{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,15]],"date-time":"2025-08-15T02:36:59Z","timestamp":1755225419474,"version":"3.43.0"},"reference-count":80,"publisher":"Association for Computing Machinery (ACM)","issue":"3","content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":["J. Emerg. Technol. Comput. Syst."],"published-print":{"date-parts":[[2025,7,31]]},"abstract":"<jats:p>\n            High value data like historical or health records, seismic or satellite images, particle collision events or original recordings, requires a long-term storage medium that is resilient, scalable, secure, and computable. DNA has been proposed as a solution and storage has been demonstrated using basewise synthesis. Separately, DNA computing demonstrations have shown complex programs executed on small datasets. Here, we demonstrate a new unified approach to DNA-based data storage and computing. We describe a novel combinatorial assembly approach to writing data into DNA. We define a trie-like DNA data structure and use it to write data in key-value form. We demonstrate our approach by writing\n            <jats:italic toggle=\"yes\">The Complete Works of William Shakespeare<\/jats:italic>\n            \u2014about 1 million words of text\u2014into DNA with raw error rates rivaling conventional media. Leveraging our DNA data structure, we define two new computing instructions\u2014\n            <jats:monospace>select<\/jats:monospace>\n            and\n            <jats:monospace>quotient<\/jats:monospace>\n            \u2014and using them, demonstrate how DNA-encoded text could be searched for exact or approximate matches to a query word. Our search demonstrations achieve perfect recall and high precision. Our approach is more scalable in cost and throughput that previous approaches and our platform is extensible to more powerful computing instructions applicable to a variety of applications.\n          <\/jats:p>","DOI":"10.1145\/3744562","type":"journal-article","created":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T11:22:57Z","timestamp":1749727377000},"page":"1-28","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Demonstration of a Scalable DNA Computing Platform: Writing and Selection"],"prefix":"10.1145","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1079-7570","authenticated-orcid":false,"given":"Swapnil P.","family":"Bhatia","sequence":"first","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1175-2585","authenticated-orcid":false,"given":"Miriam","family":"Ramliden","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1705-582X","authenticated-orcid":false,"given":"Vibha","family":"Rao","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6087-3338","authenticated-orcid":false,"given":"Grace","family":"Vezeau","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5918-4874","authenticated-orcid":false,"given":"Nina","family":"Katz-Christy","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6101-2701","authenticated-orcid":false,"given":"Seth","family":"Tolkamp","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0665-299X","authenticated-orcid":false,"given":"Matthew","family":"O\u2019Leary","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-6571-0569","authenticated-orcid":false,"given":"Hannah","family":"Jayne","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2280-2357","authenticated-orcid":false,"given":"Tyler","family":"Rockwood","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1387-044X","authenticated-orcid":false,"given":"Rithika Raj Kumar","family":"Pradeep","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3886-6585","authenticated-orcid":false,"given":"Chaitanya","family":"Joshi","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7551-6640","authenticated-orcid":false,"given":"Cat","family":"Ferrieri","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6631-1677","authenticated-orcid":false,"given":"Laurel","family":"Provencher","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8779-568X","authenticated-orcid":false,"given":"Gabriella","family":"Davis","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2291-3230","authenticated-orcid":false,"given":"Dasith","family":"Perera","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9991-6489","authenticated-orcid":false,"given":"Emily","family":"Greenwald","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1878-8126","authenticated-orcid":false,"given":"James","family":"Loomis","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9042-4830","authenticated-orcid":false,"given":"Phyllis","family":"Gitobu","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-7886-7634","authenticated-orcid":false,"given":"David","family":"Kleiman","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-2872-8388","authenticated-orcid":false,"given":"Sean","family":"Mihm","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-7274-4658","authenticated-orcid":false,"given":"David","family":"Turek","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4770-2186","authenticated-orcid":false,"given":"Hyunjun","family":"Park","sequence":"additional","affiliation":[{"name":"Catalog Technologies Inc., Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2025,8,13]]},"reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0400731101"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.7973651"},{"key":"e_1_3_3_4_2","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1145\/3600006.3613208","volume-title":"the 29th ACM Symposium on Operating Systems PrinciplesACM, New York, NY","author":"Anderson Patrick","year":"2023","unstructured":"Patrick Anderson, Erika B. Aranas, Youssef Assaf, Raphael Behrendt, Richard Black, Marco Caballero, Pashmina Cameron, Burcu Canakci, Andromachi Chatzieleftheriou, and Rebekah Clarke. 2023. Project silica: Towards sustainable cloud archival storage in glass. In the 29th ACM Symposium on Operating Systems Principles. ACM, New York, NY 166\u2013181."},{"issue":"7","key":"e_1_3_3_5_2","doi-asserted-by":"crossref","first-page":"17092","DOI":"10.1038\/nmicrobiol.2017.92","article-title":"A decade of discovery: CRISPR functions and applications","volume":"2","author":"Barrangou Rodolphe","year":"2017","unstructured":"Rodolphe Barrangou and Philippe Horvath. 2017. A decade of discovery: CRISPR functions and applications. Nature Microbiology 2, 7 (2017), 17092.","journal-title":"Nature Microbiology"},{"key":"e_1_3_3_6_2","unstructured":"Sarah Barsness Aaron Collie Michelle Gallinger Carol Kussmann Sibyl Schaefer and Gail Truman. 2017. 2017 Fixity Survey Report. Technical Report. National Digital Stewardship Alliance."},{"issue":"5210","key":"e_1_3_3_7_2","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1126\/science.7725109","article-title":"Building an associative memory vastly larger than the bra","volume":"268","author":"Baum Eric B.","year":"1995","unstructured":"Eric B. Baum. 1995. Building an associative memory vastly larger than the bra. Science 268, 5210 (1995), 583\u2013585.","journal-title":"Science"},{"issue":"1","key":"e_1_3_3_8_2","doi-asserted-by":"crossref","first-page":"4764","DOI":"10.1038\/s41467-021-24991-z","article-title":"Molecular-level similarity search brings computing to DNA data storage","volume":"12","author":"Bee Callista","year":"2021","unstructured":"Callista Bee, Yuan-Jyue Chen, Melissa Queen, David Ward, Xiaomeng Liu, Lee Organick, Georg Seelig, Karin Strauss, and Luis Ceze. 2021. 2021. Molecular-level similarity search brings computing to DNA data storage. Nature Communications 12, 1 (Aug. 2021), 4764.","journal-title":"Nature Communications"},{"key":"e_1_3_3_9_2","volume-title":"Natural Language Processing with Python: Analyzing Text with the Natural Language Toolkit","author":"Bird Steven","year":"2009","unstructured":"Steven Bird, Ewan Klein, and Edward Loper. 2009. Natural Language Processing with Python: Analyzing Text with the Natural Language Toolkit. O\u2019Reilly Media, Inc."},{"key":"e_1_3_3_10_2","unstructured":"Bob Biskeborn Mark Lantz Simeon Furrer Geoff Spratt Eiki Ozawa Eiji Nakashio Turguy Goker Robert Raymond Mark Hill and Badger Matt. 2024. INSIC International Magnetic Tape Storage Technology Roadmap 2024. Technical Report. Information Storage Industry Consortium."},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.procs.2016.05.398"},{"key":"e_1_3_3_12_2","first-page":"637","volume-title":"21st International Conference on Architectural Support for Programming Languages and Operating Systems","author":"Bornholt James","year":"2016","unstructured":"James Bornholt, Randolph Lopez, Douglas M. Carmean, Luis Ceze, Georg Seelig, and Karin Strauss. 2016. A DNA-based archival storage system. In 21st International Conference on Architectural Support for Programming Languages and Operating Systems, 637\u2013649."},{"issue":"5567","key":"e_1_3_3_13_2","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1126\/science.1069528","article-title":"Solution of a 20-variable 3-SAT problem on a DNA computer","volume":"296","author":"Braich Ravinderjit S.","year":"2002","unstructured":"Ravinderjit S. Braich, Nickolas Chelyapov, Cliff Johnson, Paul W. K. Rothemund, and Leonard Adleman. 2002. Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296, 5567 (Apr. 2002), 499\u2013502.","journal-title":"Science"},{"issue":"6113","key":"e_1_3_3_14_2","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1126\/science.1232919","article-title":"The revolution in the life sciences","volume":"338","author":"Brenner Sydney","year":"2012","unstructured":"Sydney Brenner. 2012. The revolution in the life sciences. Science 338, 6113 (2012), 1427\u20131428.","journal-title":"Science"},{"key":"e_1_3_3_15_2","volume-title":"European Physical Journal Web of Conferences","author":"Cano Eric","year":"2021","unstructured":"Eric Cano, Vladim\u00edr Bahyl, C\u00e9dric Caffy, Germ\u00e1n Cancio, Michael Davis, Oliver Keeble, Viktor Kotlyar, Julien Leduc, and Steven Murray. 2021. CERN tape archive: A distributed, reliable and scalable scheduling system. In European Physical Journal Web of Conferences, Vol. 251, Article 02037."},{"issue":"1","key":"e_1_3_3_16_2","first-page":"1","article-title":"Recent advances in DNA assembly technologies","volume":"15","author":"Chao Ran","year":"2015","unstructured":"Ran Chao, Yongbo Yuan, and Huimin Zhao. 2015. Recent advances in DNA assembly technologies. FEMS Yeast Research 15, 1 (2015), 1\u20139.","journal-title":"FEMS Yeast Research"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/0306-4379(95)98559-V"},{"key":"e_1_3_3_18_2","first-page":"281","volume-title":"Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman","author":"Chen Yuan-Jyue","unstructured":"Yuan-Jyue Chen and Georg Seelig. [n.d.]. Scaling up DNA computing with array-based synthesis and high-throughput sequencing. In Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman. Nata\u0161a Jonoska and Erik Winfree (Eds.), 281\u2013293."},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0289-6"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1226355"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0259868"},{"key":"e_1_3_3_22_2","doi-asserted-by":"crossref","DOI":"10.1128\/9781555819217","volume-title":"Mobile DNA III","author":"Craig N. L.","year":"2015","unstructured":"N. L. Craig, M. Chandler, M. Gellert, A. Lambowitz, P. A. Rice, and S. Sandmeyer (Eds.). 2015. Mobile DNA III. American Society for Microbiology Press, Washington, D.C."},{"key":"e_1_3_3_23_2","unstructured":"Forrest W. Crawford Kyle Webster Gerald L. Epstein Derek Roberts Joseph Fair and Sella Nevo. 2024. Securing Commercial Nucleic Acid Synthesis. Technical Report. RAND Corporation."},{"issue":"11","key":"e_1_3_3_24_2","doi-asserted-by":"crossref","first-page":"1775","DOI":"10.1109\/JPROC.2008.2004311","article-title":"Magnetic tape for data storage: An enduring technology","volume":"96","author":"Dee Richard H.","year":"2008","unstructured":"Richard H. Dee. 2008. Magnetic tape for data storage: An enduring technology. Proceedings of the IEEE 96, 11 (2008), 1775\u20131785.","journal-title":"Proceedings of the IEEE"},{"issue":"11","key":"e_1_3_3_25_2","doi-asserted-by":"crossref","first-page":"17552","DOI":"10.1021\/acsnano.2c06748","article-title":"Emerging approaches to DNA data storage: Challenges and prospects","volume":"16","author":"Doricchi Andrea","year":"2022","unstructured":"Andrea Doricchi, Casey M. Platnich, Andreas Gimpel, Friederikee Horn, Max Earle, German Lanzavecchia, Aitziber L. Cortajarena, Luis M. Liz-Marz\u00e1n, Na Liu, Reinhard Heckel, et al. 2022. Emerging approaches to DNA data storage: Challenges and prospects. ACS Nano 16, 11 (2022), 17552\u201317571.","journal-title":"ACS Nano"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1039\/c0ib00070a"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1038\/35002125"},{"key":"e_1_3_3_28_2","unstructured":"EMBL-EBI. 2024. Human assembly and gene annotation. Retrieved from https:\/\/www.ensembl.org\/Homo_sapiens\/Info\/Annotation"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaj2038"},{"issue":"10","key":"e_1_3_3_30_2","article-title":"Thermally induced error: Density limit for magnetic data storage","volume":"100","author":"Evans R. F. L.","year":"2012","unstructured":"R. F. L. Evans, R. W. Chantrell, U. Nowak, A. Lyberatos, and H.-J. Richter. 2012. Thermally induced error: Density limit for magnetic data storage. Applied Physics Letters 100, 10 (2012), 102402.","journal-title":"Applied Physics Letters"},{"issue":"5","key":"e_1_3_3_31_2","first-page":"22","article-title":"There\u2019s plenty of room at the bottom: An invitation to enter a new field of physics","volume":"23","author":"Feynman Richard P.","year":"1960","unstructured":"Richard P. Feynman. 1960. There\u2019s plenty of room at the bottom: An invitation to enter a new field of physics. Caltech Engineering and Science 23, 5 (1960), 22\u201336.","journal-title":"Caltech Engineering and Science"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1145\/367390.367400"},{"key":"e_1_3_3_33_2","unstructured":"Fujifilm. Fujifilm. 2018. The Role of Barium Ferrite Technology. Technical Report. Retrieved from https:\/\/fujistore.hu\/wp-content\/uploads\/2020\/03\/THE-ROLE-OF-BARIUM-FERRITE-TECHNOLOGY.pdf"},{"key":"e_1_3_3_34_2","volume-title":"Rapid Expert Consultation on Archival Data Storage Technologies for the Intelligence Community","author":"Fullerton Eric","year":"2024","unstructured":"Eric Fullerton, Steffen Hellmhold, Shashidhar Joshi, and Laura McNamara. 2024. Rapid Expert Consultation on Archival Data Storage Technologies for the Intelligence Community. The National Academies Press, Washington, DC."},{"key":"e_1_3_3_35_2","first-page":"149","volume-title":"the Spring Joint Computer Conference (AFIPS \u201967)","volume":"30","author":"Gaines B.","year":"1967","unstructured":"B. Gaines. 1967. Stochastic computing. In the Spring Joint Computer Conference (AFIPS \u201967), Vol. 30, 149\u2013156."},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1038\/35002131"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11875"},{"issue":"4","key":"e_1_3_3_38_2","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1109\/PGEC.1966.264358","article-title":"Content-addressable and associative memory systems a survey","volume":"15","author":"Hanlon A. G.","year":"1966","unstructured":"A. G. Hanlon. 1966. Content-addressable and associative memory systems a survey. IEEE Transactions on Electronic Computers EC 15, 4 (1966), 509\u2013521.","journal-title":"IEEE Transactions on Electronic Computers EC"},{"key":"e_1_3_3_39_2","unstructured":"Carla Hayden. 2023. Annual Report of the Librarian of Congress. Technical Report. Library of Congress Washington D.C."},{"issue":"24","key":"e_1_3_3_40_2","doi-asserted-by":"crossref","first-page":"6082","DOI":"10.1002\/cctc.202001107","article-title":"Looking back: A short history of the discovery of enzymes and how they became powerful chemical tools","volume":"12","author":"Heckmann Christian M.","year":"2020","unstructured":"Christian M. Heckmann and Francesca Paradisi. 2020. Looking back: A short history of the discovery of enzymes and how they became powerful chemical tools. ChemCatChem 12, 24 (2020), 6082\u20136102.","journal-title":"ChemCatChem"},{"issue":"3","key":"e_1_3_3_41_2","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/s41570-022-00456-9","article-title":"DNA synthesis technologies to close the gene writing gap","volume":"7","author":"Hoose Alex","year":"2023","unstructured":"Alex Hoose, Richard Vellacott, Marko Storch, Paul S. Freemont, and Maxim G. Ryadnov. 2023. DNA synthesis technologies to close the gene writing gap. Nature Reviews Chemistry 7, 3 (2023), 144\u2013161.","journal-title":"Nature Reviews Chemistry"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1109\/12.59856"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1137\/0216039"},{"key":"e_1_3_3_44_2","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1109\/ICDE.1998.655781","volume-title":"14th International Conference on Data Engineering","author":"Johnson T.","year":"1998","unstructured":"T. Johnson. 1998. Coarse indices for a tape-based data warehouse. In 14th International Conference on Data Engineering. IEEE, Orlando, FL, 231\u2013240."},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.5555\/534853"},{"key":"e_1_3_3_46_2","first-page":"355","volume-title":"Combinatorial Algorithms","author":"Knuth Donald E.","year":"2011","unstructured":"Donald E. Knuth. 2011. Combinatorial Algorithms. The Art of Computer Programming, Vol. 4A. Addison-Wesley, Reading, MA, Chapter 7, 355\u2013360."},{"key":"e_1_3_3_47_2","first-page":"492","volume-title":"Sorting and Searching","author":"Knuth Donald E.","year":"2011","unstructured":"Donald E. Knuth. 2011. Sorting and Searching (2nd. ed.). The Art of Computer Programming, Vol. 3. Addison-Wesley, Reading, MA, Chapter 6, 492\u2013507.","edition":"2"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2918"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1109\/2.330035"},{"issue":"1","key":"e_1_3_3_50_2","article-title":"Magnetic tape storage technology","volume":"21","author":"Lantz Mark A.","year":"2025","unstructured":"Mark A. Lantz, Simeon Furrer, Martin Petermann, Hugo Rothuizen, Stella Brach, Luzius Kronig, Ilias Iliadis, Beat Weiss, Ed R. Childers, and David Pease. 2025. Magnetic tape storage technology. ACM Transactions on Storage 21, 1, Article 6 (Jan. 2025), 70 pages.","journal-title":"ACM Transactions on Storage"},{"issue":"1","key":"e_1_3_3_51_2","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1038\/s41467-019-10258-1","article-title":"Terminator-free template-independent enzymatic DNA synthesis for digital information storage","volume":"10","author":"Lee Henry H.","year":"2019","unstructured":"Henry H. Lee, Reza Kalhor, Naveen Goela, Jean Bolot, and George M. Church. 2019. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nature Communications 10, 1 (2019), 2383.","journal-title":"Nature Communications"},{"issue":"10","key":"e_1_3_3_52_2","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1016\/j.tibtech.2020.12.008","article-title":"Novel modalities in DNA data storage","volume":"39","author":"Lim Cheng Kai","year":"2021","unstructured":"Cheng Kai Lim, Saurabh Nirantar, Wen Shan Yew, and Chueh Loo Poh. 2021. Novel modalities in DNA data storage. Trends in Biotechnology 39, 10 (2021), 990\u20131003.","journal-title":"Trends in Biotechnology"},{"key":"e_1_3_3_53_2","volume-title":"Error Control Coding","author":"Lin Shu","year":"2004","unstructured":"Shu Lin and Daniel J. Costello Jr. 2004. Error Control Coding. Prentice Hall, Upper Saddle Rive, NJ."},{"issue":"4861","key":"e_1_3_3_54_2","first-page":"10","article-title":"A last-in first-out stack data structure implemented in DNA","volume":"12","author":"Lopiccolo Annunziata","year":"2021","unstructured":"Annunziata Lopiccolo, Ben Shirt-Ediss, Emanuela Torelli, Abimbola Feyisara Adedeji Olulana, Matteo Castronovo, Harold Fellermann, and Natalio Krasnogor. 2021. A last-in first-out stack data structure implemented in DNA. Nature Communications 12, 4861 (2021), 10 pages.","journal-title":"Nature Communications"},{"issue":"9","key":"e_1_3_3_55_2","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1038\/s41559-024-02461-1","article-title":"The nature of the last universal common ancestor and its impact on the early earth system","volume":"8","author":"Moody Edmund R. R.","year":"2024","unstructured":"Edmund R. R. Moody, Sandra \u00c1lvarez-Carretero, Tara A. Mahendrarajah, James W. Clark, Holly C. Betts, Nina Dombrowski, L\u00e9n\u00e1rd L. Sz\u00e1nth\u00f3, Richard A. Boyle, Stuart Daines, Xi Chen, et al. 2024. The nature of the last universal common ancestor and its impact on the early earth system. Nature Ecology & Evolution 8, 9 (2024), 1654\u20131666.","journal-title":"Nature Ecology & Evolution"},{"issue":"1","key":"e_1_3_3_56_2","first-page":"3","article-title":"Some fundamental issues in microminiaturization","volume":"19","author":"Neiman Mikhail S.","year":"1964","unstructured":"Mikhail S. Neiman. 1964. Some fundamental issues in microminiaturization. Radiotekhnika 19, 1 (1964), 3\u201312.","journal-title":"Radiotekhnika"},{"issue":"7932","key":"e_1_3_3_57_2","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41586-022-05218-7","article-title":"Nonlinear decision-making with enzymatic neural networks","volume":"610","author":"Okumura S.","year":"2022","unstructured":"S. Okumura, G. Gines, N. Lobato-Dauzier, A. Baccouche, R. Deteix, T. Fujii, Y. Rondelez, and A. J. Genot. 2022. Nonlinear decision-making with enzymatic neural networks. Nature 610, 7932 (2022), 496\u2013501.","journal-title":"Nature"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4079"},{"issue":"1","key":"e_1_3_3_59_2","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1038\/s43586-020-00011-0","article-title":"Ancient DNA analysis","volume":"1","author":"Orlando Ludovic","year":"2021","unstructured":"Ludovic Orlando, Robin Allaby, Pontus Skoglund, Clio Der Sarkissian, Philipp W. Stockhammer, Mar\u00eda C. \u00c1vila-Arcos, Qiaomei Fu, Johannes Krause, Eske Willerslev, Anne C. Stone, et al. 2021. Ancient DNA analysis. Nature Reviews Methods Primers 1, 1 (2021), 14.","journal-title":"Nature Reviews Methods Primers"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.3115\/v1\/D14-1162"},{"issue":"11","key":"e_1_3_3_61_2","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1021\/acssynbio.8b00333","article-title":"Comprehensive profiling of four base overhang ligation fidelity by T4 DNA ligase and application to DNA assembly","volume":"7","author":"Potapov Vladimir","year":"2018","unstructured":"Vladimir Potapov, Jennifer L. Ong, Rebecca B. Kucera, Bradley W. Langhorst, Katharina Bilotti, John M. Pryor, Eric J. Cantor, Barry Canton, Thomas F. Knight, Thomas C. Evans Jr., et al. 2018. Comprehensive profiling of four base overhang ligation fidelity by T4 DNA ligase and application to DNA assembly. ACS Synthetic Biology 7, 11 (2018), 2665\u20132674.","journal-title":"ACS Synthetic Biology"},{"issue":"7939","key":"e_1_3_3_62_2","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41586-022-05453-y","article-title":"A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA","volume":"612","author":"Kj\u00e6r Kurt H.","year":"2022","unstructured":"Kurt H. Kj\u00e6r, Mikkel Winther Pedersen, Bianca De Sanctis, Binia De Cahsan, Thorfinn S. Korneliussen, Christian S. Michelsen, Karina K. Sand, Stanislav Jelavi\u0107, Anthony H. Ruter, Astrid M. A. Schmidt, et al. 2022. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612, 7939 (2022), 283\u2013291.","journal-title":"Nature"},{"key":"e_1_3_3_63_2","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/3-540-48017-X_22","volume-title":"DNA Computing","author":"Reif John H.","year":"2002","unstructured":"John H. Reif, Thomas H. LaBean, Michael Pirrung, Vipul S. Rana, Bo Guo, Carl Kingsford, and Gene S. Wickham. 2002. Experimental construction of very large scale DNA databases with associative search capability. In DNA Computing. Nata\u0161a Jonoska and Nadrian C. Seeman (Eds.), Springer, Berlin, 231\u2013247."},{"issue":"6297","key":"e_1_3_3_64_2","doi-asserted-by":"crossref","first-page":"aad8559","DOI":"10.1126\/science.aad8559","article-title":"Synthetic recombinase-based state machines in living cells","volume":"353","author":"Roquet Nathaniel","year":"2016","unstructured":"Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, and Timothy K. Lu. 2016. Synthetic recombinase-based state machines in living cells. Science 353, 6297 (2016), aad8559.","journal-title":"Science"},{"key":"e_1_3_3_65_2","unstructured":"Jeff Rothenberg. 1999. Avoiding Technological Quicksand: Finding a Viable Technical Foundation for Digital Preservation. Technical Report. Council on Library and Information Resources."},{"key":"e_1_3_3_66_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules181114268"},{"issue":"3","key":"e_1_3_3_67_2","doi-asserted-by":"crossref","first-page":"8\u2013es","DOI":"10.1145\/1288783.1288785","article-title":"Understanding disk failure rates: What does an MTTF of 1,000,000 hours mean to you","volume":"3","author":"Schroeder Bianca","year":"2007","unstructured":"Bianca Schroeder and Garth A. Gibson. 2007. Understanding disk failure rates: What does an MTTF of 1,000,000 hours mean to you? ACM Transactions on Storage 3, 3 (Oct. 2007), 8\u2013es.","journal-title":"ACM Transactions on Storage"},{"key":"e_1_3_3_68_2","volume-title":"The Complete Works of William Shakespeare","author":"Shakespeare William","year":"1994","unstructured":"William Shakespeare. 1994. The Complete Works of William Shakespeare. Vol. 100. Project Gutenberg, Urbana, Illinois. Retrieved from https:\/\/www.gutenberg.org\/cache\/epub\/100\/pg100.txtRetrieved 02-01-2024"},{"key":"e_1_3_3_69_2","first-page":"1","volume-title":"IEEE High Performance Extreme Computing Conference (HPEC \u201923)","author":"Shankar Sadasivan","year":"2023","unstructured":"Sadasivan Shankar. 2023. Energy estimates across layers of computing: From devices to large-scale applications in machine learning for natural language processing, scientific computing, and cryptocurrency mining. In IEEE High Performance Extreme Computing Conference (HPEC \u201923). IEEE, Boston, MA, 1\u20136."},{"key":"e_1_3_3_70_2","first-page":"214","volume-title":"11th International Conference on Scientific and Statistical Database Management","author":"Shoshani Arie","year":"1999","unstructured":"Arie Shoshani, Luis M. Bernardo, Henrik Nordberg, Doron Rotem, and Alex Sim. 1999. Multidimensional indexing and query coordination for tertiary storage management. In 11th International Conference on Scientific and Statistical Database Management. IEEE, Cleveland, OH, 214\u2013225."},{"issue":"1","key":"e_1_3_3_71_2","doi-asserted-by":"crossref","first-page":"14138","DOI":"10.1038\/srep14138","article-title":"A rewritable, random-access DNA-based storage system","volume":"5","author":"Hossein Tabatabaei Yazdi S. M.","year":"2015","unstructured":"S. M. Hossein Tabatabaei Yazdi, Yongbo Yuan, Jian Ma, Huimin Zhao, and Olgica Milenkovic. 2015. A rewritable, random-access DNA-based storage system. Scientific Reports 5, 1 (Sep. 2015), 14138.","journal-title":"Scientific Reports"},{"issue":"1","key":"e_1_3_3_72_2","doi-asserted-by":"crossref","first-page":"4998","DOI":"10.1038\/s41598-019-41228-8","article-title":"Demonstration of end-to-end automation of DNA data storage","volume":"9","author":"Takahashi Christopher N.","year":"2019","unstructured":"Christopher N. Takahashi, Bichlien H. Nguyen, Karin Strauss, and Luis Ceze. 2019. Demonstration of end-to-end automation of DNA data storage. Scientific Reports 9, 1 (2019), 4998.","journal-title":"Scientific Reports"},{"issue":"7329","key":"e_1_3_3_73_2","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/nature09565","article-title":"Robust multicellular computing using genetically encoded nor gates and chemical \u2019wires","volume":"469","author":"Tamsir A.","year":"2011","unstructured":"A. Tamsir, J. J. Tabor, and C. A. Voigt. 2011. Robust multicellular computing using genetically encoded nor gates and chemical \u2019wires. Nature 469, 7329 (2011), 212\u2013215.","journal-title":"Nature"},{"issue":"37","key":"e_1_3_3_74_2","doi-asserted-by":"crossref","first-page":"e2217330120","DOI":"10.1073\/pnas.2217330120","article-title":"Parallel molecular computation on digital data stored in DNA","volume":"120","author":"Wang Boya","year":"2023","unstructured":"Boya Wang, Siyuan Stella Wang, Cameron Chalk, Andrew D. Ellington, and David Soloveichik. 2023. Parallel molecular computation on digital data stored in DNA. Proceedings of the National Academy of Sciences of the United States of America 120, 37 (Sep. 2023, e2217330120.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"5","key":"e_1_3_3_75_2","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nbt.3805","article-title":"Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells","volume":"35","author":"Weinberg Benjamin H.","year":"2017","unstructured":"Benjamin H. Weinberg, N. T. Hang Pham, Leidy D. Caraballo, Thomas Lozanoski, Adrien Engel, Swapnil Bhatia, and Wilson W. Wong. 2017. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nature Biotechnology 35, 5 (2017), 453\u2013462.","journal-title":"Nature Biotechnology"},{"key":"e_1_3_3_76_2","unstructured":"National Human Genome Research Institute. 2025. DNA Sequencing Costs: Data. Retrieved from https:\/\/www.genome.gov\/about-genomics\/fact-sheets\/DNA-Sequencing-Costs-Data"},{"key":"e_1_3_3_77_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1014-9"},{"issue":"12","key":"e_1_3_3_78_2","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/s41578-020-0229-6","article-title":"Solid-state nanopore sensors","volume":"5","author":"Xue Liang","year":"2020","unstructured":"Liang Xue, Hirohito Yamazaki, Ren Ren, Meni Wanunu, Aleksandar P. Ivanov, and Joshua B. Edel. 2020. Solid-state nanopore sensors. Nature Reviews Materials 5, 12 (2020), 931\u2013951.","journal-title":"Nature Reviews Materials"},{"key":"e_1_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.1145\/356683.356685"},{"key":"e_1_3_3_80_2","first-page":"64","volume-title":"9th International Conference on Scientific and Statistical Database Management (Cat. No. 97TB100150)","author":"Yu Jie Bing","year":"1997","unstructured":"Jie Bing Yu and D. J. DeWitt. 1997. Query pre-execution and batching in paradise: A two-pronged approach to the efficient processing of queries on tape-resident raster images. In 9th International Conference on Scientific and Statistical Database Management (Cat. No. 97TB100150). IEEE, Olympia, WA, 64\u201378."},{"issue":"4","key":"e_1_3_3_81_2","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/nmat4594","article-title":"Nucleic acid memory","volume":"15","author":"Zhirnov Victor","year":"2016","unstructured":"Victor Zhirnov, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, and William L. Hughes. 2016. Nucleic acid memory. Nature Materials 15, 4 (2016), 366\u2013370.","journal-title":"Nature Materials"}],"container-title":["ACM Journal on Emerging Technologies in Computing Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3744562","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,13]],"date-time":"2025-08-13T11:22:31Z","timestamp":1755084151000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3744562"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,31]]},"references-count":80,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,7,31]]}},"alternative-id":["10.1145\/3744562"],"URL":"https:\/\/doi.org\/10.1145\/3744562","relation":{},"ISSN":["1550-4832","1550-4840"],"issn-type":[{"type":"print","value":"1550-4832"},{"type":"electronic","value":"1550-4840"}],"subject":[],"published":{"date-parts":[[2025,7,31]]},"assertion":[{"value":"2024-08-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-03-26","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-08-13","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}