Related papers: Improving sequencing by tunneling with multiplexin…
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra- and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
Feature embedding methods have been proposed in literature to represent sequences as numeric vectors to be used in some bioinformatics investigations, such as family classification and protein structure prediction. Recent theoretical…
It is shown that in a structure consisting of a superconducting ring-shaped electrode overlapped by a normal metal contact through a thin oxide barrier, measurements of the tunnel current in magnetic field can probe persistent currents in…
High-throughput and quantitative experimental technologies are experiencing rapid advances in the biological sciences. One important recent technique is multiplexed fluorescence in situ hybridization (mFISH), which enables the…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
The phenomenon of resonant tunneling transport through polar double-barrier heterostructures is systematically investigated using a combined experimental and theoretical approach. On the experimental side, GaN/AlN RTDs are grown by MBE.…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional…