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Publications in 2003

I. Articles in journals with editorial policy

  1. Binz PA, Hochstrasser DF, Appel RD. Mass spectrometry-based proteomics: current status and potential use in clinical chemistry. Clin Chem Lab Med 2003; 41: 1540-1551.

  2. Bologna G. A model for single and multiple knowledge based networks. Artif Intell Med 2003; 28: 141-163.

  3. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003; 31: 3784-3788.

  4. Gras R, Hernandez D, Hernandez P, Zangger N, Mescam Y, Frey J, Martin O, Nicolas J, Appel RD. Cooperative Metaheuristics for Exploring Proteomic Data. Artif Intell Rev 2003; 20: 95-120.

  5. Hernandez P, Gras R, Frey J, Appel RD. Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics 2003; 3: 870-878.

  6. Mostaguir K, Hoogland C, Binz PA, Appel RD. 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: 1441-1444.

II. Books, book chapters & guest edition

  1. Ducret A, Eberle AN, Faupel MD, Hofsteenge J, Jenö P, Langen H, Palagi PM, Rossier J, Sanchez JC, Stöcklin R, van Oostrum J, Voshol J. Proceedings of the Swiss Proteomics Proceedings of the Swiss Proteomics Society, 2003 Congress, Understanding biological systems (Editors). Lausanne, Switzerland: FontisMedia Publishers; 2003.

  2. Gras R, Hernandez P, Müller M, Appel RD. Scoring functions for mass spectrometric protein identification. In: Conn PM, ed. Handbook of Proteomic Methods. Humana Press; 2003: 477-486.

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

  4. Palagi PM, Quadroni M, Rossier J, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 2nd Annual Conference of the Swiss Proteomics Society (Guest Editors). Proteomics vol.3, n°8; 2003.

  5. Voordijk S, Walther D, Bouchet G, Appel RD. Image Analysis Tools in Proteomics. Encyclopedia of the human genome. Macmillian Publishers Ltd, Nature Publishing Group; 2003: 404-410.

III. Articles in journals without editorial policy

  1. Bairoch A, Gasteiger E, Gattiker A, Hoogland C, Lachaize C, Mostaguir K, Ivanyi I, Appel RD. The ExPASy proteome WWW server in 2003. Swiss Institute of Bioinformatics. 2003; http://www.expasy.org/doc/expasy.pdf.

IV. Conference proceedings

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

  2. Hochstrasser DF, Corthals G, Zimmerman C, Scherl A, Bougueleret L, Collinge J, Masselot A, Binz PA, Müller M, Bairoch A, Appel RD, Sanchez JC, Rose K. Proteomics & Mass Spectrometry in Medicine. International Mass Spectrometry Conference. Edinburgh: Aug. 2003.

  3. Martin O, Gras R, Hernandez D, Appel RD. Optimizing Genetic Algorithms Using Self-Adaptation And Explored Space Modelization. The Fifth International Workshop on Frontiers in Evolutionary Algorithms (FEA 2003). Cary, North Carolina, USA: Sept. 2003: 291-294.

V. Abstracts and posters

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

  2. Binz PA, Tuloup M, Hernandez C, Fabretti R, Hernandez P, Bologna G, Hoogland C, Mostaguir K, Walther D, Bouchet G, Palagi PM, Appel RD. Bioinformatics and Proteome Analysis in MS dominated workflows. Jahrestagung Chemie 2003 der Gesellschaft Deutscher Chemiker. München: Oct. 2003.

  3. Binz PA, Paesano S, Zanini P, Scherl A, Hoogland C, Allard L, Zimmermann C, Carrette O, Sanchez JC, Borella S, Castelnovo R, Appel RD, Hochstrasser DF. Why and How? A LIMS in a proteomics research environment. Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 170-171.

  4. Corthals G, Pasquarello C, Scherl A, Burgess J, Vaezzadeh A, Deshusses J, Hochstrasser DF, Sanchez JC, Binz PA, Appel RD. Controlling data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry. MipTec. Basel: 2003.

  5. Corthals G, Pasquarello C, Scherl A, Burgess J, Allard L, Deshusses J, Walter N, Paesano S, Carrette O, Bienvenut W, Hoogland C, Binz PA, Müller M, Appel RD, Hochstrasser DF, Sanchez JC. Tools and technologies in proteome analysis. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 9-10.

  6. Corthals GL, Pasquarello C, Scherl A, Burgess J, Vaezzadeh A, Binz PA, Deshusses J, Appel RD, Sanchez JC, Hochstrasser DF. Guiding data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry (NRMS). 16th International Mass Spectrometry Conference. Edinburgh: Aug. 2003.

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

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

  9. Hochstrasser DF, Sanchez JC, Rose K, Bougueleret L, Appel RD, Bairoch A, Corthals G. Clinical Proteomics. Proteomic Forum '03. Münich: Sept. 2003.

  10. Hochstrasser DF, Corthals G, Appel RD, Sanchez JC. Large scale proteomics in medecine. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 25.

  11. Hochstrasser DF, Sanchez JC, Corthals G, Scherl A, Rose K, Bougueleret L, Colinge J, Bairoch A, Appel RD. Proteomics & Mass Spectrometry in Medicine. 16th International Mass Spectrometry Conference. Edinburgh: Aug. 2003.

  12. Hochstrasser DF, Sanchez JC, Corthals G, Binz PA, Müller M, Appel RD, Bougueleret L, Rose K. Proteomics in laboratory medicine. EUROMEDLAB Barcelona 2003, 15th IFCC - FESCC European Congress of Clinical Chemistry and Laboratory Medicine. Barcelona: 2003.

  13. Hochstrasser DF, Corthals G, Appel RD, Sanchez JC. Proteomics in medecine. Barnett Lecture, Barnett Institute. Boston: Apr. 2003.

  14. Hochstrasser DF, Corthals G, Rose K, Bougueleret L, Appel RD, Bairoch A, Sanchez JC. The five dimensions of diseases. Second Annual HUPO Congress. Montreal: Oct. 2003.

  15. Hoogland C, Mostaguir K, Hochstrasser DF, Sanchez JC, Appel RD. SWISS-2DPAGE, 10 years later... Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 172-173.

  16. Mostaguir K, Hoogland C, Binz PA, Appel RD. The Make 2D-DB II Package - Conversion of federated 2-DE gel databases into a relational format and interconnection of distributed databases. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 73-74.

  17. Tuloup M, Hernandez C, Coro I, Hoogland C, Binz PA, Appel RD. Aldente and BioGraph : An improved peptide mass fingerprinting protein identification environment. Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 174-176.

  18. Voordijk S, Rossier G, Walther D, Bouchet G, Appel RD. New features in the Melanie 2D gel analysis software. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 91-92.

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