32 citations · 149 across the 19 of their papers we have counts for
20 papers
Hepatitis C Virus Genotyping with a Transformer Neural Network
Ariella Aro, Taimá Furuyama, Marcelo R. S. Briones +3
This study aims to explore the applicability of Transformer-based models for genetic sequence classification by evaluating their performance in predicting hepatitis C virus (HCV) g…
Automated Classification of Homeostasis Structure in Input-Output Networks
Xinni Lin, Fernando Antoneli, Yangyang Wang
Homeostasis is widely observed in biological systems and refers to their ability to maintain an output quantity approximately constant despite variations in external disturbances.…
Homeostasis in Input-Output Networks: Structure, Classification and Applications
Fernando Antoneli, Martin Golubitsky, Jiaxin Jin +1
Homeostasis is concerned with regulatory mechanisms, present in biological systems, where some specific variable is kept close to a set value as some external disturbance affects t…
Homeostasis in Gene Regulatory Networks
Fernando Antoneli, Martin Golubitsky, Jiaxin Jin +1
In this paper, we use the framework of infinitesimal homeostasis to study general design principles for the occurrence of homeostasis in gene regulatory networks. We assume that th…
Homeostasis Patterns
William Duncan, Fernando Antoneli, Janet Best +5
Homeostasis is a regulatory mechanism that keeps a specific variable close to a set value as other variables fluctuate. The notion of homeostasis can be rigorously formulated when…
Homeostatic Mechanisms in Biological Systems
Pedro P. A. Cardoso de Andrade, João L. O. Madeira, Fernando Antoneli
In this paper we investigate the homeostatic mechanism in two biologically motivated models: intracellular copper regulation and self immune recognition. The analysis is based on t…
Homeostasis in Networks with Multiple Input Nodes and Robustness in Bacterial Chemotaxis
João Luiz de Oliveira Madeira, Fernando Antoneli
A biological system achieve homeostasis when there is a regulated quantity that is maintained within a narrow range of values. Here we consider homeostasis as a phenomenon of netwo…
Push-forward method for piecewise deterministic biochemical simulations
Guilherme C. P. Innocentini, Arran Hodgkinson, Fernando Antoneli +2
A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactio…
The Structure of Infinitesimal Homeostasis in Input-Output Networks
Yangyang Wang, Zhengyuan Huang, Fernando Antoneli +1
Homeostasis refers to a phenomenon whereby the output of a system is approximately constant on variation of an input . Homeostasis occurs frequently in biochemic…
Temporal data series of COVID-19 epidemics in the USA, Asia and Europe suggests a selective sweep of SARS-CoV-2 Spike D614G variant
Taima N. Furuyama, Fernando Antoneli, Isabel M. V. G. Carvalho +2
The COVID-19 pandemic started in Wuhan, China, and caused the worldwide spread of the RNA virus SARS-CoV-2, the causative agent of COVID-19. Because of its mutational rate, wide ge…
Effective computational methods for hybrid stochastic gene networks
Guilherme C. P. Innocentini, Fernando Antoneli, Arran Hodgkinson +1
At the scale of the individual cell, protein production is a stochastic process with multiple time scales, combining quick and slow random steps with discontinuous and smooth varia…
Stochastic Modeling and Simulation of Viral Evolution
Luiza Guimarães, Diogo Castro, Bruno Gorzoni +2
RNA viruses comprise vast populations of closely related, but highly genetically diverse, entities known as quasispecies. Understanding the mechanisms by which this extreme diversi…
A Kolmogorov-Smirnov test for the molecular clock on Bayesian ensembles of phylogenies
Fernando Antoneli, Fernando Marcon, Luciano R. Lopes +1
Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-p…
Protein synthesis driven by dynamical stochastic transcription
Guilherme C. P. Innocentini, Michael Forger, Ovidiu Radulescu +1
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics…
Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage
Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini +3
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughpu…
A Model of Gene Expression Based on Random Dynamical Systems Reveals Modularity Properties of Gene Regulatory Networks
Fernando Antoneli, Renata C. Ferreira, Marcelo R. S. Briones
Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of…
A Model for the Dynamics of Gene Networks
Fernando Antoneli, Renata C. Ferreira, Francisco Bosco +1
In this work we propose a model for gene expression based on the theory of random dynamical systems (RDS) and show that it has a "modularity property" in the following sense: given…
Virus Replication as a Phenotypic Version of Polynucleotide Evolution
Fernando Antoneli, Francisco Bosco, Diogo Castro +1
In this paper we revisit and adapt to viral evolution an approach based on the theory of branching process advanced by Demetrius, Schuster and Sigmund ("Polynucleotide evolution an…
Viral Evolution and Adaptation as a Multivariate Branching Process
Fernando Antoneli, Francisco Bosco, Diogo Castro +1
In the present work we analyze the problem of adaptation and evolution of RNA virus populations, by defining the basic stochastic model as a multivariate branching process in close…
Maximal Subgroups of Compact Lie Groups
Fernando Antoneli, Michael Forger, Paola Gaviria
This report aims at giving a general overview on the classification of the maximal subgroups of compact Lie groups (not necessarily connected). In the first part, it is shown that…