Related papers: Fundamental Limits of Pooled-DNA Sequencing
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
For decades, forensic statisticians have debated whether searching large DNA databases undermines the evidential value of a match. Modern surveillance faces an exponentially harder problem: screening populations across thousands of…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
This paper studies achievable rates of nanopore-based DNA storage when nanopore signals are decoded using a tractable channel model that does not rely on a basecalling algorithm. Specifically, the noisy nanopore channel (NNC) with the…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
Label noise may affect the generalization of classifiers, and the effective learning of main patterns from samples with noisy labels is an important challenge. Recent studies have shown that deep neural networks tend to prioritize the…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
This paper studies sequential methods for recovery of sparse signals in high dimensions. When compared to fixed sample size procedures, in the sparse setting, sequential methods can result in a large reduction in the number of samples…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples…
The seminal paper by Mazumdar and Saha \cite{MS17a} introduced an extensive line of work on clustering with noisy queries. Yet, despite significant progress on the problem, the proposed methods depend crucially on knowing the exact…
Freely available and easy-to-use audio editing tools make it straightforward to perform audio splicing. Convincing forgeries can be created by combining various speech samples from the same person. Detection of such splices is important…
We consider the problem of detecting the overlap between a pair of short fragments sampled in random locations from an exponentially longer sequence, via their possibly noisy reads. We consider a noiseless setting, in which the reads are…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…