{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T11:08:35Z","timestamp":1720609715219},"reference-count":43,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2022,8]]},"DOI":"10.1016\/j.compbiolchem.2022.107696","type":"journal-article","created":{"date-parts":[[2022,5,21]],"date-time":"2022-05-21T23:31:39Z","timestamp":1653175899000},"page":"107696","update-policy":"http:\/\/dx.doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Cipher constrained encoding for constraint optimization in extended nucleic acid memory"],"prefix":"10.1016","volume":"99","author":[{"given":"Saptarshi","family":"Biswas","sequence":"first","affiliation":[]},{"given":"Sumagna","family":"Dey","sequence":"additional","affiliation":[]},{"given":"Pradyut","family":"Nath","sequence":"additional","affiliation":[]},{"given":"Subhrapratim","family":"Nath","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2022.107696_bib1","doi-asserted-by":"crossref","unstructured":"Alsaffar, Q.S., Mohaisen, H.N., Almashhdini, F.N., 2021. An encryption based on DNA and AES algorithms for hidinga compressed text in colored Image. IOP Conf. Ser. Mater. Sci. Eng, pp. 1\u201312.","DOI":"10.1088\/1757-899X\/1058\/1\/012048"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib2","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1038\/s41587-019-0240-x","article-title":"Data storage in DNA with fewer synthesis cycles using composite DNA letters","volume":"37","author":"Anavy","year":"2019","journal-title":"Nat. Biotechnol."},{"issue":"1\/2","key":"10.1016\/j.compbiolchem.2022.107696_bib3","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1504\/IJNBM.2020.107412","article-title":"Extended nucleic acid memory as the future of data storage technology","volume":"9","author":"Biswas","year":"2020","journal-title":"Int. J. Nano Biomater."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib4","doi-asserted-by":"crossref","unstructured":"Biswas, S., et al., 2019. Storing digital data in nucleic acid memory with extended genetic alphabet. Devices for Integrated Circuit (DevIC), Kalyani, India, pp. 236\u2013239.","DOI":"10.1109\/DEVIC.2019.8783912"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib5","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1016\/j.procs.2016.05.398","article-title":"Forward error correction for DNA data storage","volume":"80","author":"Blawat","year":"2016","journal-title":"Procedia Comput. Sci."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib6","doi-asserted-by":"crossref","unstructured":"Bornholt, J., Lopez, R., Carmean, D.M., Ceze, L., Seelig, G., Strauss, K., 2016. A DNA-based archival storage system. In: Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems, pp. 637\u2013649.","DOI":"10.1145\/2954680.2872397"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib7","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/s41576-019-0125-3","article-title":"Molecular digital data storageusing DNA","volume":"20","author":"Ceze","year":"2019","journal-title":"Nat. Rev."},{"issue":"6582","key":"10.1016\/j.compbiolchem.2022.107696_bib8","article-title":"High information capacity DNA-based data storage with augmented encoding characters using degenerate bases","volume":"9","author":"Choi","year":"2019","journal-title":"Sci. Rep."},{"issue":"6102","key":"10.1016\/j.compbiolchem.2022.107696_bib9","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1126\/science.1226355","article-title":"Next-generation digital information storage in DNA","volume":"337","author":"Church","year":"2012","journal-title":"Science"},{"issue":"6328","key":"10.1016\/j.compbiolchem.2022.107696_bib10","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1126\/science.aaj2038","article-title":"DNA fountain enables a robust and efficient storage architecture","volume":"355","author":"Erlich","year":"2017","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.compbiolchem.2022.107696_bib11","first-page":"331","article-title":"A new approach to generate multi s-boxes based on RNA computing","volume":"16","author":"Farhan","year":"2020","journal-title":"Int. J. Innov. Comput. Inf. Control"},{"issue":"7435","key":"10.1016\/j.compbiolchem.2022.107696_bib12","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1038\/nature11875","article-title":"Towards practical, high-capacity, low-maintenance information storage in synthesized DNA","volume":"494","author":"Goldman","year":"2013","journal-title":"Nature"},{"issue":"8","key":"10.1016\/j.compbiolchem.2022.107696_bib13","doi-asserted-by":"crossref","first-page":"2552","DOI":"10.1002\/anie.201411378","article-title":"Robust chemical preservation of digital information on DNA in silica with error-correcting codes","volume":"54","author":"Grass","year":"2015","journal-title":"Angew. Chem. Int. Ed."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib14","doi-asserted-by":"crossref","unstructured":"Hatkar, S.S., Pawar, B.K., 2016. Symmetric key algorithm using vernam cipher: VSA. In: Proceedings of the International Conference on Inventive Computation Technologies (ICICT), pp. 1\u20135. \u300810.1109\/INVENTIVE.2016.7830196\u3009.","DOI":"10.1109\/INVENTIVE.2016.7830196"},{"issue":"7","key":"10.1016\/j.compbiolchem.2022.107696_bib15","doi-asserted-by":"crossref","first-page":"345","DOI":"10.2183\/pjab.88.345","article-title":"Unnatural base pair systems toward theexpansion of the genetic alphabet in the central dogma","volume":"88","author":"Hirao","year":"2012","journal-title":"Proc. Jpn. Acad. Ser. B Phys. Biol. Sci."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib16","doi-asserted-by":"crossref","first-page":"15549","DOI":"10.1021\/ja073830m","article-title":"An efficient unnatural base pair for PCR amplification","volume":"129","author":"Hirao","year":"2007","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib17","doi-asserted-by":"crossref","unstructured":"Hirao, I., et al., 2006. An unnatural base pair system for in vitroreplication and transcription. Nucleic Acid Symposium Series No. 50, pp. 33\u201334.","DOI":"10.1093\/nass\/nrl017"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib18","doi-asserted-by":"crossref","unstructured":"Hussein, H.I., Abduallah, W.M., 2018. A modified table lookup substitution method for hiding data in DNA. In: Proceedings of the International Conference on Advanced Science and Engineering, pp. 268\u2013273. \u300810.1109\/ICOASE.2018.8548863\u3009.","DOI":"10.1109\/ICOASE.2018.8548863"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib19","unstructured":"Immink, K.A.S., Cai, K., 2018. Design of capacity-approaching constrained codes for DNA-based storage systems. IEEE Commun. Lett."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib20","doi-asserted-by":"crossref","first-page":"5839","DOI":"10.1021\/acs.jpcb.5b03293","article-title":"What sustains the unnatural base pairs (UBPs) with no hydrogen bonds","volume":"119","author":"Jahiruddin","year":"2015","journal-title":"J. Phys. Chem."},{"issue":"1","key":"10.1016\/j.compbiolchem.2022.107696_bib21","first-page":"1","article-title":"A proposal for a DNA-based computer code","volume":"1","author":"Jim\u00e9nez-S\u00e1nchez","year":"2013","journal-title":"Int. Invent. J. Biochem. Bioinform."},{"issue":"4","key":"10.1016\/j.compbiolchem.2022.107696_bib22","first-page":"8","article-title":"DNA computer code based on expanded genetic alphabet","volume":"2","author":"Jim\u00e9nez-S\u00e1nchez","year":"2014","journal-title":"J. Comput. Sci. Technol."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib23","doi-asserted-by":"crossref","first-page":"49","DOI":"10.9790\/0661-16294953","article-title":"Survey: recent modifications in Vigen\u00e8re Cipher","volume":"16","author":"Kartha","year":"2014","journal-title":"IOSR J. Comput. Eng."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib24","first-page":"3","article-title":"Replication of non-hydrogen bonded bases by DNA polymerases: a mechanism for steric matching","volume":"48","author":"Kool","year":"1998","journal-title":"Biopolym. Nucleic Acid. Sci."},{"issue":"2383","key":"10.1016\/j.compbiolchem.2022.107696_bib25","article-title":"Terminator-free template-independent enzymatic DNA synthesis for digital information storage","volume":"10","author":"Lee","year":"2019","journal-title":"Nat. Commun."},{"issue":"5","key":"10.1016\/j.compbiolchem.2022.107696_bib26","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1016\/j.bbapap.2009.08.023","article-title":"Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases","volume":"1804","author":"Lee","year":"2010","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-10978-4","article-title":"DNA assembly for nanopore data storage readout","volume":"10","author":"Lopez","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib28","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nature13314","article-title":"A semi-synthetic organism with anexpanded genetic alphabet","volume":"509","author":"Malyshev","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib29","doi-asserted-by":"crossref","unstructured":"Nguyen, T.T., Cai, K., Immink, K.A.S., Kiah, H.M., 2020. Capacity-Approaching Constrained Codes with Error Correction for DNA-Based Data Storage. arXiv:2001.02839 [cs.IT], 1\u201313 of 13.","DOI":"10.1109\/ISIT44484.2020.9174438"},{"issue":"3","key":"10.1016\/j.compbiolchem.2022.107696_bib30","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/nbt.4079","article-title":"Random access in large-scale DNA data storage","volume":"36","author":"Organick","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib31","unstructured":"Public-Domain Test Images for Homeworks and Projects, 2021. Fabien a.p. petitcolas, University of Wisconsin. Available: \u3008https:\/\/homepages.cae.wisc.edu\/~ece533\/images\/\u3009."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib32","first-page":"108","article-title":"A cryptosystem based on Vigen\u00e8re cipher with varying key","volume":"1","author":"Quist-Aphetsi","year":"2012","journal-title":"Int. J. Adv. Res. Comput. Eng. Technol."},{"issue":"2","key":"10.1016\/j.compbiolchem.2022.107696_bib33","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1248\/cpb.c17-00685","article-title":"Unnatural base pairs for synthetic biology","volume":"66","author":"Saito-Tarashima","year":"2018","journal-title":"Chem. Pharm. Bull."},{"issue":"2","key":"10.1016\/j.compbiolchem.2022.107696_bib34","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1093\/nar\/gkh241","article-title":"PCR amplification of DNA containingnon-standard base pairs by variants of reverse transcriptase from human immunodeficiency virus-1","volume":"32","author":"Sismour","year":"2004","journal-title":"Nucleic Acid. Res."},{"issue":"10","key":"10.1016\/j.compbiolchem.2022.107696_bib35","doi-asserted-by":"crossref","first-page":"2004","DOI":"10.1109\/LCOMM.2018.2866566","article-title":"Codes with run-length and GC-content constraints for DNA-based data storage","volume":"22","author":"Song","year":"2018","journal-title":"IEEE Commun. Lett."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib36","unstructured":"Standard Test Images, 2021. Mike Wakin, University of Michigan, Rice University. Available: \u3008https:\/\/www.ece.rice.edu\/~wakin\/images\/\u3009."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib37","doi-asserted-by":"crossref","unstructured":"Suyehira, K., Llewellyn, S., Zadegan, R.M., Hughes, W.L., Andersen, T., 2017. A coding scheme for nucleic acid memory (NAM). In: Proceedings of the IEEE Workshop on Microelectronics and Electron Devices (WMED).","DOI":"10.1109\/WMED.2017.7916922"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib38","doi-asserted-by":"crossref","unstructured":"Triandi, B., et al., 2018. Improve security algorithm cryptography Vigen\u00e8re Cipher using chaos functions. In: Proceedings of the 2018 6th International Conference on Cyber and IT Service Management (CITSM). IEEE, Parapat, Indonesia, pp. 1\u20135.","DOI":"10.1109\/CITSM.2018.8674376"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib39","doi-asserted-by":"crossref","unstructured":"Wang, Y., Noor-A-Rahim, Md., Gunawan, E., Guan, Y.L., Poh, C.L., 2019. Construction of bio-constrained code for DNA data storage. IEEE Commun. Lett.","DOI":"10.1109\/LCOMM.2019.2912572"},{"key":"10.1016\/j.compbiolchem.2022.107696_bib40","first-page":"1","article-title":"A rewritable, random-access DNA-based storage system","volume":"5","author":"Yazdi","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-05188-1","article-title":"Portable and error-free DNA-based data storage","volume":"7","author":"Yazdi","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.compbiolchem.2022.107696_bib42","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nature24659","article-title":"A semi-synthetic organism that stores andretrieves increased genetic information","volume":"551","author":"Zhang","year":"2017","journal-title":"Nature"},{"issue":"4","key":"10.1016\/j.compbiolchem.2022.107696_bib43","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/nmat4594","article-title":"Nucleic acid memory","volume":"15","author":"Zhirnov","year":"2016","journal-title":"Nat. Mater."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927122000767?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927122000767?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2023,4,3]],"date-time":"2023-04-03T11:24:20Z","timestamp":1680521060000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927122000767"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8]]},"references-count":43,"alternative-id":["S1476927122000767"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2022.107696","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2022,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Cipher constrained encoding for constraint optimization in extended nucleic acid memory","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2022.107696","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"107696"}}