Publications by authors named "Simone Giannerini"

Article Synopsis
  • In the mid-20th century, molecular biology and information-communication theory emerged, initially leading to a deep synergy in understanding genetic codes and their meanings.
  • Over time, despite advancements, the collaboration between these fields has faced challenges that complicate efforts in next-generation biology, including personalized therapies and protein production.
  • To overcome these challenges, a paradigm shift in theoretical biology is necessary, demanding a multidisciplinary approach that incorporates insights from various fields, including Artificial Life.
View Article and Find Full Text PDF

Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels.

View Article and Find Full Text PDF

Self-organizing precipitation processes, such as chemical gardens forming biomimetic micro- and nanotubular forms, have the potential to show us new fundamental science to explore, quantify, and understand nonequilibrium physicochemical systems, and shed light on the conditions for life's emergence. The physics and chemistry of these phenomena, due to the assembly of material architectures under a flux of ions, and their exploitation in applications, have recently been termed chemobrionics. Advances in understanding in this area require a combination of expertise in physics, chemistry, mathematical modeling, biology, and nanoengineering, as well as in complex systems and nonlinear and materials sciences, giving rise to this new synergistic discipline of chemobrionics.

View Article and Find Full Text PDF

We analyze the time series of the temperature of the sedimentary core MD01-2443 originating from the Iberian Margin with a duration of 420 kyr. The series has been tested for unit-root and a long term trend is estimated. We identify four significant periodicities together with a low climatic activity every 100 kyr, and these were associated with internal and external forcings.

View Article and Find Full Text PDF

In 1966, only a few months after the complete elucidation of the standard nuclear genetic code (Kay, 2000), the Russian theoretical physicist Yury Borisovich Rumer uncovered the existence of a particular symmetry (Rumer, 1966): when the keto-amino transformation (also known as Rumer's transformation) is applied to the bases of a codon then the degeneracy of the transformed codon was changed. In particular, if the amino acid associated to the starting codon has degeneracy 4, then the amino acid associated to the transformed codon has degeneracy 1, 2 or 3 (and vice versa). After half a century from this discovery and despite the universality of Rumer's symmetry, little is known about its origin and its possible biological significance.

View Article and Find Full Text PDF

In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries.

View Article and Find Full Text PDF

On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems-or parts of them-within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level.

View Article and Find Full Text PDF

The presence of circular codes in mRNA coding sequences is postulated to be involved in informational mechanisms aimed at detecting and maintaining the normal reading frame during protein synthesis. Most of the recent research is focused on trinucleotide circular codes. However, also dinucleotide circular codes are important since dinucleotides are ubiquitous in genomes and associated to important biological functions.

View Article and Find Full Text PDF

Circular codes, putative remnants of primeval comma-free codes, have gained considerable attention in the last years. In fact they represent a second kind of genetic code potentially involved in detecting and maintaining the normal reading frame in protein coding sequences. The discovering of an universal code across species suggested many theoretical and experimental questions.

View Article and Find Full Text PDF

In this article we show how dichotomic classes, binary variables naturally derived from a new mathematical model of the genetic code, can be used in order to characterize different parts of the genome. In particular, we analyze and compare different parts of whole chromosome 1 of Arabidopsis thaliana: genes, exons, introns, coding sequences (CDS), intergenes, untranslated regions (UTR) and regulatory sequences. In order to accomplish the task we encode each sequence in the 3 possible reading frames according to the definitions of the dichotomic classes (parity, Rumer and hidden).

View Article and Find Full Text PDF
Article Synopsis
  • The article introduces a new mathematical model of the genetic code that helps analyze the almost periodic properties of DNA and mRNA sequences used in protein coding.
  • It connects the model to number theory and group theory, drawing interesting parallels with crystal structures.
  • The research reveals that protein-coding sequences have a structured informational framework, potentially improving algorithms for accurate protein synthesis and enhancing our understanding of biological information and its relation to nucleic acids and proteins.
View Article and Find Full Text PDF

The study of correlation structures in DNA sequences is of great interest because it allows us to obtain structural and functional information about underlying genetic mechanisms. In this paper we present a study of the correlation structure of protein coding sequences of DNA based on a recently developed mathematical representation of the genetic code. A fundamental consequence of such representation is that codons can be assigned a parity class (odd-even).

View Article and Find Full Text PDF

In this article, we have applied the methods of chaos theory to channeling phenomena of positive charged particles in crystal lattices. In particular, we studied the transition between two ordered types of motion; i.e.

View Article and Find Full Text PDF

A prospective study designed to measure the accuracy of mammography (MRx), ultrasound (US), fine-needle aspiration cytology (FNAC) and one of the most recently introduced techniques, vacuum biopsy (VB), in the diagnosis of breast cancer is reported. A sample of 146 breast lesions on 135 patients were examined. The design of the study made it possible to compare MRx, US, FNAC and VB directly, because it excluded several confounding variables.

View Article and Find Full Text PDF

A PHP Error was encountered

Severity: Warning

Message: fopen(/var/lib/php/sessions/ci_sessioniommpn0658d5etgh0ijhd9mn3o28rjb0): Failed to open stream: No space left on device

Filename: drivers/Session_files_driver.php

Line Number: 177

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once

A PHP Error was encountered

Severity: Warning

Message: session_start(): Failed to read session data: user (path: /var/lib/php/sessions)

Filename: Session/Session.php

Line Number: 137

Backtrace:

File: /var/www/html/index.php
Line: 316
Function: require_once