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Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
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…
Cryptography is the science that secures data and communication over the network by applying mathematics and logic to design strong encryption methods. In the modern era of e-business and e-commerce the protection of confidentiality,…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
DNA samples crime cases analysed in forensic genetics, frequently contain DNA from multiple contributors. These occur as convolutions of the DNA profiles of the individual contributors to the DNA sample. Thus, in cases where one or more of…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
We study the unzipping of a double stranded DNA (dsDNA) by applying an external force on a single strand while leaving the other strand free. We find that the dsDNA can be unzipped to two single strands if the external force exceeds a…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
This paper reports some experimental results validating in a broader context a variant of PCR, called XPCR, previously introduced and tested on relatively short synthetic DNA sequences. Basic XPCR technique confirmed to work as expected, to…
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the…
DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. While sequencing based technologies are increasingly allowing high resolution measurements of DNA methylation,…
Drug discovery is adapting to novel technologies such as data science, informatics, and artificial intelligence (AI) to accelerate effective treatment development while reducing costs and animal experiments. AI is transforming drug…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
Human and animal tissues consist of heterogeneous cell types that organize and interact in highly structured manners. Bulk and single-cell sequencing technologies remove cells from their original microenvironments, resulting in a loss of…
This paper proposed a new method to build the large scale DNA sequences search system based on web search engine technology. We give a very brief introduction for the methods used in search engine first. Then how to build a DNA search…
We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA…