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Publications in 2002

Thesis

1. Gay, S., Datamining in proteomics: extracting knowledge from peptide mass fingerprinting spectra. 2002, Thèse de doctorat ès sciences, mention interdisciplinaire (Universitè de Genève).

Journal Articles

1. Bienvenut, W.V., Hoogland, C., Greco, A., Heller, M., Gasteiger, E., Appel, R.D., Diaz, J.J., Sanchez, J.C., and Hochstrasser, D.F., Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting. Rapid Communications in Mass Spectrometry, 2002. 16(6): p. 616-626.

2. Gay, S., Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics., 2002. 2(10): p. 1374-1391.

3. Geissbuhler, A., Lovis, C., Spahni, S., Appel, R.D., Ratib, O., Boyer, C., Hochstrasser, D.F., and Baud, R., A humanist's legacy in medical informatics: visions and accomplishments of Professor Jean-Raoul Scherrer. Methods of Information in Medicine, 2002. 41(3): p. 237-242.

4. Hochstrasser, D.F., Sanchez, J.C., and Appel, R.D., Proteomics and its trends facing nature's complexity. Proteomics., 2002. 2(7): p. 807-812.

5. Müller, M., Gras, R., Appel, R.D., Bienvenut, W.V., and Hochstrasser, D.F., Visualization and analysis of molecular scanner peptide mass spectra. Journal of the American Society for Mass Spectrometry, 2002. 13(3): p. 221-231.

6. Müller, M., Gras, R., Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Molecular scanner experiment with human plasma: improving protein identification by using intensity distributions of matching peptide masses. Proteomics., 2002. 2(10): p. 1413-1425.

Journal Articles - non peer-reviewed

1. Vargas, A.R., Balderrama, J.R., Hoogland, C., Gasteiger, E., Ivanyi, I., Bairoch, A., Appel, R.D., and Hochstrasser, D.F., El nuovo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org. Acta Nova, 2002. 2: p. 72-81.

Guest Edition

1. Appel, R.D. and Bairoch, A., Special issue on Applications of Bioinformatics to Mass Spectrometry 2002, Proteomics, Vol.2, No. 10.

2. Palagi, P.M., Quadroni, M., Rossier, J., Sanchez, J.C., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2002 Congress, Applied Proteomics 2002, FontisMedia Publishers: Lausanne, Switzerland.

3. Sanchez, J.C., Palagi, P.M., and Stöcklin, R., Special Issue on the Proceedings of the 1st Annual Conference of the Swiss Proteomics Society. 2002, Proteomics vol.2, nø7.

Abstracts & Posters

1. Appel, R.D., Hernandez, P., Tuloup, M., Walther, D., Gras, R., Müller, M., Hoogland, C., Binz, P.A., Corthals, G.L., Sanchez, J.C., and Hochstrasser, D.F. New developments in proteomatics at the Swiss Institute of Bioinformatics. in First Annual HUPO Congress. 2002. Versailles, France.

2. Binz, P.A., Gay, S., Hochstrasser, D.F., and Appel, R.D. Knowledge Discovery to understand and predict peptide mass fingerprinting spectra. in First Annual HUPO Congress. 2002. Versailles, France.

3. Binz, P.A., Müller, M., Hoogland, C., Walther, D., Gay, S., Gras, R., Bienvenut, W.V., Pasquarello, C., Paesano, S., Corthals, G., Sanchez, J.C., Bairoch, A., Hochstrasser, D.F., and Appel, R.D. The Synergy between Bioinformatics and Proteomics Research. in Danish Society for Biochemistry and Molecular Biology. 2002.

4. Bologna, G. On the validation of the DIMLP Neural Network. in FLAIRS'02. 2002. Florida.

5. Bologna, G. and Appel, R.D. A comparaison study on protein fold recognition. in 9th International Conference on Neural Information Processing. 2002. Singapore.

6. Bologna, G., Veuthey, A.L., and Appel, R.D. N-terminal myristoylation predictions by neural network ensembles. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

7. Corthals, G., Schmidt, G., Scherl, A., Pasquarello, C., Bienvenut, W., Binz, P.A., Walther, D., Voordijk, S., Appel, R.D., Hochstrasser, D.F., and Sanchez, J.C. Proteomics: tools and applications. in Association of Clinical Biochemists (UK), Pharmacogenomics Meeting. 2002. Cambridge, UK.

8. Gras, R., Müller, M., Hernandez, D., Hernandez, P., Zangger, N., Palagi, P., Binz, P.A., and Appel, R.D. Cooperative metaheuristic for proteomics. in Bioinformatics Workshop ISMIS. 2002. Lyon.

9. Gras, R., Müller, M., Hernandez, D., Hernandez, P., Zangger, N., Palagi, P., Binz, P.A., Lisacek, F., and Appel, R.D. New approaches of computational proteomics. in JOBIM 2002. 2002. St-Malo, France.

10. Hernandez, D., Gras, R., Lisacek, F., and Appel, R.D. MoDEL: Inférence de motifs avec un algorithme évolutionniste. in JOBIM. 2002.

11. Hernandez, P., Gras, R., and Appel, R.D. Ant Colony Optimization Metaheuristic Applied to Automated Protein Identification from Tandem Mass Spectrometric Data. in Second International Workshop on "AGENTS IN BIOINFORMATICS". 2002. Bologna, Italy.

12. Hernandez, P., Gras, R., and Appel, R.D. Automated Protein Identification from Tandem Mass Spectrometric Data Using Bio-Inspired Algorithms. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

13. Hernandez, P., Gras, R., Frey, J.P., and Appel, R.D. Automated Protein Identification from Tandem Mass Spectrometric Data Using Bio-Inspired Algorithms. in Congress of the Swiss Proteomics Society. 2002. Lausanne.

14. Hochstrasser, D.F., Sanchez, J.C., Corthals, G., Binz, P.A., Müller, M., Walther, D., and Appel, R.D. Bioinformatics in proteomics. in International Conference "Genomics, Proteomics and Bioinformatics for Medicine". 2002. Moscow.

15. Hochstrasser, D.F., Sanchez, J.C., Scherl, A., Corthals, G., and Appel, R.D. Proteomics: three approaches. in Endoderm. 2002. Arolla, Switzerland.

16. Mostaguir, K., Hoogland, C., and Appel, R.D. Migration des bases de donnes de gels 2-DE vers un format relationnel. in JOBIM. 2002.

17. 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 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

18. Müller, M., Gras, R., Bienvenut, W.V., Binz, P.A., Pasquarello, C., Hochstrasser, D.F., and Appel, R.D. Using Peptide Signal Intensity Distributions for a Better Interpretation of Molecular Scanner Data. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

19. Nadler, T., Huang, Y., Wagenfeld, B., Parker, B., Lotti, R., Vella, G.J., Binz, P.A., Müller, M., Gras, R., Hochstrasser, D.F., Bienvenut, W., Sanchez, J.C., Corthals, G., and Appel, R.D. Proteome Analysis by Multi-Dimensional Liquid Chromatography Gel-Electrophoresis and the Molecular Scanner. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

20. Tuloup, M., Hoogland, C., Binz, P.A., and Appel, R.D. A new Peptide Mass Fingerprinting tool on ExPASy : ALDentE. in Congress of the Swiss Proteomics Society. 2002. Lausanne.

21. Tuloup, M., Hoogland, C., Binz, P.A., and Appel, R.D. Utilisation de la transforme de Hough dans le cadre de l'identification des protines par spectromtrie de masse. in JOBIM. 2002.

22. Zangger, N., Gras, R., and Appel, R.D. A Symmetric Cooperative Metaheuristic for Biological Sequence Clustering Using Local Entropy as Similarity Criterion. in Second International Workshop on "AGENTS IN BIOINFORMATICS". 2002. Bologna, Italy.

23. Zangger, N., Gras, R., and Appel, R.D. Biological Sequence Clustering by Cooperative Agents. in Congress of the Swiss Proteomics Society. 2002. Lausanne.

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