16 papers · ranked by Valyu relevance
Xiaoluo Huang, Yu Wang, Jiaxin Xu, Ziang Nie + 5 more
DNA data storage offers a viable strategy to address the impending data explosion. Early attempts to harness DNA as a storage medium have encountered scalability limitations, largely due to the complexity of codec algorithms, the generation of biochemically harmful sequences and lack of a robust architecture. We…
Dana Cohen, Stefano Lonardi
This study seeks to investigate distinct signatures and codes within different genomic sequence locations of the human genome. The promoter and other non-coding regions contain sites for the binding of biological particles, for processes such as transcription regulation. The specific rules and sequence codes that…
Chenyang Wang, Di Wei, Zheng Wei, Dongxin Yang + 27 more
'Yunze Wang' 'Xiaotong Wang' 'Pei Wang' 'Guannan Ma' 'Xinru Zhang' 'Haolan Li' 'Chuan Tang' 'Pengfei Hou' 'Jie Wang' 'Renjun Gao' 'Guiqiu Xie' 'Cuidan Li' 'Yingjiao Ju' 'Peihan Wang' 'Liya Yue' 'Yongliang Zhao' 'Yongjie Sheng' 'Jingfa Xiao' 'Haitao Niu' 'Sihong Xu' 'Huaiyi Yang' 'Di Liu' 'Bo Duan' 'Dongbo Bu'…
Ben Cao, Xue Li, Bin Wang, Tiantian He + 3 more
DNA as a storage medium has the characteristics of high storage density and durability, but the existing DNA storage system has a high latency, and lacks the consideration of data security. In order to improve the availability of DNA storage, this paper proposes that Frequency Dictionary Mapping Coding (FDMC)…
Shibsankar Das, Krishna Gopal Benerjee, Adrish Banerjee
—In this paper, we present a novel design strategy of DNA codes with length 3n over the non-chain ring R = Z4 + uZ4 + u 2Z4 with 64 elements and u 3 = 1, where n denotes the length of a code over R. We first study and analyze a distance conserving map defined over the ring R into the length-3 DNA sequences. Then, we…
Zhaoguan Wang, Jingsong Cui, Qian Liu, Jiawei Li + 7 more
The authenticity and integrity of synthetic genomic materials containing valuable intellectual property are essential for advancing scientific knowledge and enhancing biosafety. Existing DNA tags and watermarks, however, have limited efficacy due to low mutation tolerance and inadequate digital encoding capacity. Here…
Aaron Pfennig, Alexandre Lomsadze, Mark Borodovsky
Some of recently discovered in human gut microbiome highly divergent crAssphages were reported to use multiple genetic codes. Opal or amber stop codon reassignments were present in parts of the genomes, while the standard genetic code was used in the remaining genome sections. Essentially, the phage genomes were…
Siddhartha Siddhiprada Bhoi, Paramapalli Udaya, Abhay Kumar Singh
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and sequencing processes. In this letter, our goal is to tackle the problems due to…
Kevin J. Mitchell, Nick Cheney
How does the genome encode the form of the organism? What is the nature of this genomic code? Common metaphors, such as a "blueprint" or "program", fail to capture the complex, indirect, and evolutionarily dynamic relationship between the genome and organismal form, or the constructive, interactive processes that…
Chu Cheng, Pengfeng Xiao
This article proposed the correctable decoding sequencing technology with conservative theoretical error rate of 0.0009%, and evaluated its robustness by simulation. This technology can provide a powerful new protocol for NGS platforms, enabling accurate identification of rare mutations in medicine.
Dowan Kim, Ishita Kumar, Mohamed I. Hassan, Luisa F. Barraza-Vergara + 2 more
The protection of high-value cell lines (assets) relies on physical security by limiting access to samples. We present a cybersecurity-inspired platform that protects biological assets at the genetic level. This technology uses a permutation lock design where an asset can only be decrypted using an authentication code…
Yuting Chen, Eriona Hysolli, Anlu Chen, Stephen Casper + 4 more
'Kevin Yang' 'Chenli Liu' 'George Church'] Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single…
Guodong Wang, Hongwei Liu, Xueyan Chen
searching algorithms Authors: ['Guodong Wang' 'Hongwei Liu' 'Xueyan Chen'] DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes [13] and reversible composite…
Avanish Kumar Chaturvedi, Satyadeep Pandey
In this paper, we develop a generalized framework for constructing reversible linear, reversible self dual and reversible DNA codes using a matrix-theoretic approach based on involutory matrices. The proposed concatenation scheme gives a large class of generator matrices and yields codes with good parameters. The…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Yueming Wu, Chengwei Liu, Yang Liu
With the boom in modern software development, open-source software has become an integral part of various industries, driving progress in computer science. However, the immense complexity and diversity of the open-source ecosystem also pose a series of challenges, including issues of quality, security, management…