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156
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Introduction
Rui Alves currently works at the Department of Basic Medical Sciences, Universitat de Lleida. Rui does research in Bioinformatics, Evolutionary Biology and Systems Biology. Their current project is 'Quantitative design principles for adaptive responses to environmental stress in yeast'.
Additional affiliations
January 2007 - present
October 1995 - September 1996
October 1996 - December 2000
Publications
Publications (156)
Terpenoids are valued chemicals in the pharmaceutical, biotechnological, cosmetic, and biomedical industries. Biosynthesis of these chemicals relies on polymerization of Isopentenyl di-phosphate (IPP) and/or dimethylallyl diphosphate (DMAPP) monomers, which plants synthesize using a cytosolic mevalonic acid (MVA) pathway and a plastidic methyleritr...
Phenotypic differences between species are, in significant part, determined by their proteomic diversity. The link between proteomic and phenotypic diversity can be best understood in the context of the various pathways and biological processes in which proteins participate. While the conservation pattern for individual proteins across species is e...
Global food insecurity and environmental degradation creates the need to develop more sustainable agricultural solutions. Plant synthetic biology emerges as a promising yet risky avenue to develop such solutions. While synthetic biology promises enhanced crop traits, it also harbors risks of extensive environmental damage. Here, we highlight the co...
The red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of its genome. This assembly encompasses 96.9% of the avian genes flagged as essential...
Terpenoids are valued chemicals in the pharmaceutical, biotechnological, cosmetic, and biomedical industries. Biosynthesis of these chemicals relies on polymerization of Isopentenyl di-phosphate (IPP) and/or dimethylallyl diphosphate (DMAPP) monomers, which plants synthesize using a cytosolic mevalonic acid (MVA) pathway and a plastidic methyleritr...
The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories (Catalan Linguistic Area, CLA). These territories represent a biodiversity hotspot. While covering less than 1% of Europe, they are h...
Background: Sample size is a key factor in planning a clinical trial. Decisions regarding sample size are typically based on ensuring the statistical power of the test of interest. However, this does not always guarantee a precise estimate of the treatment effect. It is important to understand the distinction between these two aspects of a trial.
M...
The red-legged partridge, Alectoris rufa (n=38 chromosomes) plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of it genome (115 scaffolds, L90=23). This assembly contains 96.9%...
Maize is the most in-demand staple crop globally. Its production relies strongly on the use of fertilizers for the supply of nitrogen, phosphorus, and potassium, which the plant absorbs through its roots, together with water. The architecture of maize roots is determinant in modulating how the plant interacts with the microbiome and extracts nutrie...
Many highly valued chemicals in the pharmaceutical, biotechnological, cosmetic, and biomedical industries belong to the terpenoid family. Biosynthesis of these chemicals relies on polymerization of Isopentenyl di-phosphate (IPP) and/or dimethylallyl diphosphate (DMAPP) monomers, which plants synthesize using two alternative pathways: a cytosolic me...
Friedreich’s ataxia is a neurodegenerative disease caused by mutations in the frataxin gene. Frataxin homologues, including bacterial CyaY proteins, can be found in most species and play a fundamental role in mitochondrial iron homeostasis, either promoting iron assembly into metaloproteins or contributing to iron detoxification. While several line...
Strigolactones mediate plant development, trigger symbiosis with arbuscular mycorrhizal fungi, are abundant in 80% of the plant kingdom and help plants gain resistance to environmental stressors. They also induce germination of parasitic plant seeds that are endemic to various continents, such as Orobanche in Europe or Asia and Striga in Africa. Th...
The evolution of Crassulacean acid metabolism (CAM) by plants has been one of the most successful strategies in response to aridity. On the onset of climate change, expanding the use of water efficient crops and engineering higher water use efficiency into C3 and C4 crops constitute a plausible solution for the problems of agriculture in hotter and...
Isoprenoids are natural products derived from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In plants, these precursors are synthesized via the cytosolic mevalonate (MVA) and plastidial methylerythritol phosphate (MEP) pathways. The regulation of these pathways must therefore be understood in detail to develop effective strat...
Phosphorelays are signal transduction circuits that sense environmental changes and adjust cellular metabolism. Five different circuit architectures account for 99% of all phosphorelay operons annotated in over 9,000 fully sequenced genomes. Here we asked what biological design principles, if any, could explain selection among those architectures i...
Phosphorelays are signal transduction circuits that combine four different phosphorylatable protein domains for sensing environmental changes and use that information to adjust cellular metabolism to the new conditions in the milieu. Five alternative circuit architectures account for more than 99% of all phosphorelay operons annotated in over 9000...
BACKGROUND
Many mobile apps have been made to quit smoking. Many do not have the support of specialists, and often are apps for self-guidance. There is no record of any study looking at the apps' adherence to patient treatments from hospitals, and therefore it is not known for sure if they serve to increase the adherence of treatments.
OBJECTIVE
A...
EasyModel is a user-friendly web application that uses Wolfram webMathematica for performing simulations and analysis of systems biology models. EasyModel lets users create new models, load models from the BioModels database, and import preexisting models from SBML files. EasyModel mainly targets the student of bioinformatics or systems biology wit...
EasyModel is a new user-friendly web application that contains ready-for-simulation versions of the BioModels Database, and allows for the intuitive creation of new models. Its main target audience is the experimental biologist and students of bioinformatics or systems biology without programming skills. Expert users can also benefit from it by imp...
Nowadays there are hundreds of programs for building and analyzing mathematical models of biological systems. These programs typically feature either a complex user interface with flexible and expandable functionality for experts or a simple user interface with basic functionality for non-expert users. Tools that can be profitably used by both audi...
Rubisco is the primary carboxylase of the Calvin cycle, the most abundant enzyme in the biosphere, and one of the best-characterized enzymes. Based on correlations between Rubisco kinetic parameters, it is widely posited that constraints embedded in the catalytic mechanism enforce tradeoffs between CO2-specificity, SC/O, and maximum carboxylation r...
Adventitial vasa vasorum are physiologic microvessels that nourish artery walls. In the presence of cardiovascular risk factors, these microvessels proliferate abnormally. Studies have reported that they are the first stage of atheromatous disease. Contrast-enhanced ultrasound (CEUS) of the carotid allows direct, quantitative and non-invasive visua...
Carotid adventitia vasa vasorum neovascularization (VVn) is associated with the initial stages of arteriosclerosis and with the formation of unstable plaque. However, techniques to accurately quantify that neovascularization in a standard, fast, non-invasive, and efficient way are still lacking. The development of such techniques holds the promise...
EasyModel aims to provide a tool for both, expert and non-expert users. An easy-to-use interface allows non-expert users to create and simulate models easily. A downloadable Mathematica notebook allows expert users to customize the code and expand on the analysis.
MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows function...
Microorganisms evolved adaptive responses to survive stressful challenges in ever-changing environments. Understanding the relationships between the physiological/metabolic adjustments allowing cellular stress adaptation and gene expression changes being used by organisms to achieve such adjustments may significantly impact our ability to understan...
Microorganisms evolved adaptive responses that enable them to survive stressful challenges in ever changing environments by adjusting metabolism through the modulation of gene expression, protein levels and activity, and flow of metabolites. More frequent challenges allow natural selection ampler opportunities to select from a larger number of phen...
Production planning models are achieving more interest for being used in the primary sector of the economy. The proposed model relies on the formulation of a location model representing a set of farms susceptible of being selected by a grocery shop brand to supply local fresh products under seasonal contracts. The main aim is to minimize overall pr...
Carotid adventitial vasa vasorum (AVV) are markers of subclinical atherosclerotic lesions. Early lesion identification is essential in reducing the high mortality risk from cardiovascular diseases (CVD). In this work we present an automated method to process contrast ultrasound images (CUI) of carotid, identify AVV, and estimate relative risk of CV...
Background and Objective
Tobacco smoking is a major risk factor for a wide range of respiratory and circulatory diseases in active and passive smokers. Well-designed campaigns are raising awareness to the problem and an increasing number of smokers seeks medical assistance to quit their habit. In this context, there is the need to develop mHealth A...
Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species ide...
Symmetric difference distance between maximum parsinomy trees
Symmetric difference distance between maximum likelihood trees
Phylogram for ML tree build using the TEF1 locus for the 96 Diaporthe species
Phylogram for MP tree build using the five loci TEF1-TUB-CAL-HIS-ITS for the 96 Diaporthe species
Phylogram for ML tree build using the five loci TEF1-TUB-CAL-HIS-ITS for the 96 Diaporthe species
Comparison of MP trees generated from the same alignment of 5 genes, when changing the position of the TEF sequences in that alignment
The numbers represent the bootstrap value for the branching in each tree. Red ?MP tree with TEF in the first position of the alignment. Mauve ?MP tree with TEF in the second position of the alignment. Green ?MP tree...
Phylogram for MP tree build using the TEF1 locus for the 96 Diaporthe species
The initial diagnosis of rare diseases is difficult because they are infrequent and doctors do not often see or recognize their symptoms. Developing tools to assist in this diagnosis would provide a way to facilitate medical practice in this area. The broader goal of this project is to develop such a tool, which we name Rare Disease Discovery, RDD...
Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe . Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species id...
Background. Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe . Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species id...
Environmental stresses induce expression changes for sets of genes that are stress specific. Saccharomyces cerevisiae is a common model organism to study these changes, many of which affect genes coding for chaperone ATPases that help the cell maintain its molecular integrity. Hence, expression also changes for genes involved in the energy metaboli...
Production planning models are achieving more interest for being used in the primary sector of the economy. The proposed model relies on the formulation of a location model representing a set of farms susceptible of being selected by a grocery shop brand to supply local fresh products under seasonal contracts. The main aim is to minimize overall pr...
Stress adaptation is achieved in Saccharomyces cerevisiae by changing gene expression across the genome in stress-specific ways. Here we analyze the expression of set of genes that is important for metabolic tuning during adaptation to various types of stress. Using mathematical modeling we predict the effect of the gene expression changes in a set...
Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial...
Supporting Appendix S1.
Additional Methods and Results for Efficient Computer-Assisted Diagnosis of Rare Diseases Using Rare Disease Discovery
Regulated expression of the Ena1 Na+-ATPase is a crucial event for adaptation to high salt and/or alkaline pH stress in the budding yeast Saccharomyces cerevisiae. ENA1 expression is under the control of diverse signaling pathways, including that mediated by the calcium-regulatable protein phosphatase calcineurin and its downstream transcription fa...
Additional Supplemental Material
(MP4)
Hypertension or high blood pressure is a condition on the rise. Not only does it affect the elderly but is also increasingly spreading to younger sectors of the population. Treating it involves exhaustive monitoring of patients. A tool adapted to the particular requirements of hypertension can greatly facilitate monitoring and diagnosis. This paper...
Hypertension or high blood pressure is a condition on the rise. Not only does it affect the elderly but is also increasingly spreading to younger sectors of the population. Treating it involves exhaustive monitoring of patients. A tool adapted to the particular requirements of hypertension can greatly facilitate monitoring and diagnosis. This paper...
Hypertension or high blood pressure is a condition on the rise. Not only does it affect the elderly but is also increasingly spreading to younger sectors of the population. Treating it involves exhaustive monitoring of patients. A tool adapted to the particular requirements of hypertension can greatly facilitate monitoring and diagnosis. This paper...
Plant Synthetic Biology is still in its infancy. However, Synthetic Biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops, such as rice, potato, or maize. With current technologies, production yields of the synthetic nutrients are a result of trial and error, and systematic rational strate...
Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS...
Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS...
Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS...
The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison o...
When designing a cloud infrastructure, it is critical to ensure beforehand that the system will be able to offer the desired level of QoS (Quality of Service). Our attention is focused here on efficient QoS accessing to a biological database in cloud computing systems. Our group developed two software applications that address important biological...
Small chemical molecules regulate biological processes at the molecular level. Those molecules are often involved in causing or treating pathological states. Automatically identifying such molecules in biomedical text is difficult due to both, the diverse morphology of chemical names and the alternative types of nomenclature that are simultaneously...
In this work we present a multi-level optimization method based on flux balance analysis models (FBA) for identifying meaningful biological objective functions that drive the cell's metabolic machinery under different conditions. Our approach identifies in a rigorous and systematic manner the most probable objective functions for a given set of exp...
El consumo de tabaco continúa siendo una importante causa de morbilidad y mortalidad.
El proceso terapéutico para abandonar el tabaco consiste en la desintoxicación física de
la nicotina y en el mantenimiento de la abstinencia de su consumo. Nuestro estudio se
sitúa en este contexto, ofreciendo una estrategia de apoyo por SMS y monitorizando al
pac...
Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functiona...
The main objective of this paper is to present a new program that facilitates the management of people who want to quit smoking, implemented through an e-treatment software called S-PC (Smoker Patient Control). S-PC is a web-based application that manages groups of patients, provides a bidirectional communication through mobile text messages and e-...
Unlabelled:
One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, e...
One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental b...
One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinformaticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental b...
Tobacco consumption continues to be an important cause of morbidity and mortality. The therapeutic process of giving up smoking consists of the physical detoxification of nicotine as well as maintaining abstinence from its consumption. Our study lies in this context, offering a strategy by means of SMS support and monitoring patients throughout the...
We have developed an assay based on rice embryogenic callus for the rapid functional characterization of metabolic genes. We validated the assay using a selection of well-characterized genes with known functions in the carotenoid biosynthesis pathway, allowing the rapid visual screening of callus phenotypes based on tissue color. We were then able...
MOTIVATION: Chemical named entity recognition is used to automatically identify mentions to chemical compounds in text and is the basis for more elaborate information extraction. However, only a small number of applications are freely available to identify such mentions. Particularly challenging and useful is the identification of International Uni...
