Related papers: Optimizing Sequencing Coverage Depth in DNA Storag…
Compression and efficient storage of neural network (NN) parameters is critical for applications that run on resource-constrained devices. Despite the significant progress in NN model compression, there has been considerably less…
In order to overcome the limitations imposed by DNA barcoding when multiplexing a large number of samples in the current generation of high-throughput sequencing instruments, we have recently proposed a new protocol that leverages advances…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
Distributed storage systems often introduce redundancy to increase reliability. When coding is used, the repair problem arises: if a node storing encoded information fails, in order to maintain the same level of reliability we need to…
In this paper, we examine the problem of information storage on memristors affected by resistive drift noise under energy constraints. We introduce a novel, fundamental trade-off between the information lifetime of memristive states and the…
In this paper, we study how often unique decoding from $t$ insertions or $t$ deletions occurs for error correcting codes. Insertions and deletions frequently occur in synchronization problems and DNA, a medium which is beginning to be used…
As consumers are increasingly engaged in social networking and E-commerce activities, businesses grow to rely on Big Data analytics for intelligence, and traditional IT infrastructures continue to migrate to the cloud and edge, these trends…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of…
Storing information in DNA molecules is of great interest because of its advantages in longevity, high storage density, and low maintenance cost. A key step in the DNA storage pipeline is to efficiently cluster the retrieved DNA sequences…
Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Modern distributed storage systems offer large capacity to satisfy the exponentially increasing need of storage space. They often use erasure codes to protect against disk and node failures to increase reliability, while trying to meet the…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Supervised learning on Deep Neural Networks (DNNs) is data hungry. Optimizing performance of DNN in the presence of noisy labels has become of paramount importance since collecting a large dataset will usually bring in noisy labels.…