Master's degree in Biomedical Research

VAQUEIRO DE CASTRO ALVES, RUI CARLOS

Category: SENIOR LECTURER
Academic profile: Doctorate
Department: BASIC MEDICAL SCIENCES
Email: rui.alves@udl.cat

Teaching

Teaching Course Subject
Master's Degree in Biomedical Research 1 METHODS IN SYSTEMS BIOLOGY
Master's Degree in Biomedical Research 1 STORYTELLING WITH DATA
Degree in Biotechnology 3 BIOINFORMATICS
Degree in Biomedical Sciences 3 BIOINFORMATICS AND SYSTEMS BIOLOGY
Degree in Biotechnology 4 BACHELOR'S THESIS
Degree in Biomedical Sciences 4 SYNTHETIC BIOLOGY IN BIOMEDICINE
Master's Degree in Biomedical Research BIOINFORMATICS
Master's Degree in Biomedical Research BIOINFORMATICS AND SYSTEMS BIOLOGY

Research

Research profile: Biologia de sistemes i models matemàtics de processos biològics
Thesis Year Direction
Design principles in two component systems and his-asp phosphorelays 2016 Rui Alves
Development of Methodologies to Analyze and Compare Metabolic Networks: Application to Specific Classes of Metabolic Pathways 2000 Michael Savageau & Ruy E. Pinto
Publications Year Authors Type
EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology 2020 Bartolomé, Jordi; Alves, Rui; Solsona, Francesc; Teixidó, Ivan Article d'investigació
Automatic Methods for Carotid Contrast-Enhanced Ultrasound Imaging Quantification of Adventitial Vasa Vasorum. 2019 Pereira T.; Muguruza J.; Mária V.; Vilaprinyo E.; Sorribas A.; Fernandez E.; Fernandez-Armenteros, J.M.; Baena J.A.; Rius F.; Betriu A.; Solsona .F; Alves R. Article d'investigació
Revisiting Trade-offs between Rubisco Kinetic Parameters 2019 Flamholz, Avi I; Prywes, Noam; Moran, Uri; Davidi, Dan; Bar-On, Yinon M; Oltrogge, Luke M; Alves, Rui; Savage, Dave; Milo, Ron Article d'investigació
Foundations of Theoretical Approaches in Systems Biology 2019 Alberto Marin-Sanguino; Julio Vera; Rui Alves Review
Non-invasive imaging techniques and assessment of carotid vasa vasorum neovascularization: promises and pitfalls 2018 Pereira, T.; Betriu, A.; Alves, R. Review
MetReS, an efficient database for genomic applications 2018 Jordi Vilaplana; Rui Alves; Francesc Solsona; Jordi Mateo; Ivan Teixidó; Marc Pifarré Article d'investigació
Quantitative operating principles of Yeast metabolism during adaptation to heat stress. 2018 Pereira T.; Vilaprinyo E.; Belli G.; Herrero E.; Salvado B.; Sorribas A.; Altés G.; Alves R. Article d'investigació
Metabolic constraints and quantitative design principles in gene expression during adaption of yeast to heat shock 2018 Pereira T, Vilaprinyo E, Belli G, Herrero E, Salvado B, Sorribas A, Altés G, Alves R. Altres
Rare Disease Discovery: an optimized disease ranking system 2017 Marc Piñol; Rui Alves; Ivan Teixidó; Jordi Mateo; Francesc Solsona; Ester Vilaprinyó Article d'investigació
TControl: A mobile app to follow up tobacco-quitting patients 2017 Pifarré M.; Carrera A.; Vilaplana J.; Cuadrado J.; Solsona S.; Abella F.; Solsona F.; Alves R. Article d'investigació
Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe 2017 Santos L.; Alves A.; Alves R. Article d'investigació
HBPF: a Home Blood Pressure Framework with SLA guarantees to follow up hypertensive patients 2016 Cuadrado, J; Vilaplana, J.; Mateo, J.; Solsona, F.; Solsona, S.; Rius, J.; Alves, R., Camafort, M.; Torres, G.; Betriu, A.; Gutierrez, J.M.; Fernández, E. Article en revista divulgativa
Computer-assisted initial diagnosis of rare diseases 2016 Rui Alves; Marc Piñol; Jordi Vilaplana; Ivan Teixidó; Joaquim Cruz; Jorge Comas; Ester Vilaprinyo; Albert Sorribas; Francesc Solsona Article d'investigació
Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modelling 2016 Comas, J; Benfeitas, R.; Vilaprinyo, E.; Sorribas, A.; Solsona, F.; Farré, G.; Berman, J.; Zorrilla, U.; Capell, T.; Sandmann, G.; Zhu, C.; Christou, P.; Alves, R. Article d'investigació
Regulation of the Na+/K+-ATPase Ena1 expression by calcineurin/Crz1 under high pH stress: A quantitative study. 2016 Petrezsélyová S; López-Malo M; Canadell D; Roque A; Serra-Cardona A; Marqués MC; Vilaprinyó E; Alves R; Yenush L; Ariño J. Article d'investigació
Global methodology for developmental neurotoxicity testing in humans and animals early and chronically exposed to chemical contaminants 2016 Arpiné A. Elnar; Nadia Ouamara; Nadiya Boyko, Xavier Coumoul; Jean-Philippe Antignac; Bruno Le Bizec; Gauthier Eppe; Jenny Renaut; Torsten Bonn; Cédric Guignard; Margherita Ferrante; Maria Liusa Chius Article d'investigació
The CHEMDNER corpus of chemicals and drugs and its annotation principles 2015 Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktäschel T, Matos S, Campos D, Tang B, Xu H, Munkhdalai T, Article d'investigació
Global optimization of hybrid kinetic/FBA models via outer-approximation 2015 Pozo C.; Miro A.; Guillén-Gosálbez, G.; Sorribas A.; Alves R.; Jiménez L. Article d'investigació
CheNER: a tool for the identification of chemical entities and their classes in biomedical literature 2015 Usié A.; Cruz J.; Comas J.; Solsona F.; Alves R. Article d'investigació
A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes 2015 Salvado B.; Vilaprinyo E.; Sorribas A.; Alves R. Article d'investigació
An in vitro system for the rapid functional characterization of 20 genes involved in carotenoid biosynthesis and accumulation 2014 Bai, C; Rivera, SM; Medina,V; Alves,R; Vilaprinyo,E; Sorribas,A; Canela,R; Capell,T; Sandmann,G.; Christou, P; Zhu, C. Article d'investigació
Database Constraints Applied to Metabolic Pathway Reconstruction Tools 2014 Jordi Vilaplana; Francesc Solsona; Ivan Teixido; Anabel Usié; Hiren Karathia; Rui Alves; Jordi Mateo Article d'investigació
Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents 2014 Usie A, Karathia H, Teixidó I, Alves R, Solsona F. Article d'investigació
CheNER: Chemical Named Entity Recognizer 2014 Usie, A.; Alves, R.; Solsona, F.; Vazquez, M.; Valencia, A. Article d'investigació
S-PC: An e-treatment application for management of smoke-quitting patients 2014 Jordi Vilaplana; Francesc Solsona; Francesc Abella; Josep Cuadrado; Rui Alves; Jordi Mateo Article d'investigació
Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization 2013 Guillén-Gosálbez, G.; Miro, A.; Alves, R.; Sorribas, A.; Jimenez, L. Article d'investigació
Relative Amino Acid Composition Signatures of Organisms and Environments 2013 Moura, A.; Savageau,MA.; Alves, R. Article d'investigació
Targeted transcriptomic and metabolic profiling reveals temporal bottlenecks in the maize carotenoid pathway that may be addressed by multigene engineering 2013 Farre G.; Rivera S.M.; Alves R.; Vilaprinyo E.; Sorribas A.; Canela R.; Naqvi S.; Sandmann G.; Capell T.; Zhu C.; Christou P. Article d'investigació
Two component systems: physiological effect of a third component 2012 Salvado B.; Vilaprinyo E.; Karathia H.; Sorribas A.; Alves R. Article d'investigació
Teaching systems biology 2011 Alves R; Vilaprinyo E; Sorribas A; Article d'investigació
Special issue on biological design principles 2011 Alves, R.; Sorribas, A. Article d'investigació
¿El aniversário de la Biologia de Sistemas? 2011 Alves, R., Salvado, B., Vilaprinyo, E., Sorribas, A. Article en revista divulgativa
Existo, luego soy una red. 2011 Sorribas,A., Vilaprinyo, E., Alves, R. Article en revista divulgativa
Saccharomyces cerevisiae as a model organism: a comparative study 2011 Karathia, H.; Vilaprinyo, E.; Sorribas, A.; Alves, R. Article d'investigació
Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models 2011 Pozo C.; Marin-Sanguino, A.; Alves R.; Guillén-Gosalbez, G.; Jimenez L.; Sorribas A. Article d'investigació
Biblio-MetReS: A bibliometric network reconstruction application and server 2011 Usie A.; Karathia H.; Teixido I.; Valls J.; Faus X.; Alves R.; Solsona F. Article d'investigació
Methods for and results from the study of design principles in molecular systems 2011 Salvado B.; Karathia H.; Chimenos AU.; Vilaprinyo E.; Omholt S.; Sorribas A.; Alves R. Article d'investigació
Seguimiento y control de pacientes fumadores en proceso de deshabituación mediante SMS. Una experiencia en e-salud 2011 Francesc Abella; Assumpció Vilarasau; Josep Cuadrado; Francesc Solsona; Rui Alves; Jordi Vilaplana; Joan Serra Article en revista divulgativa
Optimization and evolution in metabolic pathways: Global optimization techniques in Generalized Mass Action models 2010 Sorribas A.; Pozo C.; Vilaprinyo E.; Guillén-Gosálbe,z G.; Jimenez L.; Alves R. Article d'investigació
Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes 2010 Vilaprinyo E.; Alves R.; Sorribas A. Article d'investigació
Evolution based on domain combinations: the case of glutaredoxins 2009 Alves, R.; Vilaprinyó, E.; Sorribas, A.; Herrero, E. Article d'investigació
Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathays 2008 Alves R.; Vilaprinyo E.; Hernández-Bermejo, B.; Sorribas A. Article d'investigació
Integrating bioinformatics and computational biology: Perspectives and possibilities for in silico network reconstruction in molecular systems biology 2008 Alves R.; Vilaprinyo E.; Sorribas A. Article d'investigació
Hysteretic and graded responses in bacterial two-component signal transduction 2008 Igoshin O.; Alves R.; Savageau M.A. Article d'investigació
Gene expression levels in Saccharomyces cerevisisae strongly reflect energetic cost rates of gene products. 2008 Vilaprinyo, E., Alves, R., Sorribas, A. & Salvador, A. Article d'investigació
Semi-Automated Reconstruction of Biological Circuits. 2008 Alves, R.; Vilaprinyo, E. & Sorribas, A. Article d'investigació
Approximate formalisms: does anything work? 2008 Sorribas A.; Vilaprinyo, E. & Alves, R. Article d'investigació
Energetic Constraints in Adaptive gene expression responses of yeast under environmental changes. 2008 Vilaprinyo, E., Salvador, A., Alves, R.,& Sorribas, A. Article d'investigació
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae 2007 Alves R.; Sorribas A. Article d'investigació
Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations 2007 Sorribas A.; Hernández-Bermejo, B.; Vilaprinyo E.; Alves R. Article d'investigació
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock 2006 Vilaprinyo E.; Alves R.; Sorribas A. Article d'investigació
Identification of operational constraints that shape the response of yeast to heat shock 2006 Sorribas, A., Vilaprinyo, E., Alves, R. Capítol de llibre d'investigació
Tools for kinetic modeling of biochemical networks 2006 Alves R.; Antunes F.; Salvador A Article d'investigació
Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes. 2005 Alves, R.; Savageau, M.A. Article d'investigació
Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism. II. Role of glutaredoxin Grx5 2004 Alves R.; Herrero E.; Sorribas A. Article d'investigació
Predictive reconstruction of the mitochondrial iron-sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin-ferredoxin reductase (Yah1-Arh1) 2004 Alves R.; Herrero E.; Sorribas A. Article d'investigació
Evolution and cellular function of monothiol glutaredoxins: involvement in iron-sulphur cluster assembly 2004 Vilella F.; Alves R.; Rodriguez-Manzaneque, M.T.; Belli G.; Swaminathan S.; Sunnerhagen P.; Herrero E. Article d'investigació
Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function. 2003 Alves R.; Savageau, M.A. Article d'investigació
Evolution of enzymes in metabolism: a network perspective. 2002 Alves R.; Chaleil R.A.; Sternberg M.J. Article d'investigació
Effect Of Overall Feedback Inhibition In Unbranched Biosynthetic Pathways 2001 Alves R.; Savageau M.A. Article d'investigació
Reversibility In Unbranched Pathways: Preferred Positions Based On Regulatory Considerations 2001 Alves R.; Savageau, M. A. Article d'investigació
Systemic Properties Of Ensembles Of Metabolic Networks: Application Of Graphical And Statistical Methods To Simple Unbranched Pathways 2000 Alves R, Savageau MA. Article d'investigació
Comparing Systemic Properties Of Ensembles Of Biological Networks By Graphical And Statistical Methods 2000 Alves R.; Savageau M.A. Article d'investigació
Extending the method of mathematically controlled comparison to include numerical comparisons 2000 Alves R, Savageau MA. Article d'investigació
Bioenergética: Termodinâmica e Cinética em Bioquímica 1996 Alves, R., Antunes, F., Salvador, A., Pinto, R. E. Capítol de llibre docent
Regulação Metabólica 1996 Antunes, F., Alves, R., Salvador, A., Pinto, R. E. Capítol de llibre docent
Lipid Peroxidation In Mitochondrial Inner Membranes: I. An Integrative Model 1996 Antunes F.; Salvador A.; Marinho S.; Alves R.; Pinto R.E. Article d'investigació
PARSYS – A tool for theoretical analysis of metabolic processes 1996 Salvador, A., Garcia, J., Sousa, J., Antunes, F., Alves, R., Pinto, R. E. Capítol de llibre d'investigació