Care was taken to form groups balanced in terms of the students' educational background. This encouraged students to help one another.

All students

Luis Filipe Domingos Pereira De Figueiredo

Being at the PhD Program in Computational Biology was a unique opportunity to develop my Computational skills and learn more about Biology and Modeling. From the personal point of view it was an intense experience in which I meet researchers from all around the world. (2005-12-01)

Resumé

Birth: Lisboa, Portugal

Currently postdoc at EMBL-European Bioinformatics Institute-Cheminformatics and Metabolism Team
2006 - 2011 PhD project entitled "Metabolic Network Reconstruction and Analysis" at FSU Jena, under supervision of Prof. Schuster
2005 - 2006 First year student of the PhD Program in Computational Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal.
2000 - 2005 Five Year Biological Engineering Degree. Instituto Superior Técnico, Technical University of Lisbon, Portugal.

PhD Project

Supervisor: Prof. Dr. Stefan Schuster

Laboratory: Department of Bioinformatics, Friedrich-Schiller-Universität Jena

University: Friedrich-Schiller-Universität Jena

Thesis

Metabolic Pathway Analysis: from small to genome-scale networks. University of Jena (2011) pp.144. [pdf]

Publications

S. Schuster, L.F. de Figueiredo, A. Schroeter, C. Kaleta. Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach. Biosystems (2011) 105, 147-153.

C. Kaleta, L.F. de Figueiredo, I. Heiland, S. Klamt and S. Schuster. Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis. Biosystems (2011) 105, 107-108.

C. Kaleta, L.F. de Figueiredo, S. Werner, R. Guthke, M. Ristow, S. Schuster. In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans. PLoS Computational Biology (2011) 7, e1002116.

L.F. de Figueiredo, T.I. Gossmann, M. Ziegler and S. Schuster. Pathway Analysis of NAD+ metabolism. Biochemical Journal (2011) , in press.

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. Current Opinion in Biotechnology (2010) 21, 502-510.

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.. Lecture Notes in Informatics - Proceedings (2010) 173, 71-80.

S. Schuster, L. F. de Figueiredo and Christoph Kaleta. Predicting novel pathways in genome-scale metabolic networks.. Biochem Soc Trans (2010) 38, 1202-1205.

L.F. de Figueiredo, S. Schuster, C. Kaleta and D.A. Fell. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics (2009) 25, 152-158.

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.

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. Proceedings of the Vienna Conference on Mathematical Modelling (2009) 2, 736-747.

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. Proceedings of the Vienna Conference on Mathematical Modelling (2009) 2, 748-759.

Luis F. de Figueiredo, Stefan Schuster, Christoph Kaleta, and David A. Fell . Response to comment on ’Can sugars be produced from fatty acids? A test case for pathway analysis tools’. Bioinformatics (2009) , Adv. Access.

Luis F. de Figueiredo, Adam Podhorski, Angel Rubio, Christoph Kaleta, John E. Beasley, Stefan Schuster and Francisco J. Planes. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics (2009) 25, 3158-3165.

C. Kaleta, L. F. de Figueiredo, J. Behre and S. Schuster. EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks. Lecture Notes in Informatics - Proceedings (2009) 157, 179-189.