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Theoretical Approaches in Molecular Sciences

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (20 June 2024) | Viewed by 1433

Special Issue Editor

Special Issue Information

Dear Colleagues,

Many theoretical tools from various origins (mathematics, computer science, statistics, theoretical physics, etc.) are used to model the structure and dynamics of molecules, especially in biology. The general theme of this Special Issue is broad and can correspond to the following topics:

  • Enzymatic kinetics;
  • Membrane dynamics;
  • Molecular aspects of the genetic networks;
  • Molecular aspects of the metabolic networks;
  • Protein/RNA interactions;
  • Phylogenies of biological molecules;
  • Chemistry of the origin of life;
  • Molecular modeling in immunology;
  • Molecular modeling in epigenetics;
  • Molecular modeling of the cell respiration;
  • Molecular models of the biological rhythms;
  • Molecular models of the embryonic development;
  • Molecular interactions in brain functioning.

Prof. Dr. Jacques Demongeot
Guest Editor

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Published Papers (1 paper)

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Research

17 pages, 9730 KiB  
Article
An Unsupervised Classifier for Whole-Genome Phylogenies, the Maxwell© Tool
by Joël Gardes, Christophe Maldivi, Denis Boisset, Timothée Aubourg and Jacques Demongeot
Int. J. Mol. Sci. 2023, 24(22), 16278; https://doi.org/10.3390/ijms242216278 - 13 Nov 2023
Cited by 1 | Viewed by 1013
Abstract
The development of phylogenetic trees based on RNA or DNA sequences generally requires a precise and limited choice of important RNAs, e.g., messenger RNAs of essential proteins or ribosomal RNAs (like 16S), but rarely complete genomes, making it possible to explain evolution and [...] Read more.
The development of phylogenetic trees based on RNA or DNA sequences generally requires a precise and limited choice of important RNAs, e.g., messenger RNAs of essential proteins or ribosomal RNAs (like 16S), but rarely complete genomes, making it possible to explain evolution and speciation. In this article, we propose revisiting a classic phylogeny of archaea from only the information on the succession of nucleotides of their entire genome. For this purpose, we use a new tool, the unsupervised classifier Maxwell, whose principle lies in the Burrows–Wheeler compression transform, and we show its efficiency in clustering whole archaeal genomes. Full article
(This article belongs to the Special Issue Theoretical Approaches in Molecular Sciences)
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