Related papers: Models and information-theoretic bounds for nanopo…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
In this study, we examine the mechanism of nanopore-based DNA sequencing using a voltage bias across a graphene nanoribbon. Using density functional theory and a non-equilibrium Green's function approach, we determine the transmission…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
Nanopore sequencing, a next-generation sequencing technology, holds the potential to revolutionize multiple facets of life sciences, forensics, and healthcare. While previous research has focused on its technical intricacies and biomedical…
Longitudinal resolution and lateral sensitivity are decisive characteristics that determine the suitability of a nanopore sensor for sequencing a strand of DNA as well as other important polymers. Previous modeling of DNA induced ionic…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
High-throughput solid-state nanopore experiments generate continuous MHz-rate data streams in which only a small fraction of data contains informative molecular information. This creates storage and processing bottlenecks that limit…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the…
Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel…
Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
A device capable of performing real time classification of proteins in a clinical setting would allow for inexpensive and rapid disease diagnosis. One such candidate for this technology are nanopore devices. These devices work by measuring…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…