Rui Alves

Summary

Affiliation: Universitat de Lleida
Country: Spain

Publications

  1. ncbi request reprint 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
  2. pmc Two component systems: physiological effect of a third component
    Baldiri Salvado
    Departament de Ciencies Mediques Basiques, Universitat de Lleida and IRBLLEIDA, Lleida, Spain
    PLoS ONE 7:e31095. 2012
  3. pmc Saccharomyces cerevisiae as a model organism: a comparative study
    Hiren Karathia
    Departament Ciencies Mediques Basiques, Universitat de Lleida and IRBLLEIDA, Lleida, Spain
    PLoS ONE 6:e16015. 2011
  4. pmc Evolution based on domain combinations: the case of glutaredoxins
    Rui Alves
    Departament de Ciencies Mediques Basiques, Universitat de Lleida, IRBLLEIDA, Lleida, Spain
    BMC Evol Biol 9:66. 2009
  5. ncbi request reprint Tools for kinetic modeling of biochemical networks
    Rui Alves
    Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4 25008 Lleida, Spain
    Nat Biotechnol 24:667-72. 2006
  6. ncbi request reprint Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism. II. Role of glutaredoxin Grx5
    Rui Alves
    Departament de Ciencies Mediques Basiques, Universidad de Lleida, Lleida, Spain
    Proteins 57:481-92. 2004
  7. pmc In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae
    Rui Alves
    Departament de Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig 2, 25008 Lleida, Spain
    BMC Syst Biol 1:10. 2007
  8. pmc Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models
    Carlos Pozo
    Departament de Ciencies Mediques Basiques, Institut de Recerca Biomèdica de Lleida IRBLleida, Universitat de Lleida, Spain
    BMC Syst Biol 5:137. 2011
  9. doi request reprint Methods for and results from the study of design principles in molecular systems
    Baldiri Salvado
    Departament de Ciencies Mediques Basiques, Universitat de Lleida and IRBLLEIDA, Lleida, Spain
    Math Biosci 231:3-18. 2011
  10. ncbi request reprint Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximations
    Albert Sorribas
    Departament de Ciencies Mediques Basiques, Universitat de Lleida, Montserrat Roig 2, 25008 Lleida
    Biotechnol Bioeng 97:1259-77. 2007

Collaborators

Detail Information

Publications20

  1. ncbi request reprint 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...
  2. pmc Two component systems: physiological effect of a third component
    Baldiri 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...
  3. pmc Saccharomyces cerevisiae as a model organism: a comparative study
    Hiren 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...
  4. pmc Evolution based on domain combinations: the case of glutaredoxins
    Rui 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...
  5. ncbi request reprint Tools for kinetic modeling of biochemical networks
    Rui 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...
  6. ncbi request reprint Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism. II. Role of glutaredoxin Grx5
    Rui Alves
    Departament de Ciencies Mediques Basiques, Universidad de Lleida, Lleida, Spain
    Proteins 57:481-92. 2004
    ....
  7. pmc In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae
    Rui 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)...
  8. pmc Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models
    Carlos Pozo
    Departament de Ciencies Mediques Basiques, Institut de Recerca Biomèdica de Lleida IRBLleida, Universitat de Lleida, Spain
    BMC Syst Biol 5:137. 2011
    ....
  9. doi request reprint Methods for and results from the study of design principles in molecular systems
    Baldiri 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...
  10. ncbi request reprint Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximations
    Albert 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...
  11. pmc Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock
    Ester 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...
  12. ncbi request reprint Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways
    Rui 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
    ..We will analyze the similarities and differences between these formalisms, discuss the advantages and limitations of each representation, and provide a tentative "road map" for their potential utilization for different problems...
  13. doi request reprint An in vitro system for the rapid functional characterization of genes involved in carotenoid biosynthesis and accumulation
    Chao Bai
    Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering ETSEA, University of Lleida Agrotecnio Center, Avenida Alcalde Rovira Roure 191, 25198, Lleida, Spain
    Plant J 77:464-75. 2014
    ..We discuss the impact of our data on analysis and engineering of the carotenoid biosynthesis pathway. ..
  14. doi request reprint Targeted transcriptomic and metabolic profiling reveals temporal bottlenecks in the maize carotenoid pathway that may be addressed by multigene engineering
    Gemma Farre
    Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering ETSEA, University of Lleida Agrotecnio Center, Avenida Alcalde Rovira Roure 191, 25198 Lleida, Spain
    Plant J 75:441-55. 2013
    ....
  15. pmc Biblio-MetReS: a bibliometric network reconstruction application and server
    Anabel 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...
  16. doi request reprint Optimization and evolution in metabolic pathways: global optimization techniques in Generalized Mass Action models
    Albert 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...
  17. doi request reprint S-PC: An e-treatment application for management of smoke-quitting patients
    Jordi Vilaplana
    Departament d Informàtica i Enginyeria Industrial and INSPIRES, Universitat de Lleida, Av Jaume II no 69, 25001 Lleida, Spain
    Comput Methods Programs Biomed 115:33-45. 2014
    ..In addition, the system also detects patients who are not progressing appropriately, allowing the professional to improve their treatment parameters dynamically. ..
  18. doi request reprint Hysteretic and graded responses in bacterial two-component signal transduction
    Oleg 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...
  19. pmc Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes
    Rui 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...
  20. ncbi request reprint Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function
    Rui 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...