20 papers · ranked by Valyu relevance
Ken Nishikawa, Akira R. Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however…
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…
Haitham Marakeby, Eman Badr, Hanaa Torkey, Yuhyun Song + 5 more
'Scotland Leman' 'Caroline L. Monteil' 'Lenwood S. Heath' 'Boris A. Vinatzer' 'Dawn Arnold'] A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and…
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'…
Ian Holmes
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by interleaving watermark and periodic marker signals; conversion from binary to…
Eric Bouton, H. M. de Oliveira, Ricardo M. Campello de Souza, Nereide Stela Santos-Magalhães
'Nereide Stela Santos-Magalhães'] Abstract: - This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2 grams are offered as an alternative to spectrograms and scalograms.…
Robersy Sanchez, Jesús Barreto
Experimental studies reveal that genome architecture splits into natural domains suggesting a well-structured genomic architecture, where, for each species, genome populations are integrated by individual mutational variants. Herein, we show that the architecture of population genomes from the same or closed related…
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)…
Бранко Драгович, Andrei Yu. Khrennikov, N.Ž. Mišić
Ultrametric approach to the genetic code and the genome is considered and developed. p-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be treated as p-adic ultrametric networks. Ultrametric modification of the Hamming…
H. M. de Oliveira, Nereide Stela Santos-Magalhães
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting symbolic-DNA strings into complex-valued signals in order to take full advantage…
Mohamed A. E. Soliman Mahdy
Genetic information is stored within the DNA molecule in the form of a triplet code, which is a sequence of three nucleotide bases which will translate through the mRNA to amino acid. Each triplet of nucleotide bases, which codes for a single amino acid is called a codon, it is the basic unit of genetic code. Gene…
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…
Marcelo M. Brandão, Larissa Spoladore, Luzinete C. B. Faria, Andréa S. L. Rocha + 2 more
'Andréa S. L. Rocha' 'Marcio C. Silva-Filho' 'Reginaldo Palazzo'] A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a…
Chao Pan, S. M. Hossein Tabatabaei Yazdi, S Kasra Tabatabaei, Álvaro González Hernández + 2 more
'Álvaro González Hernández' 'Charles E. Schroeder' 'Olgica Milenković'] The main obstacles for the practical deployment of DNAbased data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain both…
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…
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…
Gur Pines, James D. Winkler, Assaf Pines, Ryan T. Gill + 1 more
'Sang Yup Lee'] Title: ABSTRACT The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant…
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…
Yulián A. Alvarez-Ballesteros, Mario A. Quiroz‐Juárez, José L. Del-Rio-Correa, A. M. Escobar-Ruiz
Graphical Representations and Cytogenetics Authors: ['Yulián A. Alvarez-Ballesteros' 'Mario A. Quiroz‐Juárez' 'José L. Del-Rio-Correa' 'A. M. Escobar-Ruiz'] In this work, we applied the Chaos Game Representation (CGR) to the complete human genomic sequence T2T-CHM13v2.0, analyzing the entire chromosome assembly and…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…