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Publications in 2004

Journal Articles

1. Binz, P.A., Müller, M., Hoogland, C., Zimmermann, C., Pasquarello, C., Corthals, G., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., The molecular scanner: concept and developments. Current Opinion in Biotechnology, 2004. 15(1): p. 17-23.

2. Bologna, G., Yvon, C., Duvaud, S., and Veuthey, A.L., N-Terminal myristoylation predictions by ensembles of neural networks. Proteomics, 2004. 4(6): p. 1626-1632.

3. Hernandez, D., Gras, R., and Appel, R., MoDEL: an efficient strategy for ungapped local multiple alignment. Comput.Biol.Chem., 2004. 28(2): p. 119-128.

4. Hoogland, C., Mostaguir, K., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., SWISS-2DPAGE, ten years later. Proteomics., 2004. 4(8): p. 2352-2356.

5. Lisacek, F., Chichester, C., Gonnet, P., Jaillet, O., Kappus, S., Nikitin, F., Roland, P., Rossier, G., Truong, L., and Appel, R., Shaping biological knowledge: applications in proteomics. Comparative and Functional Genomics, 2004. 5: p. 190-195.

6. Nikitin, F., Rance, B., Itoh, M., Kanehisa, M., and Lisacek, F., Using protein motif combinations to update KEGG pathway maps and orthologue tables. Genome Inform., 2004. 15(2): p. 266-275.

Guest Edition

1. Affolter, M., Gadola, S., Haeberli, A., Heller, M., Palagi, P.M., Sanchez, J.C., Solioz, M., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2004 Congress, Proteomics for Health 2004: Bern, Switzerland.

2. Appel, R.D. and Bairoch, A., Special issue on Tools and Databases for Post-Translational Modifications 2004, Proteomics, Vol.4, No. 6.

3. Palagi, P.M., Sanchez, J.C., and Stöcklin, R., Special Issue on the Proceedings of the 3rd Annual Congress of the Swiss Proteomics Society. 2004, Proteomics vol. 4, n.8.

Conference Proceedings

1. Frey, J., Gras, R., Hernandez, P., and Appel, R., A Hierarchical Model of Parallel Genetic Programming Applied to Bioinformatic Problems. Lecture Notes in Computer Science, 2004. 3019: p. 1146-1153.

Book Chapters

1. Boyer, C. and Appel, R.D., Steps towards Reliable Consumer Health Information, in Consumer Informatics: Applications and Strategies in Cyber Health Care (Health Informatics), Nelson, R. and Ball, M.J., Editors. 2004, Springer Verlag. p. 80-89.

2. 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, in Artificial Intelligence Methods and Tools for Systems Biology, Dubitzsky, W. and Azuaje, F., Editors. 2004. p. 87-106.

3. 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 Advances in Mass Spectrometry, Ashcroft, A.E., Brenton, G., and Monhagan, J.J., Editors. 2004, Elsevier B.V. p. 19-32.

Abstracts & Posters

1. Appel, R.D., Binz, P.A., Bouchet, G., Catherinet, S., Gras, R., Hernandez, C., Hernandez, D., Hernandez, P., Hoogland, C., Lisacek, F., Mostaguir, K., Müller, M., Palagi, P., Pelhatre, S., Tuloup, M., Walther, D., and Zangger, N. Current developments at the Proteome Informatics Group, Swiss Institute of Bioformatics, Geneva. in Quelle informatique et bioinformatique pour la protomique ? Journe Rhne-Alpes Genopole. 2004. INRIA Rhne-Alpes, Montbonnot (Grenoble).

2. Binz, P.A., Masselot, A., Cambria, L., Müller, M., Tuloup, M., Hernandez, C., and Appel, R.D. Phenyx: about compatibility of high-throughput and pertinence in protein identification. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

3. Binz, P.A., Masselot, A., Cambria, L., Müller, M., Tuloup, M., Hernandez, C., Walther, D., Catherinet, S., and Appel, R.D. Bioinformatics and relevance in proteomics. in Socit franaise d'lectrophorse et d'analyse protomique. 2004. Bordeaux.

4. Gras, R., Hernandez, D., Hernandez, P., Mescam, Y., and Appel, R.D. Cooperation in Metaheuristics and Application in Bioinformatics. in European Conference on Combinatorial Optimisation - ECCO XVII 2004. 2004. Beirut, Lebanon.

5. Hernandez, D., Gras, R., and Appel, R.D. Stratégies d'exploration de l'espace des alignements locaux multiples sans indels. in Quatrièmes journées francophones de recherche opérationnelle (FRANCORO IV). 2004. Fribourg, Suisse.

6. Hernandez, P., Gras, R., and Appel, R.D. Popitam loves being fed on modified MS/MS spectra. in Peptide Fragmentation and identification Workshop, NIST. 2004. Gaithersburg, Maryland.

7. Hernandez, P., Gras, R., and Appel, R.D. Popitam squints to better identify ms/ms spectra of modified peptides. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

8. Hochstrasser, D.F., Corthals, G., Sanchez, J.C., Appel, R.D., Bairoch, A., Bougueleret, L., and Rose, K. Clinical proteomics: a challenge for diagnostic laboratories and the pharma industry? in AACC 2004 Annual meeting. 2004. Los Angeles, CA.

9. Hochstrasser, D.F., Zimmermann-Ivol, C.G., Corthals, G.L., Appel, R.D., and Sanchez, J.C. Clinical Proteomics. in Congress of the Swiss Proteomics Society. 2004. Bern.

10. Hoogland, C., Lion, N., Palagi, P.M., Rossier, J., Sanchez, J.C., Stocklin, R., Tissot, J.D., and Voshol, H. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. in Swiss Proteomics Society 2004 Congress: Proteomics for Health. 2004. Bern, Switzerland.

11. Hoogland, C., Lion, N., Palagi, P.M., Sanchez, J.C., and Tissot, J.D. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. in 6th Siena Meeting From genome to proteome: Biomarker discovery & Proteome imaging. 2004. Siena, Italy.

12. Masselot, A., Binz, P.A., Cambria, L., and Appel, R.D. Phenyx: combining high-throughput and pertinence in protein identification. in Third Annual HUPO Congress (proceedings in Molecular & Cell Proteomics). 2004. Beijing.

13. Masselot, A., Binz, P.A., Cambria, L., and Appel, R.D. Phenyx: Manage Protein Identification With Flexibility and Pertinence. in Congress of the Swiss Proteomics Society. 2004. Bern.

14. Mostaguir, K., Hoogland, C., and Appel, R.D. The Make2D-DB II Tool: building a large federated 2-DE database network. in ISMB/ECCB04. 2004. Glasgow.

15. Mostaguir, K., Hoogland, C., and Appel, R.D. The Make2D-DB II Tool: building a large federated 2-DE gel databases network. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

16. Palagi, P.M., Bucher, P., Notredame, C., Schwede, T., Galisson, G., and Appel, R.D. Evolution of bioinformatics education in Switzerland and the role of the Swiss Institute of Bioinformatics. in WEB'04 - Workshop on Education in Bioinformatics 2004, ISMB2004. 2004. Glasgow, Scotland.

17. Palagi, P.M., Walther, D., Quadroni, M., Catherinet, S., Burgess, J., Zimmermann-Ivol, C.G., Sanchez, J.C., Binz, P.A., Hochstrasser, D.F., and Appel, R.D. Proteome imaging: a prerequisite for any MS-related proteomic study? in Congress of the Swiss Proteomics Society. 2004. Bern.

18. Potts, A., Walther, D., Catherinet, S., Bienvenut, W., Appel, R.D., and Quadroni, M. The application of a software tool for the two-dimensional representation of LC-MS data to the analysis of post-translational modifications and the comparison of complex peptide mixtures. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

19. Quadroni, M., Walther, D., Appel, R., Bienvenut, W., and Potts, A. Comparative mass spectrometric analysis of complex peptide mixtures using a novel software tool for two-dimensional data visualization. in Congress of the Swiss Proteomics Society. 2004. Bern.

20. Scherl, A., Francois, P., Bento, M., Deshusses, J.M., Charbonnier, Y., Converset, V., Huyghe, A., Walter, N., Hoogland, C., Appel, R.D., Sanchez, J.C., Zimmermann-Ivol, C.G., Corthals, G.L., Hochstrasser, D.F., and Schrenzel, J. Exploring the proteome and transcriptome of Staphylococcus aureus. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

21. Walther, D., Quadroni, M., Catherinet, S., Burgess, J., Zimmermann-Ivol, C.G., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D. Why not exploit ms data to its fullest? Using data-redundancy in mass spectra. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

22. Zimmermann-Ivol, C.G., Vaezzadeh, A., Converset, V., Hoogland, C., Walther, D., Catherinet, S., Tuloup, M., Hernandez, C., Müller, M., Moll, S., Corthals, G.L., Pasquarello, C., Appel, R.D., and Hochstrasser, D.F. Distribution and visualisation of urine protein profile with the Molecular Scanner. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

23. Zimmermann-Ivol, C.G., Vaezzadeh, A., Demalte, I., Converset, V., Di Dio, J., Scherl, A., Corthals, G.L., Appel, R.D., and Hochstrasser, D.F. The Molecular Scanner. in Congress of the Swiss Proteomics Society. 2004. Bern.

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