Related papers: Finite-State Semi-Markov Channels for Nanopore Seq…

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…

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 technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…

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…

Solid-state nanopores, nm-sized holes in thin, freestanding membranes, are powerful single-molecule sensors capable of interrogating a wide range of target analytes, from small molecules to large polymers. Interestingly, due to their high…

The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…

In nanopore technology, the development of multiplexed detection and release platforms with high spatial and temporal resolution remains a significant challenge due to the difficulty in distinguishing signals originating from different…

We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…

Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…

Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…

Regular perturbation is applied to the Manakov equation and motivates a generalized correlated phase-and-additive noise model for wavelength-division multiplexing over dual-polarization optical fiber channels. The model includes three…

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…

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…

Proteins are arguably the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analysing biomolecules such as proteins at single-molecule level.…

Single-molecule based 3rd generation DNA sequencing technologies have been explored with tremendous effort, among which nanopore sequencing is considered as one of the most promising to achieve the goal of $1,000 genome project towards…

Solid-state nanopores are emerging platforms for single-molecule protein sequencing due to their tolerance to hash physiology environment and compatibility with different electrical and optical detection methods. However, they suffer from…

With advancements in telecommunications, data transmission over increasingly harsher channels that produce synchronisation errors is inevitable. Coding schemes for such channels are available through techniques such as the Davey-MacKay…

Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…

Modern deep neural networks (DNNs) become frail when the datasets contain noisy (incorrect) class labels. Robust techniques in the presence of noisy labels can be categorized into two folds: developing noise-robust functions or using…