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Publications in 2003

Thesis

1. Müller, M., Molecular Scanner Data Analysis. 2003, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

Journal Articles

1. Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Mass spectrometry-based proteomics: current status and potential use in clinical chemistry. Clin.Chem.Lab Med., 2003. 41(12): p. 1540-1551.

2. Bologna, G., A model for single and multiple knowledge based networks. Artificial Intelligence in Medicine, 2003. 28(2): p. 141-163.

3. Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D., and Bairoch, A., ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 2003. 31(13): p. 3784-3788.

4. Gras, R., Hernandez, D., Hernandez, P., Zangger, N., Mescam, Y., Frey, J., Martin, O., Nicolas, J., and Appel, R.D., Cooperative Metaheuristics for Exploring Proteomic Data. Artificial Intelligence Review, 2003. 20(1-2): p. 95-120.

5. Hernandez, P., Gras, R., Frey, J., and Appel, R.D., Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics., 2003. 3(6): p. 870-878.

6. Mostaguir, K., Hoogland, C., Binz, P.A., and Appel, R.D., The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases. Proteomics., 2003. 3(8): p. 1441-1444.

Journal Articles - non peer-reviewed

1. Bairoch, A., Gasteiger, E., Gattiker, A., Hoogland, C., Lachaize, C., Mostaguir, K., Ivanyi, I., and Appel, R.D. The ExPASy proteome WWW server in 2003. 2003; Available from: http://www.expasy.org/doc/expasy.pdf.

Guest Edition

. Ducret, A., Eberle, A.N., Faupel, M.D., Hofsteenge, J., Jen”, P., Langen, H., Palagi, P.M., Rossier, J., Sanchez, J.C., Stöcklin, R., van Oostrum, J., and Voshol, J., Proceedings of the Swiss Proteomics Proceedings of the Swiss Proteomics Society, 2003 Congress, Understanding biological systems 2003, FontisMedia Publishers: Lausanne, Switzerland.

2. Palagi, P.M., Quadroni, M., Rossier, J., Sanchez, J.C., and Stöcklin, R., Special Issue on the Proceedings of the 2nd Annual Conference of the Swiss Proteomics Society. 2003, Proteomics vol.3, nø8.

Conference Proceedings

1. Martin, O., Gras, R., Hernandez, D., and Appel, R.D. Optimizing Genetic Algorithms Using Self-Adaptation And Explored Space Modelization. in The Fifth International Workshop on Frontiers in Evolutionary Algorithms (FEA 2003). 2003. Cary, North Carolina, USA.

Book Chapters

1. Gras, R., Hernandez, P., Müller, M., and Appel, R.D., Scoring functions for mass spectrometric protein identification, in Handbook of Proteomic Methods, Conn, P.M., Editor. 2003, Humana Press. p. 477-486.

2. Voordijk, S., Walther, D., Bouchet, G., and Appel, R.D., Image Analysis Tools in Proteomics, in Encyclopedia of the human genome. 2003, Macmillian Publishers Ltd, Nature Publishing Group. p. 404-410.

Abstracts & Posters

1. Binz, P.A., Bologna, G., Gay, S., Hernandez, C., Hoogland, C., Mostaguir, K., Tuloup, M., and Appel, R.D. Bioinformatics tools in proteomics: issues and perspectives. in Functional Genomics and Disease, ESF Workshop. 2003. Prague.

2. Binz, P.A., Paesano, S., Zanini, P., Scherl, A., Hoogland, C., Allard, L., Zimmermann, C., Carrette, O., Sanchez, J.C., Borella, S., Castelnovo, R., Appel, R.D., and Hochstrasser, D.F. Why and How? A LIMS in a proteomics research environment. in Congress of the Swiss Proteomics Society. 2003. Basel.

3. Binz, P.A., Tuloup, M., Hernandez, C., Fabretti, R., Hernandez, P., Bologna, G., Hoogland, C., Mostaguir, K., Walther, D., Bouchet, G., Palagi, P.M., and Appel, R.D. Bioinformatics and Proteome Analysis in MS dominated workflows. in Jahrestagung Chemie 2003 der Gesellschaft Deutscher Chemiker. 2003. Mnchen.

4. Corthals, G., Pasquarello, C., Scherl, A., Burgess, J., Allard, L., Deshusses, J., Walter, N., Paesano, S., Carrette, O., Bienvenut, W., Hoogland, C., Binz, P.A., Müller, M., Appel, R.D., Hochstrasser, D.F., and Sanchez, J.C. Tools and technologies in proteome analysis. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

5. Corthals, G., Pasquarello, C., Scherl, A., Burgess, J., Vaezzadeh, A., Deshusses, J., Hochstrasser, D.F., Sanchez, J.C., Binz, P.A., and Appel, R.D. Controlling data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry. in MipTec. 2003. Basel.

6. Corthals, G.L., Pasquarello, C., Scherl, A., Burgess, J., Vaezzadeh, A., Binz, P.A., Deshusses, J., Appel, R.D., Sanchez, J.C., and Hochstrasser, D.F. Guiding data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry (NRMS). in 16th International Mass Spectrometry Conference. 2003. Edinburgh.

7. Frey, J., Gras, R., Hernandez, P., and Appel, R.D. A Hierarchical Model of Coarse-Grained Parallel Genetic Programming. in PPAM 2003 - Fifth International Conference on Parallel Processing and Applied Mathematics. 2003. Czestochowa, Poland.

8. Gras, R., Frey, J., Hernandez, P., and Appel, R.D. Un modéle hiérarchique "coarse-grained" de parallélisation d'algorithme de programmation génétique appliqué à des problèmes de bioinformatique. in Workshop: Résolution Parallèle des Problémes NP-complets. 2003. Nice.

9. Gras, R., Hernandez, D., Hernandez, P., Zangger, N., Mescam, Y., Frey, J., Martin, O., Nicolas, J., and Appel, R.D. Cooperative metaheuristics to solve complex bioinformatics problem. in International Summer School on Metaheuristics. 2003. Tenerife.

10. Hochstrasser, D.F., Corthals, G., Appel, R.D., and Sanchez, J.C. Large scale proteomics in medecine. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

11. Hochstrasser, D.F., Corthals, G., Appel, R.D., and Sanchez, J.C. Proteomics in medecine. in Barnett Lecture, Barnett Institute. 2003. Boston.

12. Hochstrasser, D.F., Corthals, G., Rose, K., Bougueleret, L., Appel, R.D., Bairoch, A., and Sanchez, J.C. The five dimensions of diseases. in Second Annual HUPO Congress. 2003. Montreal.

13. Hochstrasser, D.F., Corthals, G., Zimmerman, C., Scherl, A., Bougueleret, L., Collinge, J., Masselot, A., Binz, P.A., Müller, M., Bairoch, A., Appel, R.D., Sanchez, J.C., and Rose, K. Proteomics & Mass Spectrometry in Medicine. in International Mass Spectrometry Conference. 2003. Edinburgh.

14. Hochstrasser, D.F., Sanchez, J.C., Corthals, G., Binz, P.A., Müller, M., Appel, R.D., Bougueleret, L., and Rose, K. Proteomics in laboratory medicine. in EUROMEDLAB Barcelona 2003, 15th IFCC - FESCC European Congress of Clinical Chemistry and Laboratory Medicine. 2003. Barcelona.

15. Hochstrasser, D.F., Sanchez, J.C., Corthals, G., Scherl, A., Rose, K., Bougueleret, L., Colinge, J., Bairoch, A., and Appel, R.D. Proteomics & Mass Spectrometry in Medicine. in 16th International Mass Spectrometry Conference. 2003. Edinburgh.

16. Hochstrasser, D.F., Sanchez, J.C., Rose, K., Bougueleret, L., Appel, R.D., Bairoch, A., and Corthals, G. Clinical Proteomics. in Proteomic Forum '03. 2003. Mnich.

17. Hoogland, C., Mostaguir, K., Hochstrasser, D.F., Sanchez, J.C., and Appel, R.D. SWISS-2DPAGE, 10 years later. in Congress of the Swiss Proteomics Society. 2003. Basel.

18. Mostaguir, K., Hoogland, C., Binz, P.A., and Appel, R.D. The Make 2D-DB II Package - Conversion of federated 2-DE gel databases into a relational format and interconnection of distributed databases. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

19. Tuloup, M., Hernandez, C., Coro, I., Hoogland, C., Binz, P.A., and Appel, R.D. Aldente and BioGraph : An improved peptide mass fingerprinting protein identification environment. in Congress of the Swiss Proteomics Society. 2003. Basel.

20. Voordijk, S., Rossier, G., Walther, D., Bouchet, G., and Appel, R.D. New features in the Melanie 2D gel analysis software. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

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