Related papers: Coded Shotgun Sequencing
Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…
Recurrent neural networks (RNNs) have been applied to a broad range of applications, including natural language processing, drug discovery, and video recognition. Their vulnerability to input perturbation is also known. Aligning with a view…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
In the Levenshtein's sequence reconstruction problem a codeword is transmitted through $N$ channels and in each channel a set of errors is introduced to the transmitted word. In previous works, the restriction that each channel provides a…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
Fairly recently, a new encryption scheme for audio data encryption has been proposed by Naskar, P.K., et al. The cryptosystem is based on substitution-permutation encryption structure using DNA encoding at the substitution stage, in which…
Secure communication is the cornerstone of modern infrastructures, yet achieving unconditional security -resistant to any computational attack- remains a fundamental challenge. The One-Time Pad (OTP), proven by Shannon to offer perfect…
As long as human beings exist on this earth, there will be confidential images intended for limited audience. These images have to be transmitted in such a way that no unauthorized person gets knowledge of them. DNA sequences play a vital…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In [Daskalakis et al.'09], building on the…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA…
Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…