Related papers: Codon Bias Patterns of $E.coli$'s Interacting Prot…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
In this paper it is shown that within a Combined Genetic Code Table, realized through a combination of Watson-Crick Table and Codon Path Cube it exists, without an exception, a strict distinction between two classes of enzymes…
Statistical analysis of protein-protein interactions shows anomalously high frequency of homodimers [Ispolatov, I., et al. (2005) Nucleic Acids Res 33, 3629-35]. Furthermore, recent findings [Wright, C.F., et al. (2005) Nature 438, 878-81]…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
The widespread adoption of large language models (LLMs) and generative AI (GenAI) tools across diverse applications has amplified the importance of addressing societal biases inherent within these technologies. While the NLP community has…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
For synergistic interactions between humans and artificial intelligence (AI) systems, AI outputs often need to be explainable to people. Explainable AI (XAI) systems are commonly tested in human user studies. However, whether XAI…
An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism's genome, a…
Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results…
We have performed a statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli. The analysis reveals that operons that regulate each other and operons that are coregulated tend…
Predicting gene functions is a challenge for biologists in the post genomic era. Interactions among genes and their products compose networks that can be used to infer gene functions. Most previous studies adopt a linkage assumption, i.e.,…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
Human-AI co-creativity involves both humans and AI collaborating on a shared creative product as partners. In a creative collaboration, interaction dynamics, such as turn-taking, contribution type, and communication, are the driving forces…
Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
In this work, we propose a novel centrality metric, referred to as star centrality, which incorporates information from the closed neighborhood of a node, rather than solely from the node itself, when calculating its topological importance.…
Sharing genome data in a privacy-preserving way stands as a major bottleneck in front of the scientific progress promised by the big data era in genomics. A community-driven protocol named genomic data-sharing beacon protocol has been…