Related papers: Complete Human Mitochondrial Genome Construction U…
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to…
Large language models (LLMs) have achieved great success in many fields, and recent works have studied exploring LLMs for graph discriminative tasks such as node classification. However, the abilities of LLMs for graph generation remain…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
The development of autonomous molecular computers capable of making independent decisions in vivo regarding local drug administration may revolutionize medical science. Recently Benenson at el (2004) have envisioned one form such a ``smart…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
This paper proposes a methodology of integrating the Linear Graph (LG) approach with Genetic Programming (GP) for generating an automated multi-domain engineering design approach by using the in-house developed LG MATLAB toolbox and the GP…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…
The emerging field of epigenetics has recently unveiled a dynamic landscape in which gene expression is not determined solely by genetic sequences but also by intricate regulatory mechanisms. This review examines the interactions between…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown…
Gene essentiality refers to the degree to which a gene is necessary for the survival and reproductive efficacy of a living organism. Although the essentiality of non-coding genes has been documented, there are still aspects of non-coding…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
The human genome remains incomplete, with multi-megabase sized gaps representing the endogenous centromeres and other heterochromatic regions. These regions are commonly enriched with long arrays of near-identical tandem repeats, known as…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…