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Luís F. de Figueiredo |
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Address:
Ernst - Abbe - Platz 2
D-07743 Jena
Deutschland
Phone: +49-3641-949583
Fax: +49-3641-946452
Email:
Contact at IGC:
Rua da Quinta Grande, 6 Apartado 14
P-2780-156 Oeiras
Portugal
Phone: +351 21 440 7909 (ext: 209)
Fax: +351 214 407 973
Email:
Education:
2000 - 2005 Graduation in Biological Engineering, IST
2005 - PhD program in Computational Biology, IGC
2006 - PhD project "Metabolic Network Reconstruction and Analysis", FSU Jena
Former Positions:
2005 Trainee (6 months), Fluxome Sciences A/S
Publications:
A. Rezola∗, L. F. de Figueiredo∗, M. Brock, J. Pey, A. Podhorski, C. Wittmann, S. Schuster, A. Bockmayr and F. J. Planes. Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics, 2011, 27:534-540 (∗both authors contributed equally; doi:10.1093/bioinformatics/btq681)
S. Schuster, L. F. de Figueiredo and C. Kaleta. Predicting novel pathways in genome-scale metabolic networks. Biochem Soc Trans, 2010, 38:1202-1205 (doi:10.1042/BST0381202)
K. Bohl∗, L. F. de Figueiredo∗, O. Hädicke, S. Klamt, C. Kost, S. Schuster and C. Kaleta. CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks. In D. Schomburg, A. Grote (editors), Lecture Notes in Informatics - Proceedings, volume P-173, Gesellschaft für Informatik, Bonn 2010, pp 71-80. (∗both authors contributed equally; ISBN:978-3-88579-267-3)
E. Ruppin, J. A. Papin, L. F. de Figueiredo and S. Schuster. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr Opin Biotechnol, 2010, 21:502-510 (doi:10.1016/j.copbio.2010.07.002)
L. F. de Figueiredo, S. Schuster, C. Kaleta and D. A. Fell. Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinformatics, 2009, 25:3330-3331 (doi:10.1093/bioinformatics/btp591)
C. Kaleta∗, L. F. de Figueiredo∗, J. Behre and S. Schuster. EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks. In I. Grosse, S. Neumann, S. Posch, F. Schreiber, P. Stadler (editors), Lecture Notes in Informatics - Proceedings , volume P-157, Gesellschaft für Informatik, Bonn 2009, pp 179-189. (∗both authors contributed equally; ISBN:978-3-88579-251-2)
L. F. de Figueiredo, A. Podhorski, A. Rubio, C. Kaleta, J. E. Beasley, S. Schuster and F. J. Planes. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics, 2009, 25:3158-3165 (doi: 10.1093/bioinformatics/btp564)
C. Kaleta, L. F. de Figueiredo and S. Schuster. Can the Whole Be Less Than the Sum of its Parts? Pathway Analysis in Genome-Scale Metabolic Networks Using Elementary Flux Patterns. Genome Research , 2009, 19: 1872-1883 (doi:10.1101/gr.090639.108)
L. F. de Figueiredo, A. Podhorski, A. Rubio, J. E. Beasley, S. Schuster and F. J. Planes. Calculating the K-shortest elementary flux modes in metabolic networks.In I. Troch and F. Breitenecker (editors), Proceedings of the Vienna Conference on Mathematical Modelling, volume 2 of ARGESIM Reports 2009, pp. 736-747. (ISBN:978-3-901608-35-3; submitted version)
C. Kaleta, L. F. de Figueiredo and S. Schuster. Detecting Metabolic Conversions in Genome-Scale Metabolic Networks on the Basis of Elementary Flux Patterns in Subnetworks. In I. Troch and F. Breitenecker (editors), Proceedings of the Vienna Conference on Mathematical Modelling, volume 2 of ARGESIM Reports 2009, pp. 748-759. (ISBN:978-3-901608-35-3)
L. F. de Figueiredo, S. Schuster, C. Kaleta, D. A. Fell. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics, 2009, 25(1):152-158 (doi:10.1093/bioinformatics/btn621)
Presentations:
L. F. de Figueiredo, S. Schuster and C. Kaleta. Metabolic pathway analysis in genome-scale networks and beyond. Talk at the 2010 International Workshop on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany, 18th May 2010.
L. F. de Figueiredo. Scaling up elementary flux mode analysis towards genome-scale metabolic networks. Talk at the JCB seminar, Jena, Germany, 8th April 2010.
L. F. de Figueiredo, Computing metabolic pathways in Systems Biology. Invited talk at the Gulbenkian Alumni Meetings (GAMeets), Oeiras, Portugal, 28th December 2009.
L. F. de Figueiredo, C. Kaleta, S. Schuster and D. A. Fell. Benchmarking tools in Metabolic Pathway Analysis. Highlights Track (Talk and Poster) at the ISMB/ECCB 2009, Stockholm, Sweden, 1st July 2009.
L. F. de Figueiredo, A. Podhorski, A. Rubio, C. Kaleta, J. Behre, J. E. Beasley, S. Schuster and F. J. Planes. Computation of elementary flux modes in systems biology. Talk at the 10th BioPathways meeting, Stockholm, Sweden, 27th June 2009.
L. F. de Figueiredo, A. Podhorski, A. Rubio, J. E. Beasley, S. Schuster and F. J. Planes. Calculating the K-shortest Elementary Flux Modes in Metabolic Networks . Talk at the 6th Vienna International Conference on Mathematical Modelling (MATHMOD 2009), Vienna, Austria, 11th February 2009.
L. F. de Figueiredo, S. Schuster,C. Kaleta, D.A. Fell. Benchmarking new tools in Metabolic Pathway Analysis by didactic examples. Talk at 13th Workshop of the International Study Group for Systems Biology (ISGSB), Elsinore, Denmark, 18th August 2008.
L. F. de Figueiredo , F. J. Planes, S. Schuster. Optimization as a Framework for Metabolic Reconstruction - Analysis of Suboptimal Solutions. Poster at:GCB 2008
L. F. de Figueiredo , F. J. Planes, S. Schuster. Optimization as a Framework for Metabolic Reconstruction. Poster at:FPBC 2008
L. F. de Figueiredo , D. A. Fell, S. Schuster. Metabolic Pathway Analysis as a Tool in Synthetic Biology - Illustration by the example of the conversion of lipids into sugars. Poster at:9th Functional Genomics 2007, GCB 2007, AMeeGuS 2007
Interests:
Last update: 09/02/2011 | © 2010-2011 Luis F. de Figueiredo