CV at a glance

An overview of my academic activity

My research activity has focused on the development of mathematical methods for the analysis of the properties of metabolic systems. I have contributed extensively to the theory of the formalism power-law and its application as Biochemical Systems Theory. This activity started during my post-doctoral stay in the University of Michigan (Ann Arbor) under the supervision of Prof. Michael A. Savageau. 

Once incorporated at the University of Lleida, I acted as a leader of the research group on modelling metabolic processes, now within the Institut de Recerca Biomedica de Lleida. The group, repeatedly credited as a consolidated Group by Generalitat de Catalunya, has focused on aspects of the evolution of metabolic pathways, with special attention to understand design and operational principles that could be identified as general principles beyond specific cases. 

On this direction, we have investigated the adaptation of yeast to heat stress to understand the evolution of the gene expression response pattern observed experimentally. We have focused on developing methods to characterize the feasible regions for the activity of various enzymes based on specific functional requirements. Collaboration with the Group of Dr.Guillen-Gosálbez of the University Rovira i Virgili, has allowed developing novel ideas to interpret the evolution of gene expression patterns. 

Optimization techniques are difficult to enforce in non-linear models. We have contributed to this field with new techniques and explored problems associated with the identification of parameters in nonlinear models and optimization methods appropriate for these models. Our results show that gene expression patterns can be explained by correlating their effects on the underlying metabolic pathways.

We have also concentrated in computational methods able of identifying metabolic networks and of providing clues on their performance and evolution. Among other results, we have developed computational tools that use text mining techniques to identify candidate elements of specific networks. These methods were connected to tools for protein structure and docking for evaluating the most probable organization in the case of FeS cluster biosynthesis.

I’ve been leading the Agritech BIG DATA virtual platform oriented to implement BIG DATA techniques as decision-support tools in the agro-food production. This platform is being developed in the Scientific and Technological Park in Lleida in collaboration with EURECAT, the Technological Center of Catalonia. One of the leading projects in this platform concerns data integration and analysis for the world-wide consortium Global Forest Biodiversity Initiative.

I have developed various management activities, among which the direction of the Department of Basic Medical Sciences and the Subdirection of the Institut de Recerca Biomedica of Lleida (IRBLleida), from its creation to the completion of the process of accreditation by the ISCIII. From May 2011 and ending in May 2019, I was Vice-chancellor for Science Policy and Technology, coordinating the institutes and research centers and leading the research strategies of our university. On the other hand, I coordinate the actions of investigation as a representative of my University in campus IBERUS, a consortium of four universities: Zaragoza, La Rioja, Pública de Navarra, and Lleida. I was also the person responsible for promoting the scientific activities of the UdL on the Scientific Park, focusing in university and enterprise collaboration.

Main research interests

Evolution of metabolism

Mathematical models and optimization methods provide a way for understanding the evolution of metabolism. Our group has explored the adaptive response of yeast o stress and have shown that the observed pattern of gene expression that allows adaptation to heat shock can be explained as an optimization result subject to physiological constraints. Those results provide new insights on evolution and on biotechnological applications.

  • Pereira T, Vilaprinyo E, Belli G, Herrero E, Salvado B, Sorribas A, Altés G, Alves R. Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress. Cell Rep. (2018) ;22(9):2421-2430. doi: 10.1016/j.celrep.2018.02.020.
  • Vilaprinyo E, Alves R, Sorribas A (2010) Minimization of biosynthetic costs in adaptive gene expression responses of yeast to environmental changes. PLoS Comput Biol 6(2): e1000674. doi:10.1371/journal.pcbi.1000674
  • Sorribas A, Pozo C, Vilaprinyo E, Guillén-Gosálbez G, Jimenez L, Alves R (2010) Optimization and evolution in metabolic pathways: global optimization techniques in Generalized Mass Action models. J.Biotechnol. 149: 141-153
  • Guillén-Gosálbez-G, Sorribas, A. (2009) Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible en zyme activity patterns leading to cellular adaptive responses. BMC Bioinformatics 2009, 10:386
  • Alves R, Vilaprinyo E, Sorribas A, Herrero E. (2009) Evolution based on domain combinations: the case of glutaredoxins. BMC Evolutionary Biology 2009, 9:66 doi:10.1186/1471-2148-9-66
  • Vilaprinyo E, Alves R, Sorribas A. (2006) Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock. BMC Bioinformatics. 7:184.

Mathematical models’ methodology

Modeling complex systems requires methods able of providing insights on the properties and regulation of such systems. My work has focused on developing such tools. Among other results, in recent years I have focused on optimization methods and in formalisms that can capture the essential properties of metabolic processes.

  • Guillén-Gosálbez G, Miró A, Alves R, Sorribas A, Jimenez L. (2013) Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization. BMC Systems Biology 7(1):113
  • Pozo C, Guillén-Gosálbez G, Sorribas A, Jimenez L. (2012) Identifying the preferred subset of enzymatic profiles in nonlinear kinetic metabolic models via multi-objective global optimization and Pareto filters. PLoS ONE 7(9): e43487. doi:10.1371/journal.pone.0043487
  • Pozo C, Marin-Sanguino A, Guillén-Gosalbez G, Jimenez L, Alves R, Sorribas A. (2011) Steady-state global optimization of non-linear dynamic models through recasting into power-law canonical models. BMC Systems Biology 5:137
  • Pozo C, Guillén-Gosálbez G, Sorribas A, Jimenez L (2011) A spatial branch-and-bound framework for the global optimization of kinetic models of metabolic networks. Industrial & Engineering Chemistry Research 50: 5225-5238 DOI: 10.1021/ie101368k
  • Sorribas A, Hernandez-Bermejo B, Vilaprinyo E, Alves R. (2007) Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations. Biotechnol Bioeng. 97(5):1259-77.
  • Alves R, Sorribas, A. (2007) In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. BMC Syst Biol. 31;1:10.

Design principles in metabolism

The existence of recurrent network motifs leads asking why some designs are prevalent. Our group has investigated this subject by using mathematical models and analysis based on the power-law formalism.

  • Salvado, B; Vilaprinyo, E; Sorribas, A and Alves,R. 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). PeerJ 3:e1183; DOI 10.7717/peerj.1183
  • Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R (2012) Two Component Systems: Physiological Effect of a Third Component. PLoS ONE 7(2): e31095. doi:10.1371/journal.pone.0031095
  • Karathia HM, Vilaprinyo E, Sorribas A, Alves R. S. cerevisiae as a model organism: Strengths & drawbacks (2011) PLoS One 6(2):e16015
  • Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R (2012) Two Component Systems: Physiological Effect of a Third Component. PLoS ONE 7(2): e31095. doi:10.1371/journal.pone.0031095
  • Salvado B, Karathia H, Usie-Chimenos A, Vilaprinyo E, Omholt S, Sorribas A, Alves R. (2011) Methods for and results from the study of design principles in molecular systems. Mathematical Biosciences 231:3–18
  • Special issue on biological design principles (editor) Mathematical Biosciences

Mathematical models of metabolic networks

Mathematical models are fundamental tools for guiding biotechnological applications. By have collaborated with other groups to apply our knowledge on real world problems.

  • 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. Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling. Plant J. (2016);87(5):455-71. doi: 10.1111/tpj.13210
  • Bai, C; Maiam R, Sol; Medina, V; Alves, R; Vilaprinyo, E; Sorribas, A; Canela, R; Capell, T; Sandmann, G; Christou, P; Zhu, C. (2014) An in vitro system for the rapid functional characterization of genes involved in carotenoid biosynthesis and accumulation. The Plant Journal (2014) doi: 10.1111/tpj.12384
  • Farré G, Maiam Rivera S, Alves R, Vilaprinyo E, Sorribas A, Canela R, Naqvi S, Sandmann G, Capell T, Zhu C, Christou P (2013) Targeted transcriptomic and metabolic profiling reveals temporal bottlenecks in the maize carotenoid pathway that may be addressed by multigene engineering. The Plant Journal doi: 10.1111/tpj.12214
  • Pozo C, Marin-Sanguino A, Guillén-Gosalbez G, Jimenez L, Alves R, Sorribas A. (2011) Steady-state global optimization of non-linear dynamic models through recasting into power-law canonical models. BMC Systems Biology 5:137

Statistical methods and theory

Although this has been secondary to my activity, I have worked on some problems related to statistical theory and applications. Recently we have started to investigate the problem of diagnostic in rare diseases.

  • Alves R, Piñol M, Vilaplana J, Teixidó I, Cruz J, Comas J, Vilaprinyo E, Sorribas A, Solsona F. Computer-assisted initial diagnosis of rare diseases. PeerJ. (2016) Jul 21;4:e2211. doi: 10.7717/peerj.2211
  • Trujillano J, Muino JM, March J, Sorribas A. (2007) A more flexible parametric estimation of univariate reference intervals: a new method based on the GS-distribution. Clin Chim Acta. 379(1-2):71-80. Epub 2006 Dec 22.
  • Sorribas, A, Muiño, JM, Voit, EO. (2006) GS-distributions: a new family of distributions for continous unimodal variables. Computational Statistics and Data Analysis 50:2769-2798

Leadership and administration

  • Vicerector for Scientific and Technologial Policies of the University of Lleida (May 2011-May 2019)
  • Responsible of the Strategic Plan of Research of the University of Lleida (2012).
  • Coordinator of the RIS3CAT Community of Technology for AgriFood Production (2013-2019), with 7 projects and a total of 10M€ of funding.
  • Leader of the Specialization and Competitivity Plan (PECT) of the Catalan region of Lleida (2014-2019). Participation in 3 approved proposals with more than 2M€ funding.
  • Representative of the University of Lleida and active member of the Pla Estratègic de Recerca, Innovació i Transferència Agroalimentària de Catalunya (2013-2020).
  • Responsible of the University of Lleida in the International Campus of Excellence IBERUS (2011-2019).
  • Responsible of the scientific and technological participation of the University of Lleida in the Scientific and Technological AgriFood Parc of Lleida (PCiTAL) (2015-2019).
  • Promoter of Agritech BIG DATA, a platform for data analytics and integration in agrofood production (Digital Innovation Hub) in collaboration with EURECAT and other Catalan institutions and entities of the agrofood activitiy.
  • Promoter of the GFBI Hub at the University of Lleida for data integration and big data analysis in forestry. GFBI is an international consortium (Global Forest Biodiversity Initiative) of more than 40 universities and technological centers around the world.
  • Subdirector of the Research Institute of Biomedicine (IRBLleida) (2004-2011)
  • Director of the Department of Basic Medical Sciences of the University of Lleida (2004-2009)
  • Representative of the University of Lleida in the core group for the candidature FoodBest to the KIC4Future call of the EIT (2012-2016).
  • IP of the group: Models Matemàtics i Estadístics en Biologia de Sistemes, Genètica de Malalties Complexes i Models Biològico-Factorials de la Personalitat (SGR2005-00951, SGR2009-809)
  • IP of the group: Modelització matemàtica i Estadística de Processos Biològics (2014 SGR 243, Quality group of the Generalitat de Catalunya)
  • Six positive evaluations (all the possible since 1981) of research activity from the Spanish science office.

Projects as IP

  • Desarrollo de métodos para la caracterización de principios de diseño y operación en Biología de sistemas BFU2008-00196/BMC (2008-2011)
  • Investigación de principios operacionales en biología de sistemas: caracterización en el caso de la respuesta de S. cerevisiae a estrés térmico. BFU2008-00196/BMC (2005-2008)
  • Desarrollo e implementación práctica de nuevos métodos para estimar intervalos de referencia y para el control de calidad en parámetros clínicos: generalización de la metodologia basada en la S-Distribution. PI020450 (2002-2005)
  • Cálculo de intervalos de normalidad criterios diagnóstico y curvas ROC en la práctica clínica: desarrollo de nuevos métodos de aplicación general basados en el concepto de S-distribution. MSCO-00/0235 (2000-2001)
  • Desarrollo de métodos basados en la S-distribution para la estimación de distribuciones condicionales y percentiles en estudios poblacionales. PAER-Ajuntament de Lleida (1999-2000)

I’m an enthusiastic photographer (https://alsote.wixsite.com/photo) and cooker (my wet laboratory activity!!). Traveling, mountaineering, and skiing are paramount for me as a mean for knowing people and cultures and for enjoying outdoors.

I admire Barcelona football team as an example of a dynamic complex system able of performing in an excellent coordination for attaining good results. I am also a passionate reader and a regular theater spectator. Books and performances approach me to the important issues of life.

Last, but not least, I consider debate and exchange of ideas with friends and colleagues (sometimes the same person bears both categories) a fundamental part of life.