CRISPR-Cas Encoding of a Digital Movie into the Genomes of a Population of Living Bacteria

CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes

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Molecular Computation of Solutions to Combinatorial Problems

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Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

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Next-Generation Digital Information Storage in DNA

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Towards Practical, High-Capacity, Low-Maintenance Information Storage in Synthesized DNA

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Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus

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DNA Fountain enables a robust and efficient storage architecture

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Whole-organism lineage tracing by combinatorial and cumulative genome editing

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Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

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Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

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Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

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A biological camera that captures and stores images directly into DNA

Lim, C. K., Yeoh, J. W., Kunartama, A. A., Yew, W. S., & Poh, C. L. (2023) · Nature Communications · doi:10.1038/s41467-023-38876-w · Cited by 25

Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration

Nivala, J., Shipman, S. L., & Church, G. M. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0097-z · Cited by 24

Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response

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Single-Error Detection and Correction for Duplication and Substitution Channels

Tang, Y., Yehezkeally, Y., Schwartz, M., & Farnoud, F. (2020) · IEEE Transactions on Information Theory · doi:10.1109/tit.2020.3006228 · Cited by 24

Deep Joint Source-Channel Coding for DNA Image Storage: A Novel Approach With Enhanced Error Resilience and Biological Constraint Optimization

Wu, W., Xiang, L., Liu, Q., & Yang, K. (2023) · IEEE Transactions on Molecular Biological and Multi-Scale Communications · doi:10.1109/tmbmc.2023.3331579 · Cited by 25

How to make DNA data storage more applicable

Akash, A., Bencúrová, E., & Dandekar, T. (2023) · Trends in biotechnology · doi:10.1016/j.tibtech.2023.07.006 · Cited by 25

DNA Molecular Storage System: Transferring Digitally Encoded Information through Bacterial Nanonetworks

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Acceleration of cancer science with genome editing and related technologies

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Sc-ncDNAPred: A Sequence-Based Predictor for Identifying Non-coding DNA in Saccharomyces cerevisiae

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Applications of CRISPR-Cas in Bioengineering, Biotechnology, and Translational Research

Lau, C. (2018) · The CRISPR Journal · doi:10.1089/crispr.2018.0026 · Cited by 22

Deciding the Confusability of Words under Tandem Repeats in Linear Time

Chee, Y. M., Chrisnata, J., Kiah, H. M., & Nguyen, T. T. (2019) · ACM Transactions on Algorithms · doi:10.1145/3338514 · Cited by 22

DNA Data Storage.

Buko, T., Tuczko, N., & Ishikawa, T. (2023) · BioTech · doi:10.3390/biotech12020044 · Cited by 21

Using Hawkeye from the Avengers to communicate on the eye

Fitzgerald, B. W. (2018) · AJP Advances in Physiology Education · doi:10.1152/advan.00161.2017 · Cited by 22

CRISPR for neuroscientists

Kalamakis, G., & Platt, R. J. (2023) · Neuron · doi:10.1016/j.neuron.2023.04.021 · Cited by 20

DNA Privacy: Analyzing Malicious DNA Sequences Using Deep Neural Networks

Bae, H., Min, S., Choi, H.-S., & Yoon, S. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.3017191 · Cited by 21

Recent progress in DNA data storage based on high-throughput DNA synthesis

Jo, S., Shin, H., Joe, S.-Y., Baek, D. J., Park, C., & Chun, H. (2024) · Biomedical Engineering Letters · doi:10.1007/s13534-024-00386-z · Cited by 25

The zettabyte era is in our DNA

Bar-Lev, D., Sabary, O., & Yaakobi, E. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00717-1 · Cited by 22

Beyond CMOS

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Advances and Challenges in Random Access Techniques for In Vitro DNA Data Storage

Zhou, Y., Bi, K., Ge, Q., & Lu, Z. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c07235 · Cited by 22

Error-Correcting Codes for Noisy Duplication Channels

Tang, Y., & Farnoud, F. (2021) · IEEE Transactions on Information Theory · doi:10.1109/tit.2021.3059095 · Cited by 20

Engineered Spore-Forming Bacillus as a Microbial Vessel for Long-Term DNA Data Storage

Liu, F., Li, J., Zhang, T., Chen, J., & Ho, C. L. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00291 · Cited by 19

DNA storage—from natural biology to synthetic biology

Bencúrová, E., Akash, A., Dobson, R. C. J., & Dandekar, T. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.01.045 · Cited by 20

A Tutorial on Coding Methods for DNA-Based Molecular Communications and Storage

Xiang, L., Liu, Q., Chen, S., Yan, K., Wu, W., & Yang, K. (2023) · IEEE Internet of Things Journal · doi:10.1109/jiot.2023.3332903 · Cited by 22

DNA storage: The future direction for medical cold data storage

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Study of Statistical Characteristics of GB-speckles, Forming at Scattering of Light on Virtual Structures of Nucleotide Gene Sequences of Enterobacteria

Ulyanov, S. S., Anatolievna, F. V., Ulianova, O. V., Zaitsev, S. S., Khizhnyakova, M. A., Saltykov, Y. V., Filonova, N. N., Subbotina, I. A., & Lyapina, A. M. (2018) · Izvestiya of Saratov University Physics · doi:10.18500/1817-3020-2018-18-2-123-137 · Cited by 17

A high storage density strategy for digital information based on synthetic DNA

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Batch Optimization for DNA Synthesis

Makarychev, K., Rácz, M. Z., Rashtchian, C., & Yekhanin, S. (2022) · IEEE Transactions on Information Theory · doi:10.1109/tit.2022.3184903 · Cited by 16

Cellular Computational Logic Using Toehold Switches

Choi, S., Lee, G., & Kim, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23084265 · Cited by 16

Fabrication and Decryption of a Microarray of Digital Dithiosuccinimide Oligomers

Shi, Q., Miao, T., Liu, Y., Hu, L., Yang, H., Shen, H., Piao, M., Huang, Z., & Zhang, Z. (2022) · Macromolecular Rapid Communications · doi:10.1002/marc.202200029 · Cited by 16

What would a synthetic connectome look like?

Rabinowitch, I. (2019) · Physics of Life Reviews · doi:10.1016/j.plrev.2019.06.005 · Cited by 18

DNA event recorders send past information of cells to the time of observation

Ishiguro, S., Mori, H., & Yachie, N. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.05.009 · Cited by 15

Long-Term Rewritable Report and Recording of Environmental Stimuli in Engineered Bacterial Populations

Zou, Z., & Ye, B. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00193 · Cited by 15

Sequences of Sequences: Spatial Organization of Coded Matter through Layer‐by‐Layer Assembly of Digital Polymers

Szweda, R., Tschopp, M., Félix, O., Decher, G., & Lutz, J. (2018) · Angewandte Chemie · doi:10.1002/ange.201810559 · Cited by 15

Synthetic Polymers with Finely Regulated Monomer Sequences: Properties and Emerging Applications

Laurent, E., Szweda, R., & Lutz, J. (2022) · Wiley eBooks · doi:10.1002/9783527815562.mme0041 · Cited by 16

Error Correction for DNA Storage

Sima, J., Raviv, N., Schwartz, M., & Bruck, J. (2023) · IEEE BITS the Information Theory Magazine · doi:10.1109/mbits.2023.3318516 · Cited by 17

Towards next-generation DNA encryption via an expanded genetic system

Huang, X., Hou, Z., Qiang, W., Wang, H., Wang, X., Chen, X., Hu, X., Dai, J., Li, L., & Zhao, G. (2024) · National Science Review · doi:10.1093/nsr/nwae469 · Cited by 15

HD-Code: End-to-End High Density Code for DNA Storage

Wu, J., Zhang, S., Zhang, T., & Liu, Y. (2021) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2021.3102122 · Cited by 15

Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the Efficiency of Prespacer Selection during Primed Adaptation

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Putative Phenotypically Neutral Genomic Insertion Points in Prokaryotes

Bernhards, C. B., Liem, A. T., Berk, K. L., Roth, P. A., Gibbons, H. S., & Lux, M. W. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00531 · Cited by 13

Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint

Li, X., Wei, Z., Wang, B., & Song, T. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.644484 · Cited by 13

DNA Punch Cards: Storing Data on Native DNA Sequences via NickingPreprint

Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J.-P., Soloveichik, D., Zhao, H., & Milenkovic, O. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/672394 · Cited by 14

Emerging preservation materials for long-term DNA-based data storage

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Molecular recording using DNA Typewriter

Liao, H., Choi, J., & Shendure, J. (2024) · Nature Protocols · doi:10.1038/s41596-024-01003-0 · Cited by 14

Data Readout Techniques for DNA‐Based Information Storage

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Engineered Living Memory Microspheroid‐Based Archival File System for Random Accessible In Vivo DNA Storage

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Filamentation initiated by Cas2 and its association with the acquisition process in cells

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Emerging Threats of Synthetic Biology and Biotechnology

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Mainstream encoding–decoding methods of DNA data storage

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Encoding of non-biological information for its long-term storage in DNA

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Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors

Yehezkeally, Y., & Schwartz, M. (2018) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit.2018.8437731 · Cited by 11

Pragmatic soft-decision data readout of encoded large DNA

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Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid‐Phase Synthesis

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Analysing bio-art’s epistemic landscape: from metaphoric to post-metaphoric structure

Ahmedien, D. A. M. (2022) · BioSocieties · doi:10.1057/s41292-022-00270-y · Cited by 10

Content-based filter queries on DNA data storage systems

El-Shaikh, A., & Seeger, B. (2023) · Scientific Reports · doi:10.1038/s41598-023-34160-5 · Cited by 10

As good as it gets: a scaling comparison of DNA computing, network biocomputing, and electronic computing approaches to an NP-complete problem

Perumal, A. S., Wang, Z., Ippoliti, G., van Delft, F. C. M. J. M., Lila Kari, A., & Nicolau, D. V. (2021) · New Journal of Physics · doi:10.1088/1367-2630/ac3883 · Cited by 11

Interfacing Neural Network Components and Nucleic Acids

Lissek, T. (2017) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2017.00053 · Cited by 10

Synthetic biology in China: Review and prospects

Zhang, X. (2019) · Scientia Sinica Vitae · doi:10.1360/ssv-2019-0299 · Cited by 10

Engineering the Activity of a Template-Independent DNA Polymerase

Milisavljevic, M., Rodriguez, T. R., Carlson, C. K., Liu, C. C., & Tyo, K. E. J. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00255 · Cited by 9

SemAI: Semantic Artificial Intelligence-Enhanced DNA Storage for Internet of Things

Wu, W., Xiang, L., Liu, Q., & Yang, K. (2024) · IEEE Internet of Things Journal · doi:10.1109/jiot.2024.3477314 · Cited by 9

Current and emerging opportunities in biological medium‐based computing and digital data storage

Bennet, D., Vo‐Dinh, T., & Zenhausern, F. (2021) · Nano Select · doi:10.1002/nano.202100275 · Cited by 9

Temporally resolved transcriptional recording in E. coli DNA using a Retro-Cascorder

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Controlled polymers: accessing new platforms for material synthesis

Kaligian, K. L., & Sprachman, M. M. (2019) · Molecular Systems Design & Engineering · doi:10.1039/c8me00095f · Cited by 9

Construction of tandem duplication correcting codes

Zeraatpisheh, M., Esmaeili, M., & Gulliver, T. A. (2019) · IET Communications · doi:10.1049/iet-com.2018.6053 · Cited by 10

Single-Error Detection and Correction for Duplication and Substitution Channels

Tang, Y., Yehezkeally, Y., Schwartz, M., & Farnoud, F. (2019) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit.2019.8849307 · Cited by 9

DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cellsPreprint

Loveless, T. B., Grotts, J. H., Schechter, M. W., Forouzmand, E., Carlson, C. K., Agahi, B. S., Liang, G., Ficht, M., Liu, B., Xie, X. S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/639120 · Cited by 9

DNA Origami Framework‐Based Spatial Nanochip for Circular ssDNA Assembly and Data Storage

Wang, S., Yang, D., Li, J., Bao, H., Pan, S., Huang, K., Shao, J., Yang, Q., Chen, X., Jiang, X., et al. (2025) · Small · doi:10.1002/smll.202410391 · Cited by 8

Deep mutational scanning identifies Cas1 and Cas2 variants that enhance type II-A CRISPR-Cas spacer acquisition

Hofmann, R., Herman, C., Mo, C. Y., Mathai, J., & Marraffini, L. A. (2025) · Nature Communications · doi:10.1038/s41467-025-60925-9 · Cited by 8

Linked data storage using DNA origami nanostructures

Zhang, C., Xie, M., Wang, L., Fan, C., & Chao, J. (2025) · Nature Communications · doi:10.1038/s41467-025-66274-x · Cited by 10

Strategies and mechanisms of precision genome engineering: From gene editing to genome writing

Huang, K., Tian, J., Zhao, W., Zhang, S., Xiang, L., Yang, M., Ls, L., Huang, Y., Zhang, N., Sun, L., et al. (2026) · iMetaOmics. · doi:10.1002/imo2.70115 · Cited by 8

Emerging and Enabling Technologies in Biodefense

Berger, K. M. (2019) · Springer eBooks · doi:10.1007/978-3-030-03053-7_13 · Cited by 9

The Entropy Rate of Some Pólya String Models

Elishco, O., Farnoud, F., Schwartz, M., & Bruck, J. (2019) · IEEE Transactions on Information Theory · doi:10.1109/tit.2019.2936556 · Cited by 8

Uncertainty of Reconstructing Multiple Messages from Uniform-Tandem-Duplication Noise

Yehezkeally, Y., & Schwartz, M. (2020) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit44484.2020.9174322 · Cited by 8

A Brain Inspired View of Life: The Scientific, Social and Cultural Implications of Interconnectivity and Complexity

Kılıç, T. (2019) · IEEE International Conference on Cognitive Informatics & Cognitive Computing (ICCI*CC) · doi:10.1109/iccicc46617.2019.9146063 · Cited by 8

Error-correcting codes for short tandem duplications and at most $p$ substitutions

Tang, Y., Lou, H., & Farnoud, F. (2021) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit45174.2021.9518049 · Cited by 8

Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology

Majikes, J. M., & Liddle, J. A. (2022) · Nanoscale · doi:10.1039/d2nr04040a · Cited by 8

Low-Redundancy Codes for Correcting Multiple Short-Duplication and Edit Errors

Tang, Y., Wang, S., Lou, H., Gabrys, R., & Farnoud, F. (2023) · IEEE Transactions on Information Theory · doi:10.1109/tit.2022.3233733 · Cited by 8

Parallelized Linear Classification with Volumetric Chemical Perceptrons

Arcadia, C. E., Tann, H., Dombroski, A., Ferguson, K., Chen, S. L., Kim, E., Rose, C., Rubenstein, B. M., Reda, S., & Rosenstein, J. K. (2018) · IEEE International Conference on Rebooting Computing (ICRC) · doi:10.1109/icrc.2018.8638627 · Cited by 8

Error-correcting Codes for Noisy Duplication Channels

Tang, Y., & Farnoud, F. (2019) · Allerton Conference on Communication, Control, and Computing · doi:10.1109/allerton.2019.8919847 · Cited by 8

Peptide-based sensing of Pb2+, molecular logic computing, information encoding, cryptography, and steganography

Lu, J., Bu, Z. Q., & Huang, W. T. (2022) · Microchemical Journal · doi:10.1016/j.microc.2022.108198 · Cited by 7

A DNA origami framework cryptosystem with nanoconfinement control of fluorescence logic permutations

Hou, X., Zhang, Y., Liu, Y., Xia, Q., Zhang, Y., Wang, J., Li, J., Wang, F., Wang, L., Liu, H., et al. (2025) · Science Advances · doi:10.1126/sciadv.aea7518 · Cited by 7

Construction of Functional Metal-Organic Frameworks and Their Applications in the Biomedical Field

Wang, S., Dai, Y., Zhang, J., Tong, Y., Yang, J., Liu, S., Dai, Z., & Meng, X. (2026) · Chemical Research in Chinese Universities · doi:10.1007/s40242-026-5247-5 · Cited by 7

Landauer’s Principle as a Special Case of Galois Connection

Kycia, R. A. (2018) · Entropy · doi:10.3390/e20120971 · Cited by 7

Enzymes as green and sustainable tools for DNA data storage

Liu, X., Yu, E., Zhao, Q., Han, H., & Li, Q. (2025) · Chemical Communications · doi:10.1039/d4cc06351a · Cited by 7

Predicting Biosecurity Threats: Deployment and Detection of Biological Weapons

Volk, K. M., & Gering, T. J. (2021) · NATO science for peace and security series. C, Environmental security · doi:10.1007/978-94-024-2086-9_13 · Cited by 7

Bio-pixels: A stem cell-based interactive–generative interface designed to redefine technologies of self-making in new media arts

Ahmedien, D. A. M. (2019) · Convergence The International Journal of Research into New Media Technologies · doi:10.1177/1354856519890096 · Cited by 7

Negative CG dinucleotide bias: An explanation based on feedback loops between Arginine codon assignments and theoretical minimal RNA rings

Jacques Demongeot, A., Moreira, A., & Seligmann, H. (2020) · BioEssays · doi:10.1002/bies.202000071 · Cited by 7

High-density information storage and random access scheme using synthetic DNA

Zhang, S., Wu, J., Huang, B., & Liu, Y. (2021) · 3 Biotech · doi:10.1007/s13205-021-02882-w · Cited by 7

On Codes for the Noisy Substring Channel

Yehezkeally, Y., & Polyanskii, N. (2021) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit45174.2021.9517943 · Cited by 7

Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions

Zhang, X., & An, X. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.876174 · Cited by 7

Surface Functionalization of Extracellular Vesicles with Nucleic Acids towards Biomedical Applications

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Barcoding Notch signaling in the developing brain

Siniscalco, A. M., Perera, R. P., Greenslade, J. E., Veeravenkatasubramanian, H., Masters, A., Doll, H. M., & Raj, B. (2024) · Development · doi:10.1242/dev.203102 · Cited by 6

Constrained coding for error mitigation in nanopore-based DNA data storage

Whritenour, K., Civelek, M., & Farnoud, F. (2025) · Scientific Reports · doi:10.1038/s41598-025-08531-z · Cited by 6

Highly active CRISPR-adaptation proteins revealed by a robust enrichment technology

Yosef, I., Mahata, T., Goren, M. G., Degany, O., Shem, A. B., & Qimron, U. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad510 · Cited by 6

Histones direct site-specific CRISPR spacer acquisition in model archaeon

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DNA Encoding-Based Nucleotide Pattern and Deep Features for Instance and Class-Based Image Retrieval

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