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Raul Isea

Publications and source records attributed to Raul Isea.

At least 19 recordsLinked to original sources
arXiv2023

A General Approach to Modeling Covid-19

The present work shows that it is possible to analytically solve a general model to explain the transmission dynamics of SARS-CoV-2. First, the within-host model is described, and later a between-host model, where the coupling between them is the viral load of SARS-CoV-2. The within-host model describes the equations involved in the life cycle of SARS-CoV-2, and also the immune response; while that the between-Host model analyzes the dynamics of virus spread from the original source of contagion associated with bats, subsequently transmitted to a host, and then reaching the reservoir (Huanan Seafood Wholesale Market in Wuhan ), until finally infecting the human population.

q-bio.PE↗
arXiv2018

Analyzing the love affair of Romeo and Juliet with modern mathematical tools

We facetiously suggest that the romance between Romeo and Juliet can be interpreted using modern terminology and include current temptations. Using this model, we consider various factors such as the time that they might spend consulting social networks, the time that they could spend alone together and along with friends as well as their tolerance of being able to waste the couple's money. The model consists of a set of differential equations which describes the relationship between them. Finally, we analyze the eigenvalues the mathematical equations in order to determine if the critical point in this model is stable or not in four different hypothetical scenarios.

physics.soc-ph↗
arXiv2017

Quantitative Prediction of Linear B-Cell Epitopes

In scientific literature, there are many programs that predict linear B-cell epitopes from a protein sequence. Each program generates multiple B-cell epitopes that can be individually studied. This paper defines a function called that combines results from five different prediction programs concerning the linear B-cell epitopes (ie., BebiPred, EPMLR, BCPred, ABCPred and Emini Prediction) for selecting the best B-cell epitopes. We obtained 17 potential linear B cells consensus epitopes from Glycoprotein E from serotype IV of the dengue virus for exploring new possibilities in vaccine development. The direct implication of the results obtained is to open the way to experimentally validate more epitopes to increase the efficiency of the available treatments against dengue and to explore the methodology in other diseases.

q-bio.QM↗
arXiv2016

Reverse vaccinology in Plasmodium falciparum 3D7

A timely immunization can be effective against certain diseases and can save thousands of lives. However, for some diseases it has been difficult, so far, to develop an efficient vaccine. Malaria, a tropical disease caused by a parasite of the genus Plasmodium, is one example. Bioinformatics has opened the way to new lines of experimental investigation One example is reverse vaccinology that aims to identify antigens that are capable of generating an immune response in a given organism using in silico studies. In this study we applied a reverse vaccinology methodology using a bioinformatics pipeline. We obtained 45 potential linear B cells consensus epitopes from the whole genome of P. falciparum 3D7 that can be used as candidates for malaria vaccines. The direct implication of the results obtained is to open the way to experimentally validate more epitopes to increase the efficiency of the available treatments against malaria and to explore the methodology in other diseases.

q-bio.GN↗
arXiv2016

Mathematical analysis of the spreading of a rumor among different subgroups of spreaders

This paper presents a system of differential equations that describes the spreading of a rumor when it is propagated by different subgroups of spreaders. The system that is developed is a generalization of the model proposed by Daley and Kendall. Finally, the system is applied to the exchange rate of the parallel dollar in Venezuela, where the source data that was used were obtained from Google Trends.

physics.soc-ph↗
arXiv2016

Can Bioinformatics Be Considered as an Experimental Biological Science?

The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an experimental science. These examples show how the development of theoretical biological models generates experimentally verifiable computer hypotheses, which necessarily must be validated by experiments in vitro or in vivo.

q-bio.OT↗
arXiv2016

A Potential Correlation Between the Temperature of the Pacific Ocean and Data from Google Trends May Yield a Warning Sign for the Outbreak of Zika

There has been a large number of reported cases of the occurrence of Zika in different countries in 2016 and it is necessary to develop an early warning system to initiate preventive campaigns against the disease. A potential early warning system based on the rise in ocean temperature of the Pacific Niño Index is proposed. The efficacy is verified using data for the outbreak in Colombia as obtained from Google Trends.

q-bio.PE↗
arXiv2016

A Preliminary Mathematical Model for the Dynamic Transmission of Dengue, Chikungunya and Zika

Aedes aegypti is a known vector of Dengue, Chikungunya and Zika and the goal of this study is to propose the first mathematical model to describe the dynamic transmission of these three diseases. We present two preliminary models that consist of the SEIR model for the human populations and an SEI model for the vector to describe (a) the single transmission dynamics of dengue, Chikungunya or Zika, and (b) any possible coinfection between two diseases in the same population. In order to do that, we obtain an analytical solution of the system of 17 and 30 coupled differential equations for each model respectively, and later obtain the eigenvalues by analyzing the Jacobian matrix in order to begin the development of a surveillance system to prevent the spread of these three diseases.

q-bio.PE↗
arXiv2014

Challenges and characterization of a Biological system on Grid by means of the PhyloGrid application

In this work we present a new application that is being developed. PhyloGrid is able to perform large-scale phylogenetic calculations as those that have been made for estimating the phylogeny of all the sequences already stored in the public NCBI database. The further analysis has been focused on checking the origin of the HIV-1 disease by means of a huge number of sequences that sum up to 2900 taxa. Such a study has been able to be done by the implementation of a workflow in Taverna.

cs.CE↗
arXiv2014

Analysis of an SEIR-SEI four-strain epidemic dengue model with primary and secondary infections

We propose an SEIR model for the populations and an SEI model for the vector to describe the transmission dynamics of a four-strain model with both primary and secondary dengue infections. In order to accomplish this, we propose and obtain an analytic solution of a system of 47 coupled differential equations. This would be the most complete epidemic model proposed to describe the dengue epidemic.

q-bio.PE↗
arXiv2013

Application of CellDesigner to the Selection of Anticancer Drug Targets: Test Case using P53

Cancer is a disease involving many genes, consequently it has been difficult to design anticancer drugs that are efficacious over a broad range of cancers. The robustness of cellular responses to gene knockout and the need to reduce undesirable side effects also contribute to the problem of effective anti-cancer drug design. To promote the successful selection of drug targets, each potential target should be subjected to a systems biology scrutiny to locate effective and specific targets while minimizing undesirable side effects. The gene p53 is considered a good candidate for such a target because it has been implicated in 50% of all cancers and is considered to encode a hub protein that is highly connected to other proteins. Using P53 as a test case, this paper explores the capacity of the systems biology tool, CellDesigner, to aid in the selection of anticancer drug targets and to serve as a teaching resource for human resource development.

q-bio.CB↗
arXiv2010

PhyloGrid: a development for a workflow in Phylogeny

In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do this, no knowledge from his/her side about the computational procedure is required.

cs.CE↗
arXiv2010

Advances in the Biomedical Applications of the EELA Project

In the last years an increasing demand for Grid Infrastructures has resulted in several international collaborations. This is the case of the EELA Project, which has brought together collaborating groups of Latin America and Europe. One year ago we presented this e-infrastructure used, among others, by the Biomedical groups for the studies of oncological analysis, neglected diseases, sequence alignments and computation phylogenetics. After this period, the achieved advances are summarised in this paper.

cs.CE↗
arXiv2010

The Virtual Institute for Integrative Biology (VIIB)

The Virtual Institute for Integrative Biology (VIIB) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, metagenomics, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomics, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: interoperability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible workflows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions.

q-bio.OT↗
arXiv2010

Identificación de nuevos medicamentos a través de métodos computacionales

Resumen: El desarrollo de nuevos medicamentos es un problema complejo que carece de una solución única y automática desde un punto de vista computacional, debido a la carencia de programas que permitan manejar grandes volúmenes de información que están distribuidos a lo largo de todo el mundo entre múltiples bases de datos. Por ello se describe una metodología que permita realizar experimentos in silico para la identificación actual de nuevos medicamentos. Abstract: The development of new drugs is a problem that nowadays has no solution in terms of computational power due to the lack of software for handling the big volume of available information; besides, these data are stored in multiple formats and are distributed all around the world. To resolve that, a development of an in silico drug design methodology.

q-bio.OT↗
arXiv2010

Identification of 11 potential malaria vaccine candidates using Bioinformatics

In this paper, we suggested eleven protein targets to be used as possible vaccines against Plasmodium falciparum causative agent of almost two to three million deaths per year. A comprehensive analysis of protein target have been selected from the small experimental fragment of antigen in the P. falciparum genome, all of them common to the four stages of the parasite life cycle (i.e., sporozoites, merozoites, trophozoites and gametocytes). The potential vaccine candidates should be analyzed in silico technique using various bioinformatics tools. Finally, the possible protein target according to PlasmoDB gene ID are PFC0975c, PFE0660c, PF08_0071, PF10_0084, PFI0180w, MAL13P1.56, PF14_0192, PF13_0141, PF14_0425, PF13_0322, y PF14_0598.

q-bio.GN↗