Curriculum Vitae. Rui Carlos Vaqueiro de Castro Alves

Curriculum Vitae Rui Carlos Vaqueiro de Castro Alves March 2010

CURRICULUM VITAE Rui Carlos Vaqueiro de Castro Alves (R. Alves) Present address: Office: Departament Ciencies Mediques Basiques Universidad de Lleida, Montserrat Roig 2 25008 Lleida Spain Home: Camp de Mart, 43, 1º, 2ª 25006 Lleida Spain Phone: +034 973 702406 Fax : +034 973 702426 E-mail: ralves@cmb.udl.es Education University of Lisbon: B. S. & Honor s Degree (Licenciatura: grade 15/20; 1994) Biochemistry Ph. D. Suma cum Laude 24/07/2000 Theoretical Biochemistry Computer Skills: Programming Skills: C, C++ and Visual C PERL Mathematica SQL Has database building and management knowledge.

Operating systems: Extensive use of LINUX, WINDOWS and MacOS and a large assortment of mathematical, graphical and text edition programs under each of these operating systems. Scientific Training and Professional Experience: 1993-94 Research stage, University of Lisbon (Laboratory of Dr. Ruy E. Pinto). 1- year research project. The research resulted in the small thesis with the title "Mathematical Model of Mitochondrial Phosphorylative Oxidation: Construction and analysis". This thesis was graded with 19 (out of 20). April/June 1995 Worked on specific enzymatic markers for different species of partridge under the orientation of Assistant Professor Deodália Dias of Faculdade de Ciências, Universidade de Lisboa. 1995-2000 In July 1995 was selected as one of the 16 students to enter the "Programa Gulbenkian de Doutoramentos em Biologia e Medicina. This program has 4 year duration. April/May 1996 October 1996- December 1999 January 2000- December 2000 January 2001- December 2001 January 2002- December 2002 January 2003- December 2005 September 2003- December 2005 January 2006 - Worked on Controlled Mathematical Comparisons of Signal Transduction Pathways during a short stay of a month at Lleida University, Spain, under Prof. Albert Sorribas. Worked with Prof. Michael Savageau at the Microbiology and Immunology Department, Medical School, University of Michigan to complete the work for his Ph. D. and in a short Post doctoral stay. Research assistant at the Microbiology And Immunology Dept. of the University of Michigan Medical School, in Prof. Michael Savageau s Lab. Research Fellow at the Imperial Cancer Research Fund and Imperial College of London, in Prof. Michael Sternberg s Lab. Invited Professor, Biostatistics Group at the University of Lleida Medical School. Invited Research Fellow, Biostatistics Group at the University of Lleida Medical School. Post Graduate Researcher, Biomedical Engineering Department, UC Davis Ramon y Cajal Researcher, Dept. Ciencies Mediques Basiques, University of Lleida

Teaching & Organizing 1997 Teaching Assistant in 2 Sessions of the Course "Cellular and Molecular Networks". Head: Prof. Michael Savageau. University of Michigan. USA. 1998 Teaching Assistant in the Practical Sessions of "Power Law Modeling In Biology" (DE-IGC) 1 October - 3 October 1998, Oeiras, Portugal Course for 1 st year students of the PGDBM (Gulbenkian Ph. D. Program in Biology and Medicine). Gulbenkian Science Institute. Portugal. 2000 Teaching Assistant in the Practical Sessions of "Modeling In Biology" (DE-IGC) 22 May - 27 May 2000, Oeiras, Portugal Course for 1 st year students of the PGDBM (Gulbenkian Ph. D. Program in Biology and Medicine). Gulbenkian Science Institute. Portugal. 2002 Invited Professor, Biomathematics and Biostatistics Group, University of Lleida. Spain. 2002 Co-supervisor of Ph. D. student José Maria Muiño, University of Lleida. Spain. 2003 2003 2004 2005 2005 Invited Professor, University of Lleida Medical School, Bioinformatics. Spain. Invited Lecturer of the Biochemical Systems Analysis course, UC Davis. USA. Invited Lecturer of the Biochemical Systems Analysis course, UC Davis. USA. Invited Professor to the PGDB Ph.D. Program, Gulbenkian Science Institute. Portugal. Organizer and Teacher, Integrative Computational Molecular Biology Course. Universidad de Lleida, small course for Ph. D. students, Lleida. Spain. 2006 Responsible for and teacher of the course Gene Prediction for a Master s Degree in Computational Biology at the University of Lisbon, School of Sciences. Portugal. 2006 Invited Lecturer, University of Munich, Munich. Germany. 2006 Invited Professor for PGBC, Ph.D. Program, IGC, Oeiras. Gulbenkian Science Institute. Portugal. 2006 Teacher of the course Integrative Computational Biology for Graduate students, at the University of Lleida. Spain. 2007 Teacher of the course Bioinformatics for 1 st year Ph. D. students from University of Coimbra. Portugal. 2007 Teacher of the course Mathematical Modeling in Biology for 1 st year Ph. D. students from University of Coimbra. Portugal. 2007 Teacher of the course Career Workshop for 1 st year Ph. D. students from the Gulbenkian Program of Computational Biology. Gulbenkian Science Institute. Portugal.

2007 Organizer and Teacher of the Course Bioinformatics for Biotechnology Students at the University of Lleida. Spain. 2008 Organizer and Teacher of the Course Mathematical Modelling in Biology for 1 st year Ph. D. students from the Gulbenkian Program of Computational Biology. Gulbenkian Science Institute. Portugal. 2008 Organizer and Teacher of the Course Bioinformatics for Biotechnology Students at the University of Lleida. Gulbenkian Science Institute. Portugal. 2009 Organizer and Teacher of the Course Mathematical Modelling in Biology for 1 st year Ph. D. students from the Gulbenkian Program of Computational Biology, Gulbenkian Science Institute. Portugal. 2009 Teacher at the workshop Teaching Systems Biology FEBS Congress, Prague. Czech Republic. 2009 Teacher at the workshop Systems Biology Portuguese Biophysics Society Santarém, Portugal. Editorial Boards 2010-2011 Guest Editor on a special issue of the Elsevier journal Mathematical Biosciences dedicated to Biological Design Principles. (To be publish in May 2011). Additional activities 1997-98 Co-Organizer, International Symposium on Power-Law Modeling of Biological Systems, Lisbon, Portugal, 4 th of October-7 th of October 1998 1998 Organizer, "Power Law Modeling In Biology" (Instituto Gulbenkian de Ciencia) 1 st of October 3 rd of October 1998 Short Course. 2000 Organizer, "Modeling In Biology" (Instituto Gulbenkian de Ciencia) April Short Course. 2001 Co-Organizer, "4 th Gulbenkian Autumn Meeting/1 st Portuguese Meeting on Theoretical and Computational Biology" (Instituto Gulbenkian de Ciencia). 2003 Internal Seminar Series, Organizer, Department de Ciencies Mediques Basiques, Universidad de Lleida 2003 Programa de Doutoramentos Gulbenkian em Bioinformatica, Organizing Committee 2004 International Symposium on Molecular Biology Systems, Organizing Committee, Lake Tahoe, California, USA 2005 Integrative Computational Molecular Biology, Organizer, Course for Ph. D. students, University of Lleida, Spain

2006 Departmental Seminar Series, Organizer, University of Lleida, Spain 2006 Departmental Research Discussion Group, Organizer, Course for Ph. D. students, University of Lleida, Spain 2006 Integrative Computational Biology, Organizer, Course for Ph. D. students, University of Lleida, Spain 2006 Exhibition of Original Comic Art Pages, Personal collection, University of Coimbra,Portugal 2007 Mathematical Modeling in Biology, Co-Organizer, Course for Ph. D. students, University of Coimbra, Portugal 2007- Elected member of the Claustre de la Universitat de Lleida (University Senate) 2008 Mathematical Modelling in Biology, Organizer, Course for Ph. D. students from the Gulbenkian Program of Computational Biology, Oeiras, Portugal 2008 Member of the Committee for defining and writing the Internal Rules of Functioning for the research institute IRBLLeida 2008 Head of the Education Programming Committee of IRBLleida 2008- Member of the Educational Committee of IRBLleida 2008- Member of the Research Committee of IRBLleida 2009- Elected member of the Junta de la Facultat de Medicina de la Universitat de Lleida (Medical School Senate) 2009 Mathematical Modelling in Biology, Organizer, Course for Ph. D. students from the Gulbenkian Program of Computational Biology, Oeiras, Portugal 2009 Member of the Scientific committee, 11th International Conference for Molecular Systems Biology 2009, Shangai, China 2010-2011 Co-Organizer of the meeting 12th International Conference for Molecular Systems Biology, to be held in May 2011, in Lleida, Spain. Honors and awards 1995-1999 Joint Ph. D. Fellowship, PGDBM, Instituto Gulbenkian de Ciência (IGC) and PRAXIS, Portugal 1996 Joint FLAD/PGDBM Grant for equipment acquisition 2001 Research Fellowship, ICRF/BBSRC, UK

2002 Invited Professor Fellowship, Spanish Government 2003-2004 Post-Doctoral Fellowship, Fundaçao para a Ciencia e Tecnologia, Portugal. 2005- Ramón y Cajal Award (Fellowship and Research Grant) Participation in Competitively Funded Projects 2001-2004 A novel function of transthyretin: involvement in proteolysis. IP Monica Sousa, FCT Portugal 2003-2005 Gene Circuits and Biochemical Networks. IP Michael Savageau, NIH, USA 1998-2000 Gene Circuits and Biochemical Networks. IP Michael Savageau, DoD, USA 2005-2007 Investigacion de principios operacionales en biologia de sistemas: caracterización en el caso de la respuesta S. cerevisiae a estrés térmico. IP Albert Sorribas, MCyT, Spain 2006 Desarrollo y Aplicación de Técnicas de Biología Molecular Computacional Integrativa a Estudios de Reconstrucción Sistémica. IP Rui Alves, Ramon y Cajal Project, Spain 2007-2008 Coordinated Action between Portugal and Spain, Spain 2008-2010 Desarrollo y aplicacion de metodologias computacionales integradas para Biologia Molecular de Sistemas. IP Rui Alves, MCyT, Spain 2008-2010 Background Reactivity of Proteins. IP Armindo Salvador, FCT, Portugal Under Review Under Review Under Review MetRES (Metabolic REconstruction Server): desarrollo y aplicación en en estudio de principios de diseño biológico (Submitted to the Spanish National Research Plan), Spain BMEISIS: Biomed, Economics, Informatics & Science Integrated Solutions Tecnio Xarxa Centre (Submitted to the Generalitat de Catalunya), Spain Development of tools to assist in the diagnostic, understanding, and treatment of rare diseases: Application to Iron-Sulfur cluster related diseases. (Submitted to the Marato 2010 project call on rare diseases), Spain Membership in professional societies Sociedade Portuguesa de Bioquímica Sociedade Española de Bioquímica y Biologia Molecular Sociedad Española de Microbiologia Community Service

Scientific Referee for various Journals (PNAS, PLOS Journals, BMC Journals, Bioinformatics, Mathematical Biosciences, J. Theoret. Biol., Biomedical Engineering Journals, etc.) and for competitive projects from Spanish funding agencies. Articles in scientific journals 1. Antunes, F., Salvador, A., Marinho, S., Alves, R., Pinto, R. E. (1996) "Lipid Peroxidation In Mitochondrial Inner Membranes: I. An Integrative Model". Free Radic. Biol. Med., 21, 917-943. 2. Alves, R. & Savageau M. A. (2000) Comparing Systemic Properties Of Ensembles Of Biological Networks By Graphical And Statistical Methods, Bioinformatics, 16: 527-533 3. Alves, R. & Savageau M. A. (2000) Systemic Properties Of Ensembles Of Metabolic Networks: Application Of Graphical And Statistical Methods To Simple Unbranched Pathways, Bioinformatics, 16: 534-547 4. Alves, R. & Savageau M. A. (2000) Extending the method of mathematically controlled comparison to include numerical comparisons, Bioinformatics, 16:786-798 5. Alves, R. & Savageau M. A. (2000) Effect Of Overall Feedback Inhibition In Unbranched Biosynthetic Pathways, Biophysical Journal,79: 2290-2304 6. Alves, R. & Savageau M. A. (2001) Reversibility In Unbranched Pathways: Preferred Positions Based On Regulatory Considerations, Biophysical Journal, 80: 1174-1185 7. Alves, R., Chaleil, R. A. G. & Sternberg M. J. E. (2002) Evolution of Enzymes in Metabolism: A Network Perspective. Journal of Molecular Biology, 320:751-770. 8. Alves, R. & Savageau M. A. (2003) Comparative analysis of prototype twocomponent systems with either bifunctional or monofunctional sensors: Differences in molecular structure and physiological function. Mol. Microbiol. 48: 25-51. 9. Alves, R., Herrero, E. & Sorribas, A. (2004) Predictive Reconstruction of the Mitochondrial Iron-Sulfur Cluster Assembly Metabolism : I- The role of the protein pair Ferredoxin/Ferredoxin Reductase (Yah1/Arh1). Proteins: Structure Function and Bioinformatics, 56:354-366. 10. Vilella, F., Alves, R., Rodríguez-Manzaneque, M. T., Belli, G., Sunnerhagen, P. & Herrero, H. (2004). Evolution and cellular function of monothiolic Glutaredoxins: involvement in iron/sulfur cluster assembly. Comparative and Functional Genomics, 5:328-341. 11. Alves, R., Herrero, E. & Sorribas, A. (2004) Predictive Reconstruction of the Mitochondrial Iron-Sulfur Cluster Assembly Metabolism : II- The role of the protein glutaredoxin Grx5. Proteins: Structure Function and Bioinformatics, 57:481-492. 12. Alves, R. & Savageau, M. A. (2005) Evidence of selection for low cognate amino-acid bias in amino-acid biosynthetic enzymes. Mol. Microbiol.,56:1017-1034. 13. 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. 7:184-203. 14. Alves, R., Antunes, F. & Salvador, A. (2006). Tools for Kinetic Modeling. Nature Biotechnology. 24:667-672. 15. Sorribas, A., Hernandez-Bermejo, B., Vilaprinyo, E., Alves, R. (2007) Use of Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations. Bioengineering & Biotechnology, 97:1259-1277.

16. Alves, R., & Sorribas, A. (2007) In silico pathway identification and reconstruction by cooperative use of computational biology methods: The case of Iron- Sulfur assembly metabolism in Saccharomyces cerevisiae. BMC Systems Biology 1:10 17. Alves, R., Vilaprinyo, E., Sorribas, A. (2008) Integrative Computational Biology: Perspectives and Possibilities for in silico network reconstruction in Molecular Systems Biology. Currenr Bioinformatics, 3: 98-129 18. Igoshin, O., Alves, R., Savageau, M.A. (2007) Hysteretic and graded responses in bacterial two-component signal transduction. Mol. Microbiol. 68: 1196-1215 19. Alves, R., Vilaprinyo, E., Hernandez-Bermejo,B. & Sorribas A. (2008) Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways. Biotechnology & Genetic Engineering Reviews, 25: 1-40. 20. Alves, R.,Vilaprinyo, E. & Sorribas, A. (2008) Semi-Automated Reconstruction of Biological Circuits. Philippine Information Technology Journal 1: 32. 21. Vilaprinyo, E., Alves, R., Sorribas, A. & Salvador, A. (2008) Gene expression levels in Saccharomyces cerevisisae strongly reflect energetic cost rates of gene products. Philippine Information Technology Journal 1: 37. 22. Vilaprinyo, E., Salvador, A., Alves, R.,& Sorribas, A. (2008) Energetic Constraints in Adaptive gene expression responses of yeast under environmental changes. Philippine Information Technology Journal 1: 36. 23. Sorribas A., Vilaprinyo, E. & Alves, R.(2008) Approximate formalisms: does anything work?. Philippine Information Technology Journal 1: 34. 24. Alves, R., Vilaprinyo, E. Sorribas, A. & Herrero, E. (2009) Evolution based on domain combinations: the case of glutaredoxins. BMC Evolutionary Biology.9:66 25. Vilaprinyo, E., Alves, R., Sorribas, A. (2010) Minimization of biosynthetic costs in adaptive gene expression responses of yeast to environmental changes. Plos Comp. Biol. 6, e1000674 26. Sorribas, A., Pozo, C., Vilaprinyo, E., Guillén-Gosálbez, G., Jiménez, L., Alves, R. (2010) Optimization and evolution in metabolic pathways: global optimization techniques in Generalized Mass Action models. J. Biotechnol., Accepted for publication. 27. Alves, R. Vilaprinyo, E. & Sorribas, A. (2010)Teaching Undergraduate Systems Biology. Submitted. 28. Karathia, H. & Alves, R. (2010) S. cerevisiae as a model organism: streghts and drawbacks. Submitted. 29. Moles, E. Vilaprinyo, E., Karathia, H., Sorribas, A., Alves, R. (2010) FeSC biogenesis pathways: Prevalence and modularity. In preparation. 30. Karathia, H. & Alves, R. (2010) A framework the comparison of complete proteomes between organisms with fully sequence genomes. In preparation. Chapters in books 1. Alves, R., Antunes, F., Salvador, A., Pinto, R. E. (1996) "Bioenergética: Termodinâmica e Cinética em Bioquímica". In Halpern, M. (Ed.) "Bioquímica". Porto: Lidel. 2. Antunes, F., Alves, R., Salvador, A., Pinto, R. E. (1996) "Regulação Metabólica". In Halpern, M. (Ed.) "Bioquímica". Porto: Lidel. 3. Salvador, A., Garcia, J., Sousa, J., Antunes, F., Alves, R., Pinto, R. E. (1996) "PARSYS A tool for theoretical analysis of metabolic processes". In Yamakawa, T.,

Matsumoto, G. (Eds.) "Methodologies for the Conception, Design, and Application of Intelligent Systems" Vol. 2, pp 963-966. Singapore: World Scientific 4. Sorribas, A., Vilaprinyo, E., Alves, R. (2006) Identification of operational constraints that shape the response of yeast to heat shock. ISSY25 25th International Specialised Symposium on Yeasts - Yeast systems biology - from models to applications ISBN 951-38-6307-7 and 951-38-6308-5; ISSN 0357-987 and 1455-0873 Manuals, reports and Dissertations 1. Alves, R. (1994) "Construção e Análise de um Modelo Matemático da Fosforilação Oxidativa Mitocondrial" (Construction and Analysis of a Model for Mitochondrial Phosphorylative Oxidation), Monograph, Faculdade de Ciências, Universidade de Lisboa. 2. Alves, R. (1996) "Some Methodologies for Simulation of Metabolic Networks. Application to a Signal Transduction Pathway", Monograph, Departamento de Ensino, Fundação Calouste Gulbenkian, Oeiras 3. Alves, R., Preto da Silva, M.; Tavares, A. (1996) "The Origins of Life", Monograph, Departamento de Ensino, Fundação Calouste Gulbenkian, Oeiras 4. Alves, R. (2000) "Development of Methodologies to Analyze and Compare Metabolic Networks: Application to Specific Classes of Metabolic Pathways". Ph. D. Dissertation, Universidade de Lisboa Invited Seminars 2002 - "Evolutionary Design Principles in Subcelular Networks", Sociedade Catalana de Biologia, Universidad de Lerida, Lerida, España 2003 - "Predictive Reconstruction of Iron-Sulfur Cluster Metabolism in Saccharomyces cerevisiae" Instituto de Biologia Molecular e Celular, Porto, Portugal 2004 Design Principles in Molecular Biology, University of Coimbra, Coimbra, Portugal 2004 Design Principles in Molecular Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal 2004 - Predictive Reconstruction of the Mitochondrial Iron-Sulfur Cluster Assembly Metabolism :- The role of the protein pair Ferredoxin/Ferredoxin Reductase (Yah1/Arh1). SEBBM Meeting, Lleida, Spain. 2005 - Evolutionary Design Principles & Metabolic Reconstruction, Section of Microbiology, UC Davis, Davis, USA, February 2005. 2005 - Evolutionary Design Principles & Metabolic Reconstruction, EMBL, Heidelberg, Germany, February 2005. 2005 - Evolutionary Design Principles & Metabolic Reconstruction, IGC, Oeiras, Portugal, February 2005.

2005 Evolution of amino acid bias in the composition of proteins, Universidad de Lleida, Lleida, Spain, March 2005. 2005 Amino Acid Bias in Amino Acid Biosynthesis, Small Genomes Meeting, University of Winsconsin, Madison, USA, September 2005. 2006 Mathematically controlled comparisons, University of Munich, Munich, Germany, July 2006. 2006 Amino Acid Signatures, Meeting of the Spanish Society of Microbiology, Lleida, Spain, September 2006. 2007 Generic and specific constraints shaping adaptive gene expression profiles in yeast, University of Coimbra, Coimbra, Portugal, April 2007. 2007 In silico Metabolic Reconstruction of Fe-S Clusters in Yeast, University of Coimbra, Coimbra, Portugal, April 2007. 2007 In silico Metabolic Reconstruction of Fe-S Clusters in Yeast, Instituto Gulbenkian de Ciencia, Oeiras, Portugal, June 2007. 2008 Design Principles in Bacterial two component systems, Instituto Gulbenkian de Ciencia, Oeiras, Portugal, July. 2008 - Network reconstruction & design principles Systems Biology for Medical Applications Summer School, Tenerife, Spain, October 2009 - Biomedical Applications of Metabolic Reconstruction, 2nd InternationalSymposium-Cum-Training Course on Molecular Medicine and Drug Research, Karachi, Pakistan, January 2009 Iron Sulphur Cluster Biogenesis, 11th international conference on molecular systems biology, Shangai, People s Republic of China, June 2009 Systems Biology in Europe FEBS Meeting, Prague, Check Republic, July 2009 Biological Design Principles, Catalan society of Biology, October, Barcelona. 2009 Network Reconstruction & Biological Design Principles, Systems Biology workshop, Portuguese Society of Biophysics, Santarém, Portugal, October 2009 In silico methods for the study of biological design principles and network reconstruction, Parc Cientific, Barcelona, Spain, November 2009 Network Reconstruction & Biological Design Principles, Universitat Autonoma de Barcelona, Barcelona, Spain, December Abstracts, Posters and Lectures in Meetings

1. Alves, R.; Salvador, A.; Antunes, F.; Pinto, R. E. (1994) "Comparison of the accuracy of the GMA and S system approach in predicting the steady state behavior of a complex kinetic model", Poster & Short Seminar Symposium of Integrative Biochemistry, Barcelona, Spain. 2. Alves, R., Salvador, A., Antunes, F., Pinto, R. E. (1995) "O 2 binding to cytochrome oxidase: Different kinetic models", Poster, 1 st Portuguese-Spanish Biophysics Congress, Lisboa, Portugal. 3. Alves, R.; Savageau, M. (1997) "Analysis of the design of two component systems in bacteria", Communication, 3 rd PGDBM meeting, Curia, Portugal 4. Alves, R.; Savageau, M. (1998) "Regulatory design of unbranched pathways", Communication, 4 th PGDBM meeting, Curia, Portugal 5. Alves, R.; Savageau, M. (1998) "Regulatory design of unbranched pathways revisited: illustration of a statistical approach to mathematically controlled comparisons", Communication, "PowBioSys: International Symposium on Power-Law Modeling of Biological Systems", Oeiras, Portugal 6. Alves, R.; Savageau, M. (1999) " A Theoretical Study on the Selection of Two Alternative Designs for Two Component Systems", Communication, 5 th PGDBM meeting, Curia, Portugal 7. Alves, R.; Savageau, M (2000) "Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways", Communication, VI International Symposium on Biochemical Systems Theory, Tenerife, Spain 8. Alves, R., Sternberg M. J. E. (2001) Evolution of Enzymes in Metabolism: A Network Perspective,Communication, 4 th Gulbenkian Autumn Meeting/1st Portuguese Meeting on Theoretical and Computational Biology, Portugal. 9. Alves, R., Sternberg M. J. E. (2002) Evolution of Enzymes in Metabolism, Communication, VII Biochemical Systems Theory Meeting, Norway. 10. Muiño, J. M.; Alves, R.; Sorribas, A. (2003) A New and Generalized Theoretical Formalism for Growth Functions, Poster, ACMS meeting, Madrid, Spain. 11. Alves, R. & Sorribas, A. (2004) A. Predictive Reconstruction of the Mitochondrial Iron-Sulfur Cluster Assembly Metabolism :- The role of the protein pair Ferredoxin/Ferredoxin Reductase (Yah1/Arh1), Communication, International Symposium on Molecular Biology Systems, Lake Tahoe, California, USA 12. Alves, R. & Savageau, M. A. (2004) Amino acid Bias in Amino acid Biosynthesis, Communication, International Symposium on Molecular Biology Systems, Lake Tahoe, California, USA 13. E. Vilaprinyo, R. Alves, A. Sorribas. (2006) Identification of quantitative design principles of the response of yeast to stress conditions, Communication, 1 st International Symposium on Systems Biology-From genomes to in silico and back, 1 th -2 th June, 2006, Murcia, Spain 14. A. Sorribas, E. Vilaprinyo, R. Alves. (2006) Identification of operational constraints that shape the response of yeast to heat shock., Poster, ISSY25 25th International Specialised Symposium on Yeasts "Yeast systems biology - from models to applications", 18 th -21 th June, Hanasaari, Espoo, Finland 15. E. Vilaprinyo, R. Alves, A. Sorribas. (2006) Identification of Operational Constraints That Shape the Response of Yeast to Stress Conditions., Communication, International Conference On Molecular Systems Biology. 31 th July -4 th August, 2006, Munich, Germany

16. Alves, R. & Savageau, M. A. (2006) Amino Acid Signatures, Communication, International Symposium on Molecular Biology Systems, Munich, Germany 17. Alves, R. & Sorribas, A. (2006) In silico metabolic reconstruction: FeSC biogenesis in yeast, Communication, International Symposium on Molecular Biology Systems, Munich, Germany 18. 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., Communication, International Symposium on Molecular Biology Systems, Munich, Germany. 19. 19. Alves, R., (2007) Metabolic Reconstruction, Poster, Workshop on Biochemical Engineering, Ohio State University, Institute of Mathematical Biosciences, Columbus, Ohio, USA. 20. Alves, R., (2007) Career Development, Comunicación, Workshop on Carrer Development, Instituto Gulbenkian de Ciencia, Oeiras, Portugal. 21. Sorribas, A., Vilaprinyo, E. & Alves, R., (2008) Approximate formalisms: does anything work?, Communication, International Symposium on Molecular Biology Systems, University of Manila, Manila, Philipines. 22. Vilaprinyo, E., Salvador, A., Alves, R.,& Sorribas, A., (2008) Gene expression levels in Saccharomyces cerevisisae strongly reflect energetic cost rates of gene products, Communication, International Symposium on Molecular Biology Systems, University of Manila, Manila, Philipines. 23. Vilaprinyo, E., Alves, R., Sorribas, A. & Salvador, A., (2008) Energetic Constraints in Adaptive gene expression responses of yeast under environmental changes., Communication, International Symposium on Molecular Biology Systems, University of Manila, Manila, Philipines. 24. Alves, R., Vilaprinyo, E., & Sorribas, (2008) Semi-Automated Reconstruction of Biological Circuits., Communication, International Symposium on Molecular Biology Systems, University of Manila, Manila, Philipines. 25. Alves, R., (2008) Bacterial Two Component Systems, Communication, 1st Portuguese Meeting of Systems Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal. 26. Alves, R., (2008) Bacterial Two Component Systems, Invited Lecture, 2 nd Portuguese Meeting of Systems Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal. Past Students Ph. D.: Ester Vilaprinyo Richard Fassani M. Sc.: Raphael Challeill Undergraduate: Jordi Roselló

Ernest Molès Oriol Senan Current Students Ph. D.: Hiren Karathia Baldiri Salvador Anabel Usie Xavier Faust Post. Docs.: Alexandra Moura Undergraduate: Verónica Teixidò Languages: Native Language: Portuguese. Reads: English, French, Spanish, Catalan and Italian. Speaks: English, French, Spanish and Catalan. Writes: English, French, Spanish and Catalan. Hobbies: Biking, Jogging, Swimming, Reading, Listening to Music, Collecting Comic Books, Colecting, original comic book art. Theatre (attending and performing), Movies, Concerts, Mountain Hiking.