Related papers: Codon Bias Patterns of $E.coli$'s Interacting Prot…
We analyse forty seven chloroplastid genes of the large subunit of RuBisCO, from the Algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base bias defines our score called the Codon-Impact-Parameter. This…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
In this paper, we study the performance of network-coded cooperative diversity systems with practical communication constraints. More specifically, we investigate the interplay between diversity, coding, and multiplexing gain when the relay…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Brain can be represented as a network, where regions are the nodes and relations between the regions are edges. Within a network, co-existence of cooperative and competitive relationships between different nodes is called coopetition.…
Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…
Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been…
Biomedical sciences are increasingly recognising the relevance of gene co-expression-networks for analysing complex-systems, phenotypes or diseases. When the goal is investigating complex-phenotypes under varying conditions, it comes…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…
Current Explainable AI (XAI) focuses on explaining a single application, but when encountering related applications, users may rely on their prior understanding from previous explanations. This leads to either overgeneralization and AI…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
Generative AI (genAI) tools promise productivity gains, yet miscalibrated trust and usage friction still hinder adoption. Moreover, genAI can be exclusionary, failing to adequately support diverse users. One such aspect of diversity is…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
In the present article, we propose a paradigm shift on evolving Artificial Neural Networks (ANNs) towards a new bio-inspired design that is grounded on the structural properties, interactions, and dynamics of protein networks (PNs): the…
It is well known that correlations in microarray data represent a serious nuisance deteriorating the performance of gene selection procedures. This paper is intended to demonstrate that the correlation structure of microarray data provides…
Variational Auto-Encoders (VAEs) are capable of learning latent representations for high dimensional data. However, due to the i.i.d. assumption, VAEs only optimize the singleton variational distributions and fail to account for the…
This work is concerned with the development of a well-founded, theoretically justified, and least complicated metric for the classification of proteins with reference to enzymes. As the signature of an enzyme family, a catalytic domain is…
This review examines the evidence in the literature for physiological co-modulation during human-animal interaction. The aim of this work is to identify studies that assessed co-modulation via simultaneous measurement of physiological…