753 KiB  
Article
Reconstruction of Multiple Strings of Constant Weight from Prefix–Suffix Compositions
by Yaoyu Yang and Zitan Chen
Entropy 2025, 27(1), 39; https://doi.org/10.3390/e27010039 - 6 Jan 2025
Cited by 1 | Viewed by 628
Abstract
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and suffixes of every possible length. We [...] Read more.
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and suffixes of every possible length. We provide necessary and sufficient conditions for which unique reconstruction up to the reversal of the strings is possible. Additionally, we present two algorithms for reconstructing strings from the compositions of prefixes and suffixes of constant-length constant-weight strings. Full article
(This article belongs to the Special Issue Coding and Algorithms for DNA-Based Data Storage Systems)
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17 pages, 1972 KiB  
Article
A DNA Data Storage Method Using Spatial Encoding Based Lossless Compression
by Esra Şatır
Entropy 2024, 26(12), 1116; https://doi.org/10.3390/e26121116 - 20 Dec 2024
Viewed by 1055
Abstract
With the rapid increase in global data and rapid development of information technology, DNA sequences have been collected and manipulated on computers. This has yielded a new and attractive field of bioinformatics, DNA storage, where DNA has been considered as a great potential [...] Read more.
With the rapid increase in global data and rapid development of information technology, DNA sequences have been collected and manipulated on computers. This has yielded a new and attractive field of bioinformatics, DNA storage, where DNA has been considered as a great potential storage medium. It is known that one gram of DNA can store 215 GB of data, and the data stored in the DNA can be preserved for tens of thousands of years. In this study, a lossless and reversible DNA data storage method was proposed. The proposed approach employs a vector representation of each DNA base in a two-dimensional (2D) spatial domain for both encoding and decoding. The structure of the proposed method is reversible, rendering the decompression procedure possible. Experiments were performed to investigate the capacity, compression ratio, stability, and reliability. The obtained results show that the proposed method is much more efficient in terms of capacity than other known algorithms in the literature. Full article
(This article belongs to the Special Issue Coding and Algorithms for DNA-Based Data Storage Systems)
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12 pages, 404 KiB  
Article
Properties of Maxentropic DNA Synthesis Codes
by Kees Schouhamer Immink, Jos H. Weber and Kui Cai
Entropy 2024, 26(12), 1028; https://doi.org/10.3390/e26121028 - 27 Nov 2024
Viewed by 601
Abstract
Low-weight codes have been proposed for efficiently synthesizing deoxyribonucleic acid (DNA) for massive data storage, where a multiple of DNA strands are synthesized in parallel. We report on the redundancy and information rate of maxentropic low-weight codes for asymptotically large codeword length. We [...] Read more.
Low-weight codes have been proposed for efficiently synthesizing deoxyribonucleic acid (DNA) for massive data storage, where a multiple of DNA strands are synthesized in parallel. We report on the redundancy and information rate of maxentropic low-weight codes for asymptotically large codeword length. We compare the performance of low-complexity nibble replacement (NR) codes, which are designed to minimize the synthesis time, with the performance of maxentropic low-weight codes. Finally, the asymptotic redundancy and information rate of codes with a runlength limitation are investigated. Full article
(This article belongs to the Special Issue Coding and Algorithms for DNA-Based Data Storage Systems)
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