Susana Vinga KDBIO Group INESC-ID R Alves Redol 9 1000-029 Lisboa, PORTUGAL Tel. (+351) 213 100 397 Fax: (+351) 213 145 843

Research interests

New projects on this topic will start in 2010. HIVCONTROL - Control based on dynamic modeling of HIV-1 infection for therapy design (PTDC/EEACRO/100128/2008, S.Vinga PI) and PneumoSyS - A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease (PTDC/SAU-MII/100964/2008, A.R.Neves PI).

My curriculum vitae. My Researcher ID profile.

Present Position

Post-doctoral Researcher in the Knowledge Discovery and Bioinformatics group (KDBIO) @ Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID)

Invited Assistant Professor at Faculdade de Ciências Médicas/Universidade Nova de Lisboa (FCM/UNL)

Education

Mar. 2001- Feb. 2005 - PhD student in Biology/Bioinformatics - grant SFRH / BD / 3134 / 2000 from Portuguese Science Foundation (FCT) - under the supervision of Jonas S Almeida in Biomathematics Group @ ITQB/UNL (Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa).
PhD Thesis title: Biological sequence analysis by vector maps: alignment-free comparison of DNA and proteins - defense on the 25 Feb. 2005.

2000-2002 - Graduate Courses in Probability and Statistics (Mathematics Department, Instituto Superior Técnico - Lisboa)

1999 - Mechanical Engineering ( Instituto Superior Técnico - Lisboa )

1998/99 - ERASMUS Program Politecnico di Milano - Italy: Biomedical Engineering

1990/2000 - Music/Piano Course (Instituto Gregoriano de Lisboa)

Presentations and publications

Papers

• A Survey on Methods for Modeling and Analyzing Integrated Biological Networks
  N. Tenazinha, and S. Vinga
  IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 2010, in press
  

• Subcellular metabolic organization in the context of Dynamic Energy Budget and Biochemical Systems theories
  S. Vinga, A. R. Neves, H. Santos, B. W. Brandt, and S. A. L. M. Kooijman
  Philosophical Transactions of the Royal Society B, 2010, in press (provisional: 365(1558), online 18th Oct, print issue date 27 Nov)
  

• Optimization strategies for metabolic networks
  A. Domingues, S. Vinga, and J. M. Lemos
  BMC Systems Biology 2010, 4:113 (Aug 13)
  

• Entropic Profiler - Detection of conservation in genomes using Information Theory
  Francisco Fernandes and Ana T. Freitas and Jonas S. Almeida and Susana Vinga
  BMC Research Notes 2009, 2:72 (May 5)
  - see also companion webpage with additional information and ENTROPIC PROFILER tool

• Identification of neutral biochemical network models from time series data
  Marco Vilela and Susana Vinga and Marco A Grivet Mattoso Maia and Eberhard O Voit and Jonas S. Almeida
  BMC Systems Biology 2009, 3:47 (May 5)
  

• Biological sequences as pictures - a generic two dimensional solution for iterated maps
  Jonas S. Almeida and Susana Vinga
  BMC Bioinformatics 2009, 10:100 (Mar 31)
  

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

• ccrB typing tool: an online resource for staphylococci ccrB sequence typing.
  Oliveira, D.C., Santos, M., Milheirico, C., Carrico, J.A., Vinga, S., Oliveira, A.L., and de Lencastre, H.
  J Antimicrob Chemother 2008, 61:959-60
  

• An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.
  Casimiro, A.C., Vinga, S., Freitas, A.T., and Oliveira, A.L.
  BMC Bioinformatics 2008, 9:89 (Feb 7)
  

• Local Renyi entropic profiles of DNA sequences.
  Vinga, S. and Almeida, J.S.
  BMC Bioinformatics 2007, 8:393 (Oct 16).
  - see also companion webpage with additional information and MATLAB functions

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

• clfB typing in Staphylococcus aureus: online database for display, clustering analysis and storage of clfB DNA sequences.
  Gomes, A. R., Carrico, J., Vinga, S., Oliveira, A. L., Zavolan, M., and de Lencastre, H.
  International Journal of Antimicrobial Agents 2007, 29: S360-S360.

• Computing distribution of scale independent motifs in biological sequences.
  Almeida, J. S. and Vinga, S.
  Algorithms Mol Biol. 2006, 1:18 (Oct 18).

• Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones
  Oliveira, D.C., Milheiriço, C., Vinga, S. and de Lencastre, H.
  Journal of Antimicrobial Chemotherapy 2006, 58(1):23-30.

• Analysis of the Genetic Variability of Virulence-related Loci in Epidemic Clones of Methicillin-resistant Staphylococcus aureus
  Gomes, A. R., Vinga, S., Zavolan, M. and de Lencastre, H.
  Antimicrobial Agents and Chemotherapy 2005, 49(1):366-379.

• Rényi continuous entropy of DNA sequences
  Vinga, S. and Almeida, J. S.
  Journal of Theoretical Biology 2004, 231(3):377-388.
  - see also companion webpage with additional information and MATLAB functions

• Comparative evaluation of word composition distances for the recognition of SCOP relationships
  Vinga, S., Gouveia-Oliveira, R. and Almeida, J. S.
  Bioinformatics 2004, 20(2):206-215.
  - see also companion webpage with additional information

• Alignment-free sequence comparison - a review
  Vinga , S. and Almeida, J.
  Bioinformatics 2003, 19(4):513-523.
  - see also Matlab^© companion toolbox: NASC (non-aligned sequence comparison)

• Universal sequence map (USM) of arbitrary discrete sequences
  Almeida, J.S. and Vinga, S.
  BMC Bioinformatics 2002, 3:6 (Feb 5)
  

Book chapters

• Biological sequence analysis by vector-valued functions: revisiting alignment-free methodologies for DNA and protein classification
  in Advanced Computational Methods for Biocomputing and Bioimaging, T.D. Pham, H. Yan, and D.I. Crane, Editors.
  Nova Science Publishers, New York. 2007
  

National Journal Articles

• Análise e comparação de sequências biológicas através de funções vectoriais
  Boletim da Sociedade Portuguesa de Estatística, pp. 24-39, Oct. 2007.
  

Invited talks

• 30 Oct - 1 Nov 2009 8th Short Course of the Portuguese Biophysical Society: Systems Biology . Reverse Engineering of Biochemical Networks. Santarém, Portugal.
  
• 3-5 Oct 2008 - II Iberian Mathematical Meeting . Dynamical analysis and design of biochemical kinetic networks. Badajoz, Spain.
  
• 11-14 Jun 2007 - CBI07: International Workshop on Collaborative Bioinformatics 2007 (RIBIO/EMBnet) Dynamic modeling and control of metabolic networks. Malaga, Spain.
  
• 9 Oct 2006 - IV Encontro de Eng.ª Biomédica IST/FML Biological sequence analysis by vector-valued functions: alignment-free methodologies for DNA and protein classification. Lisboa, Portugal. [Abstract]
  
• 30 Nov-3 Dec 2005 - MicroBiotec'2005 Information theory and stochastic modeling of biological sequences. Póvoa de Varzim, Portugal. [Abstract]
  

Posters

• 22-26 Sep 2008 - ECCB'08 Metabolic network structure analysis: a case study on glycolysis in Lactococcus lactis [Abstract | Poster]
             
  

• 22-29 Aug 2008 - ICSB'08 Describing saturation phenomena in models of regulated metabolic networks [Abstract | Poster]
             
  

• 26-28 Sep 2007 - GCB'07 Combining Autosmooth and Alternating Regression for the Estimation of S-System Parameters [Abstract | Poster]
             
  

• 9-12 Sep 2007 - FOSBE'07 Mannitol production in Lactococcus lactis: dynamic modeling, metabolic control and regulation [Abstract | Poster]
             
  

• 21-25 July 2007 - ISMB/ECCB'07 Whole genome analysis through Rényi Entropic Profiles [Abstract | Poster]
             
  

• 6-10 August 2006 - ISMB'06 Chaos Game Representation and Vector Quantization (CGR-VQ): a new computational tool for the identification of transcription factor binding sites [Abstract | Poster]
             
  

• 31 July - 4 August 2006 - ICMSB'2006 Exploring metabolic and genetic control of the glycolytic pathway of Lactococcus lactis [Abstract | Poster]
             
  

• 5-8 October 2005 - WSGP'2005 Local DNA Sequence Information Using Rényi Entropic Profiles [Abstract]
             
  

• 28 September - 1 October 2005 - ECCB'05 Rényi entropic profiles of DNA sequences and statistical significance of motifs [Abstract | Poster]
             
  

• 31 July - 4 August 2004 - ISMB/ECCB'04 Rényi entropy of DNA sequences [Abstract | Poster]
             
  

• 27-30 September 2003 - ECCB'2003 W-metric for protein sequence comparison in SCOP database [Abstract | Poster]

              

• 2-6 July 2002 - ECMTB'2002 Sequence Comparison by Universal Sequence Mapping (USM) - alignment-free and scale independent analysis of texts [Abstract | Poster]

              

• 21-25 July 2001 - ISMB'01 Sequence Analysis by Iterative Maps - beyond graphical representation [Abstract | Poster]

           

Past courses

• MATLAB introductory course. Nov 2007. IGC, Oeiras.
  
• Categorical Data Analysis. Oct 2001. Theory: Fri 19 (10am-1pm) + Practice: Mon 22 (11am-1pm). ITQB1. Oeiras.

Links

        [Biblos-Biomath Group Library][ITQB-internal page][ISI Web of Knowledge][Ciencia hoje][Bioinformatics.org][EUROPEANA]
        [Molecular Biology Resource][NCBI][ISCB][ESMTB][OCES]
        Toolbox: [Chaos Game Representation - CGR] [Universal Sequence Maps - USM] [NASC] [W-metric&SCOP][Rényi entropy]
        Probability and Statistics: [Virtual Laboratories in Probability and Statistics][Concepts and Applications of Inferential Statistics][StatSoft]
        Dictionary: [Portuguese 1 2][English] [Ciberdúvidas da Língua Portuguesa][Eurodicautom] [Online spell check]
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Last Update: 23 Aug 2010