Research Topics
Genomes and Genes | Rui AlvesSummaryAffiliation: Universitat de Lleida Country: Spain Publications
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Detail Information
Publications
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiaeRui Alves
Departament de Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig 2, 25008 Lleida, Spain
BMC Syst Biol 1:10. 2007..One such class of pathways is involved in the biogenesis of Iron-Sulfur Clusters (ISC)...
Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin-ferredoxin reductase (Yah1-Arh1)Rui Alves
Departament de Ciencies Mediques Basiques, Universidad de Lleida, Lleida, Spain
Proteins 56:354-66. 2004..Only when this mode of action of either of the two proteins in FeSC synthesis is considered can previously reported results be reproduced...- Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism. II. Role of glutaredoxin Grx5Rui Alves
Departament de Ciencies Mediques Basiques, Universidad de Lleida, Lleida, Spain
Proteins 57:481-92. 2004.... - Tools for kinetic modeling of biochemical networksRui Alves
Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4 25008 Lleida, Spain
Nat Biotechnol 24:667-72. 2006..Virtual Cell is the most versatile program and provides the simplest and clearest functionality for setting up multicompartmentalization... - Evolution based on domain combinations: the case of glutaredoxinsRui Alves
Departament de Ciencies Mediques Basiques, Universitat de Lleida, IRBLLEIDA, Lleida, Spain
BMC Evol Biol 9:66. 2009..GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear... - Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical modelsCarlos Pozo
Departament de Ciencies Mediques Basiques, Institut de Recerca Biomèdica de Lleida IRBLleida, Universitat de Lleida, Spain
BMC Syst Biol 5:137. 2011.... - Saccharomyces cerevisiae as a model organism: a comparative studyHiren Karathia
Departament Ciencies Mediques Basiques, Universitat de Lleida and IRBLLEIDA, Lleida, Spain
PLoS ONE 6:e16015. 2011..However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking... - Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximationsAlbert Sorribas
Departament de Ciencies Mediques Basiques, Universitat de Lleida, Montserrat Roig 2, 25008 Lleida
Biotechnol Bioeng 97:1259-77. 2007..The practical use of the SC formalism for modeling is illustrated with a few examples. Similar models are built using different formalisms and compared to emphasize advantages and limitations of the different approaches... 
Methods for and results from the study of design principles in molecular systemsBaldiri Salvado
Departament de Ciencies Mediques Basiques, Universitat de Lleida and IRBLLEIDA, Lleida, Spain
Math Biosci 231:3-18. 2011..We conclude by discussing the importance of these principles for both, understanding the natural evolution of complex networks at the molecular level and for creating artificial biological systems with specific features...- Two component systems: physiological effect of a third componentBaldiri Salvado
Departament de Ciencies Mediques Basiques, Universitat de Lleida and IRBLLEIDA, Lleida, Spain
PLoS ONE 7:e31095. 2012..The presence of a third component that modulates RR activity decreases the parameter space where a bistable response of the TCS module to signals is possible... - Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shockEster Vilaprinyo
Departament de Ciencies Mediques Basiques, Universitat de Lleida, Montserrat Roig 2, 25008 Lleida, Spain
BMC Bioinformatics 7:184. 2006..The experimental determination of changes in gene expression profiles provides a descriptive picture of the adaptive response to stress. However, it does not explain why a particular profile is selected for any given response... - Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathwaysRui Alves
Departament de Ciècies Mèiques Bàiques, Institut de Recerca Biomèica de Lleida IRBLLEIDA, Universitat de Lleida, Montserrat Roig, 2, 25008 Lleida, Spain
Biotechnol Genet Eng Rev 25:1-40. 2008.... - Biblio-MetReS: a bibliometric network reconstruction application and serverAnabel Usié
Department d Informàtica i Enginyeria Industrial, Universitat de Lleida, Av, Jaume II n 69, 25001 Lleida, Spain
BMC Bioinformatics 12:387. 2011..However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available... - Optimization and evolution in metabolic pathways: global optimization techniques in Generalized Mass Action modelsAlbert Sorribas
Departament de Ciencies Mediques Basiques, Institut de Recerca Biomèdica de Lleida IRBLleida, University of Lleida, Montserrat Roig, 2, 25008 Lleida, Spain
J Biotechnol 149:141-53. 2010..Our methodology can be used with a special class of nonlinear kinetic models known as GMA models and it allows for a systematic characterization of the physiological requirements that may underlie the evolution of adaptive strategies... - Hysteretic and graded responses in bacterial two-component signal transductionOleg A Igoshin
Department of Bioengineering, Rice University, Houston, TX 77251 1892, USA
Mol Microbiol 68:1196-215. 2008..The implications of this potential bistability in the design of the EnvZ/OmpR network and other TCS are discussed... - Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymesRui Alves
Biomedical Engineering Department, University of California-Davis, Davis, CA, USA
Mol Microbiol 56:1017-34. 2005..Thus, selection for low cognate bias plays a significant role in shaping the amino acid composition for a large class of cellular proteins... - Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological functionRui Alves
Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II Ann Arbor, MI 48109-0620, USA
Mol Microbiol 48:25-51. 2003..These results provide a functional rationale for the selection of each design that is consistent with available experimental evidence for several two-component systems...