PUBLICATIONS

A. M. Luescher, R. Heckel, and R. N. Grass, “Exploring the intersection of natural sciences and information technology via entropy and randomness,” Nat Commun, vol. 16, no. 1, p. 6969, July 2025, doi: published: 10.1038/s41467-025-62353-1; open access: 10.3929/ethz-c-000782746. Available: https://www.nature.com/articles/s41467-025-62353-1

R. Con and J. Ribeiro, “Channels with Input-Correlated Synchronization Errors,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195433; open access: 10.48550/arXiv.2504.14087. Available: https://arxiv.org/abs/2504.14087. [Accessed: Oct. 29, 2025]

P. Beelen, R. Con, A. Gruica, M. Montanucci, and E. Yaakobi, “Reed-Solomon Codes Against Insertions and Deletions: Full-Length and Rate-1/2 Codes,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195607; open access: 10.48550/arXiv.2501.11371. Available: https://arxiv.org/abs/2501.11371. [Accessed: Oct. 29, 2025]

R. Gross, R. Con, and E. Yaakobi, “Improved Constructions of Linear Codes for Insertions and Deletions,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195209; open access: 10.48550/arXiv.2509.26077. Available: https://arxiv.org/abs/2509.26077. [Accessed: Oct. 29, 2025]

F. Walter and Y. Yehezkeally, “Coding for Strand Breaks in Composite DNA,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195278; open access: 10.48550/arXiv.2501.15851. Available: https://arxiv.org/abs/2501.15851

J. Bariffi, A. Wachter-Zeh, and E. Yaakobi, “Sequence Reconstruction Over Coloring Channels for Protein Identification,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195624; open access: 10.48550/arXiv.2508.02229. Available: https://doi.org/10.48550/arXiv.2508.02229

A. Banerjee, Y. Yehezkeally, A. Wachter-Zeh, and E. Yaakobi, “Correcting Multiple Substitutions in Nanopore-Sequencing Reads,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195286; open access: 10.48550/arXiv.2505.02447. Available: https://doi.org/10.48550/arXiv.2505.02447

A. Banerjee, R. Con, A. Wachter-Zeh, and E. Yaakobi, “Decoding Insertions/Deletions via List Recovery,” in 2025 IEEE International Symposium on Information Theory (ISIT), Ann Arbor, MI, USA: IEEE, June 2025, pp. 1–6. doi: published: 10.1109/ISIT63088.2025.11195412; open access: 10.48550/arXiv.2505.02452. Available: https://doi.org/10.48550/arXiv.2505.02452

S. Santhosh et al., “An Efficient Guanine O6 Phosphitylation Repair Strategy for High-Quality DNA Library Synthesis via Digital Nucleic Acid Photolithography.” Chemistry, June 04, 2025. doi: 10.26434/chemrxiv-2025-f706f. Available: https://chemrxiv.org/engage/chemrxiv/article-details/683c888cc1cb1ecda0aa827c

T. Michel et al., “Color-corrected and high-contrast catadioptric relay for maskless high-resolution nucleic acid photolithography,” Opt. Express, vol. 33, no. 8, p. 17068, Apr. 2025, doi: published: 10.1364/OE.557937; open access: 10.48550/ARXIV.2411.06466. Available: https://opg.optica.org/abstract.cfm?URI=oe-33-8-17068

A. Banerjee, L. Welter, A. G. I. Amat, A. Wachter-Zeh, and E. Rosnes, “Sequential Decoding of Multiple Traces Over the Syndrome Trellis for Synchronization Errors,” in ICASSP 2025 - 2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Hyderabad, India: IEEE, Apr. 2025, pp. 1–5. doi: published: 10.1109/ICASSP49660.2025.10889909; open access: 10.48550/arXiv.2410.07120. Available: https://doi.org/10.48550/arXiv.2410.07120

Z. Ye, O. Sabary, R. Gabrys, E. Yaakobi, and O. Elishco, “More on codes for combinatorial composite DNA,” Des. Codes Cryptogr., vol. 93, no. 8, pp. 3437–3462, 2025, doi: 10.1007/s10623-025-01634-8. Available: https://link.springer.com/10.1007/s10623-025-01634-8. [Accessed: Oct. 29, 2025]

R. Con, R. Gabrys, and E. Yaakobi, “One Code Fits All: Strong Stuck-At Codes for Versatile Memory Encoding,” IEEE Trans. Inform. Theory, vol. 71, no. 3, pp. 1666–1675, 2025, doi: published: 10.1109/TIT.2025.3526747; open access: 10.48550/arXiv.2403.19061. Available: https://arxiv.org/abs/2403.19061. [Accessed: Oct. 29, 2025]

R. Con, D. Fathollahi, R. Gabrys, M. Wootters, and E. Yaakobi, “Robust Gray Codes Approaching the Optimal Rate,” IEEE Trans. Inform. Theory, vol. 71, no. 3, pp. 1647–1665, 2025, doi: published: 10.1109/TIT.2024.3522986; open access: 10.48550/arXiv.2406.17689. Available: https://arxiv.org/abs/2406.17689. [Accessed: Oct. 29, 2025]

D. Bar-Lev, O. Sabary, R. Gabrys, and E. Yaakobi, “Cover Your Bases: How to Minimize the Sequencing Coverage in DNA Storage Systems,” IEEE Trans. Inform. Theory, vol. 71, no. 1, pp. 192–218, 2025, doi: published: 10.1109/TIT.2024.3496587; open access: 10.48550/arXiv.2305.05656. Available: https://ieeexplore.ieee.org/document/10750859/

R. Con and R. Li, “Oblivious Deletion Codes.” arXiv, 2025. doi: 10.48550/ARXIV.2506.18878. Available: https://arxiv.org/abs/2506.18878. [Accessed: Oct. 29, 2025]

R. Con, Z. Guo, R. Li, and Z. Zhang, “Random Reed-Solomon Codes Achieve the Half-Singleton Bound for Insertions and Deletions over Linear-Sized Alphabets,” LIPIcs, Volume 334, ICALP 2025, vol. 334, p. 60:1-60:21, 2025, doi: published: 10.4230/LIPIcs.ICALP.2025.60; open access: 10.48550/arXiv.2407.07299. Available: https://arxiv.org/abs/2407.07299. [Accessed: Oct. 29, 2025]

R. Con, “Anonymous Shamir’s secret-sharing via Reed-Solomon Codes Against Permutations, Insertions, and Deletions,” IEEE Trans. Inform. Theory, pp. 1–1, 2025, doi: published: 10.1109/TIT.2025.3622889; open access: 10.48550/arXiv.2412.17003. Available: https://arxiv.org/abs/2412.17003. [Accessed: Oct. 29, 2025]

Z. Lu, H. M. Kiah, Y. Zhang, R. N. Grass, and E. Yaakobit, “Coding for Synthesis Defects,” in 2024 IEEE Information Theory Workshop (ITW), Shenzhen, China: IEEE, Nov. 2024, pp. 621–626. doi: published: 10.1109/ITW61385.2024.10806998; open access: 10.48550/arXiv.2405.02080. Available: https://arxiv.org/abs/2405.02080

A. Zrihan, E. Yaakobi, and Z. Yakhini, “Studying the Cycle Complexity of DNA Synthesis,” in 2024 IEEE Information Theory Workshop (ITW), Shenzhen, China: IEEE, Nov. 2024, pp. 633–638. doi: published: 10.1109/ITW61385.2024.10807020; open access: 10.48550/arXiv.2412.05865. Available: https://arxiv.org/abs/2412.05865

A. M. Luescher, W. J. Stark, and R. N. Grass, “DNA-Based Chemical Unclonable Functions for Cryptographic Anticounterfeit Tagging of Pharmaceuticals,” ACS Nano, p. acsnano.4c10870, Oct. 2024, doi: published: 10.1021/acsnano.4c10870; open access: 10.3929/ethz-b-000703583. Available: https://pubs.acs.org/doi/10.1021/acsnano.4c10870

A. Banerjee, Y. Yehezkeally, A. Wachter-Zeh, and E. Yaakobi, “Correcting a Single Deletion in Reads from a Nanopore Sequencer,” in 2024 IEEE International Symposium on Information Theory (ISIT), Athens, Greece: IEEE, July 2024, pp. 103–108. doi: published: 10.1109/ISIT57864.2024.10619468; open access: 10.48550/arXiv.2401.15939. Available: https://arxiv.org/abs/2401.15939

D. Bar-Lev, T. Etzion, E. Yaakobi, and Z. Yakhini, “Representing Information on DNA Using Patterns Induced by Enzymatic Labeling,” in 2024 IEEE International Symposium on Information Theory (ISIT), Athens, Greece: IEEE, July 2024, pp. 1943–1948. doi: published: 10.1109/ISIT57864.2024.10619227; open access: 10.48550/arXiv.2405.08475. Available: https://arxiv.org/abs/2405.08475

O. Sabary, I. Preuss, R. Gabrys, Z. Yakhini, L. Anavy, and E. Yaakobi, “Error-Correcting Codes for Combinatorial Composite DNA,” in 2024 IEEE International Symposium on Information Theory (ISIT), Athens, Greece: IEEE, July 2024, pp. 109–114. doi: published: 10.1109/ISIT57864.2024.10619334; open access: 10.48550/arXiv.2401.15666. Available: https://arxiv.org/abs/2401.15666

S. Singhvi, R. Con, H. M. Kiah, and E. Yaakobi, “An Optimal Sequence Reconstruction Algorithm for Reed-Solomon Codes,” in 2024 IEEE International Symposium on Information Theory (ISIT), Athens, Greece: IEEE, July 2024, pp. 2832–2837. doi: published: 10.1109/ISIT57864.2024.10619163; open access: 10.48550/arXiv.2403.07754. Available: https://arxiv.org/abs/2403.07754

F. Walter, O. Sabary, A. Wachter-Zeh, and E. Yaakobi, “Coding for Composite DNA to Correct Substitutions, Strand Losses, and Deletions,” in 2024 IEEE International Symposium on Information Theory (ISIT), Athens, Greece: IEEE, July 2024, pp. 97–102. doi: published: 10.1109/ISIT57864.2024.10619202; open access: 10.48550/arXiv.2404.12868. Available: https://arxiv.org/abs/2404.12868

A. Banerjee, Y. Yehezkeally, A. Wachter-Zeh, and E. Yaakobi, “Error-Correcting Codes for Nanopore Sequencing,” IEEE Transactions on Information Theory, vol. 70, no. 7, pp. 4956–4967, July 2024, doi: published: 10.1109/TIT.2024.3380615; open access: 10.48550/arXiv.2305.10214. Available: https://ieeexplore.ieee.org/document/10478160

I. Preuss, B. Galili, Z. Yakhini, and L. Anavy, “Sequencing Coverage Analysis for Combinatorial DNA-Based Storage Systems,” IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, vol. 10, no. 2, pp. 297–316, June 2024, doi: published: 10.1109/TMBMC.2024.3408053; open access: 10.1101/2024.01.10.574966. Available: https://ieeexplore.ieee.org/document/10543138

I. Preuss, M. Rosenberg, Z. Yakhini, and L. Anavy, “Efficient DNA-based data storage using shortmer combinatorial encoding,” Sci Rep, vol. 14, no. 1, p. 7731, Apr. 2024, doi: published: 10.1038/s41598-024-58386-z; open access: 10.1101/2021.08.01.454622. Available: https://www.nature.com/articles/s41598-024-58386-z

A. L. Gimpel, W. J. Stark, R. Heckel, and R. N. Grass, “Challenges for error-correction coding in DNA data storage: photolithographic synthesis and DNA decay,” Digital Discovery, 2024, doi: published: 10.1039/D4DD00220B; open access: 10.1101/2024.07.04.602085. Available: https://xlink.rsc.org/?DOI=D4DD00220B

J. Behr et al., “An open-source advanced maskless synthesizer for light-directed chemical synthesis of large nucleic acid libraries and microarrays.” ChemRxiv, Feb. 22, 2024. doi: 10.26434/chemrxiv-2024-j4c90. Available: https://chemrxiv.org/engage/chemrxiv/article-details/65ba15e39138d231611ab534

S. Gantenbein et al., “Three-dimensional printing of mycelium hydrogels into living complex materials,” Nat. Mater., vol. 22, no. 1, pp. 128–134, Jan. 2023, doi: 10.1038/s41563-022-01429-5. Available: https://www.nature.com/articles/s41563-022-01429-5

N. Kleger et al., “Light-Based Printing of Leachable Salt Molds for Facile Shaping of Complex Structures,” Advanced Materials, vol. 34, no. 32, p. 2203878, 2022, doi: 10.1002/adma.202203878. Available: https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.202203878

X. Chen, S. K. Ammu, K. Masania, P. G. Steeneken, and F. Alijani, “Diamagnetic Composites for High-Q Levitating Resonators,” Advanced Science, vol. 9, no. 32, p. 2203619, 2022, doi: 10.1002/advs.202203619. Available: https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202203619

R. Shafir, O. Sabary, L. Anavy, E. Yaakobi, and Z. Yakhini, “Sequence Reconstruction Under Stutter Noise in Enzymatic DNA Synthesis,” in 2021 IEEE Information Theory Workshop (ITW), Oct. 2021, pp. 1–6. doi: 10.1109/ITW48936.2021.9611362. Available: https://ieeexplore.ieee.org/document/9611362

J. Lietard, A. Leger, Y. Erlich, N. Sadowski, W. Timp, and M. M. Somoza, “Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries,” Nucleic Acids Research, vol. 49, no. 12, p. 6687, July 2021, doi: 10.1093/nar/gkab505. Available: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8266620/

I. Amit et al., “CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data,” Nat Commun, vol. 12, no. 1, p. 3042, May 2021, doi: 10.1038/s41467-021-22417-4. Available: https://www.nature.com/articles/s41467-021-22417-4

O. Sabary, Y. Orlev, R. Shafir, L. Anavy, E. Yaakobi, and Z. Yakhini, “SOLQC: Synthetic Oligo Library Quality Control tool,” Bioinformatics, vol. 37, no. 5, pp. 720–722, Mar. 2021, doi: 10.1093/bioinformatics/btaa740. Available: https://doi.org/10.1093/bioinformatics/btaa740

M. Schreck et al., “3D Printed Scaffolds for Monolithic Aerogel Photocatalysts with Complex Geometries,” Small, vol. 17, no. 50, p. 2104089, 2021, doi: 10.1002/smll.202104089. Available: https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.202104089

L. C. Meiser, J. Koch, P. L. Antkowiak, W. J. Stark, R. Heckel, and R. N. Grass, “DNA synthesis for true random number generation,” Nat Commun, vol. 11, no. 1, p. 5869, Nov. 2020, doi: 10.1038/s41467-020-19757-y. Available: https://www.nature.com/articles/s41467-020-19757-y

P. L. Antkowiak et al., “Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction,” Nat Commun, vol. 11, no. 1, p. 5345, Oct. 2020, doi: 10.1038/s41467-020-19148-3. Available: https://www.nature.com/articles/s41467-020-19148-3

A. Lenz, Y. Liu, C. Rashtchian, P. H. Siegel, A. Wachter-Zeh, and E. Yaakobi, “Coding for Efficient DNA Synthesis,” in 2020 IEEE International Symposium on Information Theory (ISIT), June 2020, pp. 2885–2890. doi: 10.1109/ISIT44484.2020.9174272. Available: https://ieeexplore.ieee.org/document/9174272

A. Lenz, P. H. Siegel, A. Wachter-Zeh, and E. Yaakobi, “Coding Over Sets for DNA Storage,” IEEE Transactions on Information Theory, vol. 66, no. 4, pp. 2331–2351, Apr. 2020, doi: 10.1109/TIT.2019.2961265. Available: https://ieeexplore.ieee.org/abstract/document/8937735

J. Koch, S. Gantenbein, K. Masania, W. J. Stark, Y. Erlich, and R. N. Grass, “A DNA-of-things storage architecture to create materials with embedded memory,” Nat Biotechnol, vol. 38, no. 1, pp. 39–43, Jan. 2020, doi: 10.1038/s41587-019-0356-z. Available: https://www.nature.com/articles/s41587-019-0356-z

L. Anavy, I. Vaknin, O. Atar, R. Amit, and Z. Yakhini, “Data storage in DNA with fewer synthesis cycles using composite DNA letters,” Nat Biotechnol, vol. 37, no. 10, pp. 1229–1236, Oct. 2019, doi: 10.1038/s41587-019-0240-x. Available: https://www.nature.com/articles/s41587-019-0240-x

K. Hölz, E. Schaudy, J. Lietard, and M. M. Somoza, “Multi-level patterning nucleic acid photolithography,” Nat Commun, vol. 10, no. 1, p. 3805, Aug. 2019, doi: 10.1038/s41467-019-11670-3. Available: https://www.nature.com/articles/s41467-019-11670-3

R. Heckel, G. Mikutis, and R. N. Grass, “A Characterization of the DNA Data Storage Channel,” Sci Rep, vol. 9, no. 1, p. 9663, July 2019, doi: 10.1038/s41598-019-45832-6. Available: https://www.nature.com/articles/s41598-019-45832-6

R. Heckel, I. Shomorony, K. Ramchandran, and D. N. C. Tse, “Fundamental limits of DNA storage systems,” in 2017 IEEE International Symposium on Information Theory (ISIT), June 2017, pp. 3130–3134. doi: 10.1109/ISIT.2017.8007106. Available: https://ieeexplore.ieee.org/abstract/document/8007106

M. Sack et al., “Express photolithographic DNA microarray synthesis with optimized chemistry and high-efficiency photolabile groups,” J Nanobiotechnol, vol. 14, no. 1, p. 14, Mar. 2016, doi: 10.1186/s12951-016-0166-0. Available: https://doi.org/10.1186/s12951-016-0166-0

R. N. Grass, R. Heckel, M. Puddu, D. Paunescu, and W. J. Stark, “Robust chemical preservation of digital information on DNA in silica with error-correcting codes,” Angew Chem Int Ed Engl, vol. 54, no. 8, pp. 2552–2555, Feb. 2015, doi: 10.1002/anie.201411378. Available: https://onlinelibrary.wiley.com/doi/10.1002/anie.201411378

N. Kretschy, A.-K. Holik, V. Somoza, K.-P. Stengele, and M. M. Somoza, “Next-Generation o-Nitrobenzyl Photolabile Groups for Light-Directed Chemistry and Microarray Synthesis,” Angewandte Chemie International Edition, vol. 54, no. 29, pp. 8555–8559, 2015, doi: 10.1002/anie.201502125. Available: https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201502125

D. Paunescu, M. Puddu, J. O. B. Soellner, P. R. Stoessel, and R. N. Grass, “Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA ‘fossils,’” Nat Protoc, vol. 8, no. 12, pp. 2440–2448, Dec. 2013, doi: 10.1038/nprot.2013.154. Available: https://www.nature.com/articles/nprot.2013.154