Forward Error Correction for DNA Data Storage

Blawat, Meinolf, Gaedke, Klaus, Hütter, Ingo, Chen, Xiao-Ming, Turczyk, Brian, Inverso, Samuel, Pruitt, Benjamin W., Church, George M.·2016·Procedia Computer Science
DOI 10.1016/j.procs.2016.05.398

Cited by (331)

Items 101–200 of 331

  1. DNA storage: The future direction for medical cold data storage
    Peilin Shen, Yi Zheng, CongYu Zhang, Shuo Li, Yongru Chen, Yongsong Chen, Yuchen Liu, Zhiming Cai · 2025 · Synthetic and Systems Biotechnology
  2. Study of Statistical Characteristics of GB-speckles, Forming at Scattering of Light on Virtual Structures of Nucleotide Gene Sequences of Enterobacteria
    Sergey S. Ulyanov, Feodorova Valentina Anatolievna, Onega V. Ulianova, S. S. Zaitsev, Maria A. Khizhnyakova, Yu. V. Saltykov, Nadejda N. Filonova, I. A. Subbotina, Anna M. Lyapina · 2018 · Izvestiya of Saratov University Physics
  3. DNA storage—from natural biology to synthetic biology
    Elena Bencúrová, Aman Akash, Renwick C. J. Dobson, Thomas Dandekar · 2023 · Computational and Structural Biotechnology Journal
  4. Storage‐D: A user‐friendly platform that enables practical and personalized DNA data storage
    Xiaoluo Huang, Junting Cui, Wei Qiang, Jianwen Ye, Yu Wang, Xinying Xie, Yuanzhen Li, Junbiao Dai · 2024 · iMeta
  5. Reconstruction Algorithms for DNA-Storage Systems
    Omer Sabary, Alexander Yucovich, Guy Shapira, Eitan Yaakobi · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  6. DNA-QLC: an efficient and reliable image encoding scheme for DNA storage
    Yanfen Zheng, Ben Cao, Xiaokang Zhang, Shuang Cui, Bin Wang, Qiang Zhang · 2024 · BMC Genomics
  7. A high storage density strategy for digital information based on synthetic DNA
    Shufang Zhang, Beibei Huang, Xiangming Song, Tao Zhang, Hanjie Wang, Yuhong Liu · 2019 · 3 Biotech
  8. Error Rate-Based Log-Likelihood Ratio Processing for Low-Density Parity-Check Codes in DNA Storage
    Xiaozhou Lu, Jaeho Jeong, Jae-Won Kim, Jong‐Seon No, Hosung Park, Albert No, Sunghwan Kim · 2020 · IEEE Access
  9. Image storage onto synthetic DNA
    Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy · 2021 · Signal Processing Image Communication
  10. A Robust and Efficient Representation‐based DNA Storage Architecture by Deep Learning
    Yanqing Su, Ling Chu, Wanmin Lin, Xiangyu Yao, Peng Xu, Wenbin Liu · 2024 · Small Methods
  11. Deep DNA Storage: Scalable and Robust DNA Storage via Coding Theory and Deep Learning
    Daniella Bar-Lev, Itai Orr, Omer Sabary, Tuvi Etzion, Eitan Yaakobi · 2021 · arXiv (Cornell University)
  12. Error Correction for DNA Storage
    Jin Sima, Netanel Raviv, Moshe Schwartz, Jehoshua Bruck · 2023 · IEEE BITS the Information Theory Magazine
  13. Innovation in Constrained Codes
    Kees A. Schouhamer Immink · 2022 · IEEE Communications Magazine
  14. “Multi-layer” encryption of medical data in DNA for highly-secure storage
    Jiaxin Xu, Yu Wang, Xue Chen, Lingwei Wang, Haibo Zhou, Hui Mei, Shanze Chen, Xiaoluo Huang · 2024 · Materials Today Bio
  15. Designing DNA codes from reversible self-dual codes over GF(4)
    Hyun Jin Kim, Whan-Hyuk Choi, Yoonjin Lee · 2020 · Discrete Mathematics
  16. Data and image storage on synthetic DNA: existing solutions and challenges
    Melpomeni Dimopoulou, Marc Antonini · 2022 · EURASIP Journal on Image and Video Processing
  17. Storing Images in DNA via base128 Encoding
    Kun Wang, Ben Cao, Tao Ma, Yunzhu Zhao, Yanfen Zheng, Bin Wang, Shihua Zhou, Qiang Zhang · 2024 · Journal of Chemical Information and Modeling
  18. Mainstream encoding–decoding methods of DNA data storage
    Chenyang Wang, Guannan Ma, Di Wei, Xinru Zhang, Peihan Wang, Cuidan Li, Jing Xing, Zheng Wei, Bo Duan, Dongxin Yang et al. · 2022 · CCF Transactions on High Performance Computing
  19. Encoding of non-biological information for its long-term storage in DNA
    Р.Р. Гарафутдинов, Dmitry A. Chemeris, Assol R. Sakhabutdinova, O.Yu. Kiryanova, Constantin I. Mikhaylenko, Alexey V. Chemeris · 2022 · Biosystems
  20. Image storage in DNA using Vector Quantization
    Melpomeni Dimopoulou, Marc Antonini · 2020 · European Signal Processing Conference (EUSIPCO)
  21. Data Readout Techniques for DNA‐Based Information Storage
    Bingyi Liu, Fei Wang, Chunhai Fan, Qian Li · 2025 · Advanced Materials
  22. HL-DNA: A Hybrid Lossy/Lossless Encoding Scheme to Enhance DNA Storage Density and Robustness for Images
    Yi Li, David Hung-Chang Du, Li Ou, Bingzhe Li · 2022 · IEEE International Conference on Computer Design: VLSI in Computers and Processors (ICCD)
  23. Modelling, Characterization of Data-Dependent and Process-Dependent Errors in DNA Data Storage
    Yixin Wang, Md. Noor‐A‐Rahim, Erry Gunawan, Yong Liang Guan, Chueh Loo Poh · 2023 · IEEE Transactions on Computational Biology and Bioinformatics
  24. Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads
    Seong‐Joon Park, Sunghwan Kim, Jaeho Jeong, Albert No, Jong‐Seon No, Hosung Park · 2023 · Bioinformatics
  25. Experimental Assessment of PCR Specificity and Copy Number for Reliable Data Retrieval in DNA Storage
    Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph M. Lopez, Karin Strauß, Luís Ceze · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  26. Achievable Rates of Concatenated Codes in DNA Storage under Substitution Errors
    Andreas Lenz, Lorenz Welter, Sven Puchinger · 2020 · arXiv (Cornell University)
  27. VSD: A Novel Method for Video Segmentation and Storage in DNA Using RS Code
    Jingwei Hong, Abdur Rasool, Shuo Wang, Djemel Ziou, Qingshan Jiang · 2024 · Mathematics
  28. Constructions and Properties of Efficient DNA Synthesis Codes
    Kees A. Schouhamer Immink, Kui Cai, Tuan Thanh Nguyen, Jos H. Weber · 2024 · IEEE Transactions on Molecular Biological and Multi-Scale Communications
  29. Symbolwise MAP Estimation for Multiple-Trace Insertion/Deletion/Substitution Channels
    Ryo Sakogawa, Haruhiko Kaneko · 2020 · IEEE International Symposium on Information Theory (ISIT)
  30. Rate-Distance Trade-offs for List-Decodable Insertion-Deletion Codes
    Bernhard Haeupler, Amirbehshad Shahrasbi · 2022 · IEEE Information Theory Workshop (ITW)
  31. Construction of DNA Codes From Composite Matrices and a Bio-Inspired Optimization Algorithm
    Steven T. Dougherty, Adrian Korban, Serap Şahinkaya, Deniz Üstün · 2022 · IEEE Transactions on Information Theory
  32. A dual-rule encoding DNA storage system using chaotic mapping to control GC content
    Xuncai Zhang, Baonan Qi, Ying Niu · 2024 · Bioinformatics
  33. Design of DNA Storage Coding with Enhanced Constraints
    Xiangjun Li, Shihua Zhou, Lewang Zou · 2022 · Entropy
  34. A Combinatorial Perspective on Random Access Efficiency for DNA Storage
    Anina Gruica, Daniella Bar-Lev, Alberto Ravagnani, Eitan Yaakobi · 2024 · IEEE International Symposium on Information Theory (ISIT)
  35. A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine
    Deruilin Liu, Demin Xu, Liuxin Shi, Jiayuan Zhang, Kewei Bi, Bei Luo, Chen Liu, Yuxiang Li, Guangyi Fan, Wen Wang et al. · 2025 · Gigabyte
  36. Advancing Archival Data Storage: The Promises and Challenges of DNA Storage System
    Alex Sensintaffar, Yixun Wei, Li Ou, David H. C. Du, Bingzhe Li · 2025 · ACM Transactions on Storage
  37. Stable DNA Storage Encoding Scheme Based on Repeating Substring Tree
    Jieqiong Wu, Penghao Wang, Yanfen Zheng, Bin Wang, Qiang Zhang, Pan Zheng · 2025 · IEEE Transactions on Computational Biology and Bioinformatics
  38. Current and emerging opportunities in biological medium‐based computing and digital data storage
    Devasier Bennet, Tuan Vo‐Dinh, Frédéric Zenhausern · 2021 · Nano Select
  39. Generative Adversarial Networks for DNA Storage Channel Simulator
    Sanghoon Kang, Yunfei Gao, Jaeho Jeong, Seong‐Joon Park, Jae-Won Kim, Jong‐Seon No, Hahyeon Jeon, Jeong Wook Lee, Sunghwan Kim, Hosung Park et al. · 2023 · IEEE Access
  40. Achieving handle-level random access in an encrypted DNA archival storage system via frequency dictionary mapping coding
    Ben Cao, Xue Li, Bin Wang, Tiantian He, Yanfen Zheng, Xiaokang Zhang, Qiang Zhang · 2025 · Patterns
  41. Automated routing of droplets for DNA storage on a digital microfluidics platform
    Ajay Manicka, Andrew Stephan, Sriram Chari, Gemma Mendonsa, Peyton Okubo, John Stolzberg-Schray, Anil Reddy, Marc D. Riedel · 2023 · Digital Discovery
  42. Embracing errors is more effective than avoiding them through constrained coding for DNA data storage
    Franziska Weindel, Andreas L. Gimpel, Robert N. Grass, Reinhard Heckel · 2023 · Allerton Conference on Communication, Control, and Computing
  43. An Encoding Table Corresponding to ASCII Codes for DNA Data Storage and a New Error Correction Method HMSA
    Xuncai Zhang, Fuzhen Zhou · 2024 · IEEE Transactions on NanoBioscience
  44. Sequence Reconstruction Under Stutter Noise in Enzymatic DNA Synthesis
    Roy Shafir, Omer Sabary, Leon Anavy, Eitan Yaakobi, Zohar Yakhini · 2021 · IEEE Information Theory Workshop (ITW)
  45. Nanoscale storage encryption: data storage in synthetic DNA using a cryptosystem with a neural network
    Yue Teng, Shan Yang, Liyan Liu, Ruicun Liu, Chen Yaofeng, Jinyu Li, Qian Yang, Tuoyu Liu, Yujun Cui, Peng Cheng et al. · 2022 · Science China Life Sciences
  46. Low-Redundancy Codes for Correcting Multiple Short-Duplication and Edit Errors
    Yuanyuan Tang, Shuche Wang, Hao Lou, Ryan Gabrys, Farzad Farnoud · 2023 · IEEE Transactions on Information Theory
  47. RBS: A Rotational Coding Based on Blocking Strategy for DNA Storage
    Ziniu Mu, Ben Cao, Penghao Wang, Bin Wang, Qiang Zhang · 2023 · IEEE Transactions on NanoBioscience
  48. DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement
    Congzhou Chen, Hongyu Wang, Enqiang Zhu, Xiaolong Shi, Jin Xu · 2020 · IEEE Access
  49. Overcoming High Nanopore Basecaller Error Rates for DNA Storage Via Basecaller-Decoder Integration and Convolutional Codes
    Shubham Chandak, Joachim Neu, Kedar Tatwawadi, Jay Mardia, Billy T. Lau, Matthew A. Kubit, Reyna Hulett, Peter B. Griffin, Mary K. Wootters, Tsachy Weissman et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  50. DNA-Correcting Codes: End-to-End Correction in DNA Storage Systems
    Avital Boruchovsky, Daniella Bar-Lev, Eitan Yaakobi · 2025 · IEEE Transactions on Information Theory
  51. Towards high-density storage of text and images into DNA by the “Xiao-Pang” codec system
    Mingwei Lu, Yang Wang, Wei Qiang, Junting Cui, Yu Wang, Xiaoluo Huang, Junbiao Dai · 2023 · Science China Life Sciences
  52. Efficient DNA-Based Image Coding and Storage
    Cihan Ruan, Rongduo Han, Yixiao Li, Shan Gao, Haoyu Wu, Nam Ling · 2023 · IEEE International Symposium on Circuits and Systems proceedings
  53. Efficient Explicit and Pseudo-Random Constructions of Constrained Codes for DNA Storage
    Xuan He, Yajuan Liu, Tong Wang, Xiaohu Tang · 2024 · IEEE Transactions on Communications
  54. Cracking the code on DNA storage
    Samuel Greengard · 2017 · Communications of the ACM
  55. A Survey Paper on DNA-Based Data Storage
    Shubham Taluja, Jagrit Bhupal, Siva Rama Krishnan · 2020 · International Conference on Emerging Trends in Information Technology and Engineering (ICETITE)
  56. Design of Nonbinary Error Correction Codes With a Maximum Run-Length Constraint to Correct a Single Insertion or Deletion Error for DNA Storage
    Xiaozhou Lu, Sunghwan Kim · 2021 · IEEE Access
  57. Integrating FPGA Acceleration in the DNAssim Framework for Faster DNA-Based Data Storage Simulations
    Alessia Marelli, Thomas Chiozzi, Nicholas Battistini, Lorenzo Zuolo, Rino Micheloni, Cristian Zambelli · 2023 · Electronics
  58. DNA-Correcting Codes: End-to-end Correction in DNA Storage Systems
    Avital Boruchovsky, Daniella Bar-Lev, Eitan Yaakobi · 2023 · IEEE International Symposium on Information Theory (ISIT)
  59. Robust Indexing for the Sliced Channel: Almost Optimal Codes for Substitutions and Deletions
    Jin Sima, Netanel Raviv, Jehoshua Bruck · 2024 · IEEE Transactions on Information Theory
  60. Advancing DNA Steganography with Incorporation of Randomness
    Meiying Cui, Yixin Zhang · 2020 · ChemBioChem
  61. High-density information storage and random access scheme using synthetic DNA
    Shufang Zhang, Jianjun Wu, Beibei Huang, Yuhong Liu · 2021 · 3 Biotech
  62. Sequence-Subset Distance and Coding for Error Control in DNA-based Data Storage
    Wentu Song, Kui Cai, Kees A. Schouhamer Immink · 2018 · arXiv (Cornell University)
  63. Polymerase Elongation onto Patterned DNA for Random Accessed DNA Data Storage
    Taeseok Kang, Doyeon Lim, Won Jin Lee, Youngjun Song · 2025 · BioChip Journal
  64. An Encoding Scheme to Enlarge Practical DNA Storage Capacity by Reducing Primer-Payload Collisions
    Yixun Wei, Bingzhe Li, David H. C. Du · 2024 · International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS)
  65. Data recovery methods for DNA storage based on fountain codes
    Peter Michael Schwarz, Bernd Freisleben · 2024 · Computational and Structural Biotechnology Journal
  66. Robust image coding on synthetic DNA: Reducing sequencing noise with inpainting
    Eva Gil San Antonio, Mattia Piretti, Melpomeni Dimopoulou, Marc Antonini · 2021 · Proceedings - International Conference on Pattern Recognition/Proceedings/International Conference on Pattern Recognition
  67. Decoding for Optimal Expected Normalized Distance over the t-Deletion Channel
    Daniella Bar-Lev, Yotam Gershon, Omer Sabary, Eitan Yaakobi · 2021 · IEEE International Symposium on Information Theory (ISIT)
  68. ReLume: Enhancing DNA storage data reconstruction with flow network and graph partitioning
    Lei Xie, Ben Cao, Xiaoru Wen, Yanfen Zheng, Bin Wang, Shihua Zhou, Pan Zheng · 2025 · Methods
  69. INNSE: Invertible neural network-based DNA image storage with self-correction encoding
    Yanfen Zheng, Xiaokang Zhang, Lijun Sun, Ben Cao, Bin Wang, Qiang Zhang, Pan Zheng · 2025 · Computational and Structural Biotechnology Journal
  70. Embracing Errors Can Be More Efficient Than Avoiding Them Through Constrained Coding for DNA Data Storage
    Franziska Weindel, Andreas L. Gimpel, Robert N. Grass, Reinhard Heckel · 2025 · IEEE Transactions on Molecular Biological and Multi-Scale Communications
  71. Catalytic DNA‐Assisted Mass Production of Arbitrary Single‐Stranded DNA
    Qiao Zhang, Kai Xia, Meng Jiang, Qingting Li, Weigang Chen, Mingzhe Han, Wei Li, Rongqin Ke, Fei Wang, Yongxing Zhao et al. · 2022 · Angewandte Chemie
  72. 10 Years of Natural Data Storage
    Dixita Limbachiya, Manish K. Gupta, Vaneet Aggarwal · 2022 · IEEE Transactions on Molecular Biological and Multi-Scale Communications
  73. Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing
    Huiran Yeom, Namphil Kim, Amos Chungwon Lee, Jinhyun Kim, Hamin Kim, Hansol Choi, Seo Woo Song, Sunghoon Kwon, Yeongjae Choi · 2023 · ACS Synthetic Biology
  74. Short Systematic Codes for Correcting Random Edit Errors in DNA Storage
    Serge Kas Hanna · 2024 · IEEE International Symposium on Information Theory (ISIT)
  75. The DNA Word Design Problem: A New Constraint Model and New Results
    Michael Codish, Michael Frank, Vitaly Lagoon · 2017 · International Joint Conference on Artificial Intelligence
  76. Bee Identification Problem for DNA Strands
    Johan Chrisnata, Han Mao Kiah, Alexander Vardy, Eitan Yaakobi · 2022 · IEEE International Symposium on Information Theory (ISIT)
  77. On the Positional Single Error Correction and Double Error Detection in Racetrack Memories
    Awais Saeed, Ubaid U. Fayyaz, Ahsan Tahir, Seokin Hong, Tayyeb Mahmood · 2023 · IEEE Access
  78. Sequence Design and Reconstruction Under the Repeat Channel in Enzymatic DNA Synthesis
    Roy Shafir, Omer Sabary, Leon Anavy, Eitan Yaakobi, Zohar Yakhini · 2023 · IEEE Transactions on Communications
  79. DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage
    Yiming Li, Haoling Zhang, Yuxin Chen, Yue Shen, Zhi Ping · 2024 · Briefings in Bioinformatics
  80. Soft-Decision Decoding for DNA-Based Data Storage
    Mu Zhang, Kui Cai, Kees A. Schouhamer Immink, Pingping Chen · 2018 · International Symposium on Information Theory and its Applications
  81. Reversible $$G^k$$-codes with applications to DNA codes
    Adrian Korban, Serap Şahinkaya, Deniz Üstün · 2022 · Designs Codes and Cryptography
  82. Extended nucleic acid memory as the future of data storage technology
    Saptarshi Biswas, Subhrapratim Nath, Jamuna Kanta Sing, Subir Kumar Sarkar · 2020 · International Journal of Nano and Biomaterials
  83. Intelligent Approaches to Optimizing Big Data Storage and Management: REHDFS system and DNA Storage
    Manar Sais, Najat Rafalia, Jâafar Abouchabaka · 2022 · Procedia Computer Science
  84. OligoArchive-DSM: Columnar Design for Error-Tolerant Database Archival using Synthetic DNA
    Eugenio Marinelli, Yiqing Yan, Virginie Magnone, Marie-Charlotte Dumargne, Pascal Barbry, Thomas Heinis, Raja Appuswamy · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Efficient and low-complexity variable-to-variable length coding for DNA storage
    Yunfei Gao, Albert No · 2024 · BMC Bioinformatics
  86. The Coverage Depth Problem in Dna Storage Over Small Alphabets
    Matteo Bertuzzo, Alberto Ravagnani, Eitan Yaakobi · 2025 · IEEE International Symposium on Information Theory (ISIT)
  87. Towards learning-based image compression for storage on DNA support
    Sophie Strebel, Noémie Monnier, Davi Nachtigall Lazzarotto, Michela Testolina, Touradj Ebrahimi · 2023 · SPIE Applications of Digital Image Processing
  88. Optimizing fountain codes for DNA data storage
    Peter Michael Schwarz, Bernd Freisleben · 2024 · Computational and Structural Biotechnology Journal
  89. DP-ID: Interleaving and Denoising to Improve the Quality of DNA Storage Image
    Qi Xu, Yitong Ma, Zuhong Lu, Kun Bi · 2024 · Interdisciplinary Sciences Computational Life Sciences
  90. In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)
    Golam Md Mortuza, Jorge Eduardo Guerrero, Shoshanna Llewellyn, Michael D. Tobiason, George David Dickinson, William L. Hughes, Reza Mohammad Zadegan, Tim Andersen · 2023 · BMC Bioinformatics
  91. New Binary Code Design to Correct One Deletion and One Insertion Error
    Thi-Huong Khuat, Hosung Park, Sunghwan Kim · 2023 · IEEE Transactions on Communications
  92. Neural network execution using nicked DNA and microfluidics
    Arnav Solanki, Zak Griffin, Purab Ranjan Sutradhar, Karisha Pradhan, Caiden Merritt, Amlan Ganguly, Marc D. Riedel · 2023 · PLoS ONE
  93. Coding, Decoding and Retrieving a Message Using DNA: An Experience from a Brazilian Center Research on DNA Data Storage
    Caio Perez Gomes, André G. C. Martins, Sabrina E. Nunes, Bruno Ramos, Henrique Reis Wisinewski, João Lucas Maehara Said dos Reis, Ariel P. Lima, Thiago Yuji Aoyagi, Icaro Gonçales, Danilo S. Maia et al. · 2024 · Micromachines
  94. Two RRNS-Based Error Correction Schemes for DNA Storage Channels
    Jia Luo, Liwei Mu, Y. J. Wendy Huang, Yonglin Yan, Guojun Han, Yonglin Zhong · 2024 · IEEE Communications Letters
  95. Using Artificial Neural Networks to Model Errors in Biochemical Manipulation of DNA Molecules
    Alan J. X. Guo, Hao Qi · 2021 · IEEE Transactions on Computational Biology and Bioinformatics
  96. DNA archival storage, a bottom up approach
    Omer Sella, Amir Apelbaum, Thomas Heinis, Jasmine Quah, Andrew William Moore · 2021 · ACM Workshop on Hot Topics in Storage and File Systems (HotStorage)
  97. A Quaternary Code Correcting a Burst of at Most Two Deletion or Insertion Errors in DNA Storage
    Thi-Huong Khuat, Sunghwan Kim · 2021 · Entropy
  98. Unclonable Polymers and Their Cryptographic Applications
    Ghada Almashaqbeh, Ran Canetti, Yaniv Erlich, Jonathan M. Gershoni, Tal Malkin, Itsik Pe’er, Anna Roitburd‐Berman, Eran Tromer · 2022 · Lecture notes in computer science
  99. DNA codes from skew dihedral group ring
    Steven T. Dougherty, Adrian Korban, Serap Şahinkaya, Deniz Üstün · 2022 · Advances in Mathematics of Communications
  100. Optimal Almost-Balanced Sequences
    Daniella Bar-Lev, Adir Kobovich, Orian Leitersdorf, Eitan Yaakobi · 2024 · IEEE International Symposium on Information Theory (ISIT)