Journal Papers

• Barão M. and Lemos J.M. Nonlinear control of HIV-1 infection with a singular perturbation model. Biomedical Signal Processing and Control 2007, 2(3):248-257 (Jul).

• Vilela M., Borges C.C., Vinga S., Vasconcelos, A. T., Santos H., Voit E.O. and Almeida J.S. Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics 2007, 8:305 (Aug 21).

• Vinga S. and Almeida J.S. Local Renyi entropic profiles of DNA sequences. BMC Bioinformatics 2007, 8:393 (Oct 16).

• Vilela M., Chou I.C., Vinga S., Vasconcelos A.T., Voit E.O. and Almeida J.S. Parameter optimization in S-system models. BMC Systems Biology 2008, 2:35 (Apr 16).

• Castro R., Neves A. R., Fonseca L. L., Pool W. A., Kok J., Kuipers O. P. and Santos H. Characterization of the individual glucose uptake systems of Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU permease. Molecular Microbiology 2009, 71:795-806.

• Fernandes F., Freitas A.T., Almeida J.S. and Vinga S. Entropic Profiler - Detection of conservation in genomes using Information Theory. BMC Research Notes 2009, 2:72 (May 5).

• Vilela M., Vinga S., Maia M. A. G. M., Voit E.O. and Almeida J.S. Identification of neutral biochemical network models from time series data. BMC Systems Biology 2009, 3:47 (May 5).

• Vinga S., Neves A. R., Santos H., Brandt B. W. and Kooijman S. A. L. M. Subcellular metabolic organization in the context of Dynamic Energy Budget and Biochemical Systems theories. Philos Trans R Soc Lond B Biol Sci. 2010 Nov 12;365(1557):3429-42.

• Domingues A., Vinga S. and Lemos J. M. Optimization strategies for metabolic networks. BMC Syst Biol. 2010 Aug 13;4:113.

• Tenazinha N. and Vinga S. A Survey on Methods for Modeling and Analyzing Integrated Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 2010 Nov 24. [Epub ahead of print]

• Neves A. R., Pool W. A., Solopova A., Kok J., Santos H. and Kuipers O. P. Towards Enhanced Galactose Utilization by Lactococcus lactis. Appl. Environ. Microbiol. 2010, 76(21):7048-7060. Epub 2010 Sep 3.

• Deus HF, Correa MC, Stanislaus R, Miragaia M, Maass W, de Lencastre H, Fox R, Almeida JS. S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. BMC Bioinformatics 2011, 12.

• Gaspar P, Neves AR, Gasson MJ, Shearman CA, Santos H High Yields of 2,3-Butanediol and Mannitol in Lactococcus lactis through Engineering of NAD(+) Cofactor Recycling Applied and Environmental Microbiology 2011, 77(19):6826-6835.

Book chapters

• Eberhard O. Voit. What if the Fit is Unfit? In: "Applied Statistics for Biological Networks", Matthias Dehmer, Frank Emmert-Streib, and Armindo Salvador (Eds). Wiley and Sons, 2011 (expected).

• P. Gaspar, A. R. Neves, H. Santos, P. F. de Palencia, C. Pelaez, & T. Requena. Engineering And Re-routing Of The Metabolism Of Lactic Acid Bacteria. In: “Molecular Aspects of Lactic Acid Bacteria for Traditional and New Applications”, B. Mayo, P. López, G. Pérez-Martinez (Eds), Chapter 9, pp 265-289, Research Signpost, Kerala, India, 2008.

Conferences

• Barão, M. and Lemos, J.M. (2008) An Efficient Kullback-Leibler Optimization Algorithm for Probabilistic Control Design. In Proc. of the 16th Mediterranean Conference on Control and Automation (MED'08). June 25-27, Ajaccio, Corsica, France.

• Wang X., Almeida J.S, and Oliveira A.L. (2008) Ontology Design Principles and Normalization Techniques in the Web. In Proc of the Data Integration in the Life Sciences (DILS'2008). June 25-27, University of Evry, France.

• Vinga S., Thomaseth K., Lemos J.M., Neves A.R., Santos H. and Freitas A.T. (2008) Structural analysis of metabolic networks: a case study on Lactococcus lactis. In Proc. of the 8th Portuguese Conference on Automatic Control (CONTROLO'2008). July 21-23, Vila Real, Portugal.

• Domingues A., Lemos J.M. and Vinga S. (2009) Optimization strategies for metabolic networks. In Proc. of the European Control Conference (ECC'09). August 23-26, Budapest, Hungary.

• Domingues A., Vinga S., Gaspar P., Neves A.R., Santos H. and Lemos J.M. (2009) Consistent Parameter Estimation in Metabolic Networks: A case study. In Proc. Jornadas de Bioinformatica. November 3-6, Lisboa, Portugal.

• P. Gaspar, A. R. Neves, M. J. Gasson, C. A. Shearman and H. Santos (2010) In vivo metabolite profiling of Lactococcus lactis mutants towards the optimal production of reduced compounds. Metabolomics 2010. June 27 – July 1, 2010, Amsterdam (The Netherlands).

• Hartmann A., Vinga S. and Lemos J. M. (2011) Unified modeling of several perturbation experiments in systems biology: a case study on the glucose uptake of Lactococcus lactis. In Proc. Bioinformatics'2011 - International Conference on Bioinformatics Models, Methods and Algorithms. 26-29 January. Rome, Italy.
  

Technical Reports

• Beyer W. Combining Autosmooth and Alternating Regression for the Estimation of S-System Parameters. INESC-ID Technical Report nº 29/2008. Jan 2008.

• Domingues A., Lemos J.M. and Vinga S. Optimization strategies for metabolic networks. INESC-ID Technical Report nº 58/2008. Dec 2008.

• Lemos J.M. Bayesian Parameter Estimation in Nonlinear Dynamic Regression Models. INESC-ID Technical Report nº 26/2009. Apr 2009.

• Tenazinha N. and Vinga S. Parameter estimation in S-System and GMA models: an overview. INESC-ID Technical Report nº 31/2009. May 2009.

• Pisco A. Simultaneous Estimation of States and Parameters in Metabolic Networks – from Filtering Techniques to Systems Biology, INESC-ID Technical Report nº 48/2009. Sep 2009.

• N. Tenazinha, A. Sorribas and S. Vinga, Model identification from dynamic data: coping with saturation and cooperativity in metabolic networks, INESC-ID Tec. Rep. 22/2010, Apr 2010.

• Thomaseth K., Vinga S., Lemos J. M., Neves A. R. and Santos H. Identification of Generalized Mass Action models of metabolic networks from NMR data: a case study on Lactococcus lactis, INESC-ID Tec. Rep. 3/2011, Jan 2011.

Posters

• Beyer W., Freitas A.T., Lemos J.M, Vilela M., Almeida J.S. and Vinga S. (2007) Combining Autosmooth and Alternating Regression for the Estimation of S-System Parameters. GCB'07 - German Conference on Bioinformatics. 26-28 Sep. Potsdam, Germany. [Abstract | Poster | Matlab code]
  

• Vinga S., Piedade R., Lemos J.M., Gaspar P., Neves A.R., Santos H. and Freitas A.T. (2007) Mannitol production in Lactococcus lactis: dynamic modeling, metabolic control and regulation. FOSBE'07 - Foundations of Systems Biology in Engineering. 9-12 Sep. Stuttgart, Germany. [Abstract | Poster]
  

• Vinga S., and Almeida J.S. Whole genome analysis through Rényi Entropic Profiles. ISMB/ECCB'07 International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology. Vienna, Austria. 2007. [Abstract | Poster]
  

• Tenazinha N. and Vinga S. (2008) Describing saturation phenomena in models of regulated metabolic networks. ICSB'08 - International Conference on Systems Biology. 22-29 Aug. Göteborg, Sweden. [Abstract | Poster]
  

• Vinga S., Thomaseth K., Lemos J.M., Neves, A.R., Santos H. and Freitas A.T. (2008) Metabolic network structure analysis: a case study on glycolysis in Lactococcus lactis. ECCB'08 - European Conference on Computational Biology. 22-26 Sep. Cagliari, Italy. [Abstract | Poster]
  

• Fernandes F., Freitas A.T., Almeida J.S., and Vinga S. (2009) ENTROPIC PROFILER – efficient whole genome analysis using information theory and statistical concepts. ISMB/ECCB'09 - 17th Annual International Conference on Intelligent Systems for Molecular Biology - 8th European Conference on Computational Biology. 27 Jun - 2 Jul. Stockholm, Sweden. [Abstract | Poster]
  

• Tenazinha N. and Vinga S. (2009) Modeling integrated biochemical networks: methods, advances and perspectives. ISMB/ECCB'09 - 17th Annual International Conference on Intelligent Systems for Molecular Biology - 8th European Conference on Computational Biology. 27 Jun - 2 Jul. Stockholm, Sweden. [Abstract | Poster]
  

• Simoes M. and Vinga S. (2009) A web-based application for evaluating parameter identifiabity of biochemical models in polynomial form. ISMB/ECCB'09 - 17th Annual International Conference on Intelligent Systems for Molecular Biology - 8th European Conference on Computational Biology. 27 Jun - 2 Jul. Stockholm, Sweden. [Abstract | Poster]
  

• Vilela M., Vinga S., Maia M. G. M., Voit E. and Almeida J.(2009) Neutral Network models for Biochemical Systems. ISMB/ECCB'09 - 17th Annual International Conference on Intelligent Systems for Molecular Biology - 8th European Conference on Computational Biology. 27 Jun - 2 Jul. Stockholm, Sweden. [Abstract | Poster]
  

• Paixão A. L., Gaspar P., Pacheco I., Neves A. R. and Santos H. (2009) Towards the construction of a food-grade Lactococcus lactis strain for in situ production of mannitol in dairy products. MicroBiotec'09 28-30 Nov 2009. Vilamoura, Portugal. Prémio de melhor comunicação no simpósio temático S7 – Industrial and Food Microbiology and Biotechnology.
  

• Gaspar P., Neves A. R., Gasson M. J., Shearman C. A. and Santos H. (2009) Strategies to improve mannitol production in Lactococcus lactis. FEMS'2009 3rd Congress of European Microbiologists.28 Jun-2 Jul 2009. Gothenburg, Sweden.
  

• Hartmann A., Vinga S. and Lemos J.M. (2010) System identification of metabolic networks using Nonlinear Bayesian filtering. RECOMB'2010 - 14th International Conference on Research in Computational Molecular Biology. 25-28 April. Lisbon, Portugal. [Abstract | Poster]
  

• Gaspar P., Neves A. R., Gasson M. J., Shearman C. A. and Santos H. (2010) In vivo metabolite profiling of Lactococcus lactis mutants towards the optimal production of reduced compounds. Metabolomics 2010. June 27 – July 1, 2010, Amsterdam (The Netherlands).
  

Invited talks

• Vinga S. Dynamic modeling and control of metabolic networks. CBI07: International Workshop on Collaborative Bioinformatics 2007 (RIBIO/EMBnet) Malaga, Spain. 11-14 Jun 2007.
  

• Santos H. Dynamics of intracellular metabolite pools by NMR: input for systems biology. Workshop on Metabolomics and Environmental Biotechnology, EC-US Task Force on Biotechnology Research, Mallorca, Spain. 16-17 Jun 2008.

• Vinga S. Metabolic network structure analysis: a case study on glycolysis in Lactococcus lactis. First Portuguese Forum on Computational Biology FPBC-2008. Oeiras, Portugal. 10-12 Jul 2008.

• Vinga S. Dynamical analysis and design of biochemical kinetic networks. II Iberian Mathematical Meeting. Badajoz, Spain. 3-5 Oct 2008.

• Santos H., Neves A.R., Gaspar P., Castro R., Carvalho A.L. Time series measurements of metabolite pools in bacteria by in vivo nuclear magnetic resonance. Frontiers in Multi-Scale Systems Biology, Georgia Tech, Atlanta, USA. 18-21 Oct 2008.

• Vinga S. Reverse Engineering of Biochemical Networks. 8th short course of the Portuguese Biophysical Society on Systems Biology. Santarém, Portugal. 31 Oct 2009.

• Vinga S. Reverse engineering of biochemical networks - understanding systems biology of cells. Universidade da Madeira, Funchal, Portugal. 8 Jan 2010.

• Vinga S. New applications of alignment-free methods for biological sequence analysis and comparison. 13th Portugaliae Genetica - Genome Anatomy. IPATIMUP, Porto, Portugal. 18-19 Mar 2010.

Dissertations

PhD Thesis

• Miguel José Simões Barão. Métodos de Controlo Probabilístico. PhD Thesis, Instituto Superior Técnico, Universidade Técnica de Lisboa. Sep 2008.

• Marco Antônio Mattos Vilela. Automated reverse engineering of metabolic pathways from time series. PhD Thesis, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. May 2009.

MSc Thesis

• Rodrigo Madrugo Piedade. Dynamic modelling of metabolic networks. MSc Thesis, Instituto Superior Técnico, Universidade Técnica de Lisboa. Jan 2008.

• Angela Miguel Miranda Oliveira Pisco. Simultaneous Estimation of States and Parameters in Metabolic Networks – from Filtering Techniques to Systems Biology. MSc Thesis, Instituto Superior Técnico, Universidade Técnica de Lisboa. Sep 2009.

• Alexandre João Borralho Domingues. Optimization and Control for Metabolic Networks. MSc Thesis, Instituto Superior Técnico, Universidade Técnica de Lisboa. Nov 2009.

Graduate Thesis

• Pedro Miguel Baptista dos Reis. SDLink - Interfaces com o utilizador para ferramentas baseadas em tecnologias da web semântica: uma aplicação às ciências da vida. Relatório Final de Licenciatura, DEETC - Instituto Superior de Engenharia de Lisboa (ISEL). Sep 2010.

Software

• AutoSmooth application (2007) The application and algorithm are provided both as open source (MATLAB) code and as stand-alone applications that can be used without requiring commercial licenses. The application can also be managed conveniently as a BioinformaticStation.org module.

• S-systems inference application (2008) The application and algorithm are provided both as open source (MATLAB) code and as stand-alone applications that can be used without requiring commercial licenses. The application can also be managed conveniently as a BioinformaticStation.org module.

• GUI-SIMGLY (2008) Glycolysis simulation. The MATLAB files and examples are available here.

• Entropic Profiler (2009) The web-based application is available here.

Others

• Projecto DynaMo na Newsletter do INESC-ID - News-ID Abril-Maio-Junho Nº2.2009 [In Portuguese].