Related papers: Improving sequencing by tunneling with multiplexin…

In the presence of security countermeasures, a malware designed for data exfiltration must do so using a covert channel to achieve its goal. Among existing covert channels stands the domain name system (DNS) protocol. Although the detection…

Reliable detection of single electron tunneling in quantum dots (QD) is paramount to use this category of device for quantum information processing. Here, we report charge sensing in a degenerately phosphorus-doped silicon QD by means of a…

DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…

DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…

The design and analysis of communication systems typically rely on the development of mathematical models that describe the underlying communication channel. However, in some systems, such as molecular communication systems where chemical…

Many approaches to transform classification problems from non-linear to linear by feature transformation have been recently presented in the literature. These notably include sparse coding methods and deep neural networks. However, many of…

A single electron shared between two levels threaded by a magnetic flux is an irreducibly simple quantum system in which interference is predicted to occur. We demonstrate tuning of the tunnel coupling between two such electronic levels…

We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA sequences by plasmonic nanopores could pave a way to new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time…

An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…

The analysis of single-cell RNA sequencing (scRNA-seq) data often involves fitting a latent variable model to learn a low-dimensional representation for the cells. Validating such a model poses a major challenge. If we could sequence the…

One of the long-standing goals of quantum transport is to use the noise, rather than the average current, for information processing. However, achieving this requires on-demand control of quantum fluctuations in the electric current. In…

In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…

Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…

Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…

Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution…

Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…

Deep sequencing has become one of the most popular tools for transcriptome profiling in biomedical studies. While an abundance of computational methods exists for "normalizing" sequencing data to remove unwanted between-sample variations…

Real-time detection of single electron tunneling through a T-shaped double quantum dot is simulated, based on a Monte Carlo scheme. The double dot is embedded in a dissipative environment and the presence of electrons on the double dot is…

We present a novel neural network for processing sequences. The ByteNet is a one-dimensional convolutional neural network that is composed of two parts, one to encode the source sequence and the other to decode the target sequence. The two…