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Publications in 2005

Thesis

1. Hernandez, D., Stratégies d'optimisation combinatoire pour le problème de l'alignement local multiple sans indels, et application aux séquences prot‚iques. 2005, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

2. Hernandez, P., Peptide Identification by Tandem Mass Spectrometry: A Tag-Oriented Open-Modification Search Method. 2005, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

Journal Articles

1. Hoogland, C., Lion, N., Palagi, P.M., Sanchez, J.C., and Tissot, J.D., SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. Proteomics, 2005. 5(12): p. 3045-3047.

2. 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., MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics., 2005. 5(9): p. 2381-2384.

3. Ruch, P., Baud, R., Chichester, C., Geissbuhler, A., Lisacek, F., Marty, J., Rebholz-Schuhmann, D., Tbahriti, I., and Veuthey, A.L., Extracting key sentences with latent argumentative structuring. Studies in Health Technology and Informatics, 2005. 116: p. 835-840.

4. 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., Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth. Journal of Microbiological Methods, 2005. 60(2): p. 247-257.

5. Scherl, A., Zimmermann-Ivol, C.G., Di, D.J., Vaezzadeh, A.R., Binz, P.A., mez-Droz, M., Cochard, R., Sanchez, J.C., Gluckmann, M., and Hochstrasser, D.F., Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect. Rapid Communications in Mass Spectrometry, 2005. 19(5): p. 605-610.

6. Stephan, C., Hamacher, M., Bluggel, M., Korting, G., Chamrad, D., Scheer, C., Marcus, K., Reidegeld, K.A., Lohaus, C., Schafer, H., Martens, L., Jones, P., Muller, M., Auyeung, K., Taylor, C., Binz, P.A., Thiele, H., Parkinson, D., Meyer, H.E., and Apweiler, R., 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame. Proteomics, 2005. 5(14): p. 3560-3562.

Journal Articles - non peer-reviewed

1. Orchard, S., Hermjakob, H., Binz, P.A., Hoogland, C., Taylor, C.F., Zhu, W., Julian, R.K., Jr., and Apweiler, R., Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics, 2005. 5(2): p. 337-339.

Guest Edition

1. Aebersold, R., Affolter, M., Agurri, A., Elia, G., Gruissem, W., Neri, D., Palagi, P.M., Sanchez, J.C., Schlapbach, R., Rossier, J.S., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2005 Congress, Expanding proteomics 2005: Zurich, Switzerland.

2. Palagi, P.M., Sanchez, J.C., and Stöcklin, R., Special Issue on the Proceedings of the 4th Annual Congress of the Swiss Proteomics Society. 2005, Proteomics vol. 45, n.12.

Conference Proceedings

1. Lisacek, F., Chichester, C., Kaplan, A., and Sandor, A. Discovering paradigm shift patterns in biomedical abstracts: Application to neurodegenerative diseases. in CEUR Workshop Proceedings. 2005.

Book Chapters

1. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A., Protein Identification and Analysis Tools on the ExPASy Server, in The Proteomics Protocols Handbook, Walker, J.M., Editor. 2005, Humana Press. p. 571-607.

2. Hoogland, C., Mostaguir, K., and Appel, R.D., 2-DE Databases on the World-Wide Web, in The Proteomics Protocols Handbook, Walker, J.M., Editor. 2005, Humana Press. p. 259-266.

3. Palagi, P.M., Walther, D., Bouchet, G., Voordijk, S., and Appel, R.D., Computer Analysis of 2D Images, in The Proteomics Protocols Handbook, Walker, J.M., Editor. 2005, Humana Press. p. 267-277.

Abstracts & Posters

1. Appel, R.D. Current and future challenges in proteome informatics. in BC2, Basel Computational Biology Conference 2005. 2005. Basel.

2. Appel, R.D., Masselot, A., Budin, N., Evalet, O., Cambria, L., and Binz, P.A. What's in MS spectra? What's in databases? Take the best to identify active proteins. in HUPO 4th Annual Congress. 2005. Munich.

3. Binz, P.A. Aspects de bioinformatique applique l'tude du phosphoprotome. in Atelier phosphoprotome. 2005. Cap d'Agde, France.

4. Binz, P.A. Phenyx: understand and manage. in Proteomics Methods Forum. 2005. York, UK.

5. Binz, P.A., Masselot, A., and Appel, R.D. Proteome Bioinformatics: critically evaluating MS data. in Swiss Proteomics Society 2004 Congress: Expanding proteomics. 2005. Zurich, Swizerland.

6. Binz, P.A., Masselot, A., Budin, N., and Nahas, N. Discover Multiple Facets of the Innovative Phenyx Platform and Achieve Increased Confidence in Protein Identification. in HUPO 4th Annual Congress. 2005. Munich, Germany.

7. Binz, P.A., Masselot, A., Walther, D., and Appel, R.D. Interpretation of protein identification results: more questions than answers? The confidence and validation issue. in BSPR/EBI Meeting - From Proteins to Systems. 2005. Cambridge.

8. Hernandez, P., Gras, R., Hernandez, C., and Appel, R.D. Peptide identification and characterization using tandem mass spectrometry data: an open-modification search approach with Popitam. in Swiss Proteomics Society 2005 Congress: Expanding proteomics. 2005.

9. Hochstrasser, D.F., Appel, R.D., Paesano, S., Binz, P.A., Sanchez, J.C., and Zimmermann, C. Proteomics & Clinical Chemistry. in Fourth HUPO annual meeting. 2005. Munich.

10. Hochstrasser, D.F., Scherl, A., Binz, P.A., Zimmerman, C., Sanchez, J.C., and Appel, R.D. Complex Specimen struggling to survive. in BSPR/EBI Meeting - From Proteins to Systems. 2005. Cambridge.

11. Hochstrasser, D.F., Walther, D., Quadroni, M., Catherinet, S., Tuloup, M., Binz, P.A., Burgess, J., Vaezzadeh, A., Zimmerman, C., Corthals, G.L., Sanchez, J.C., and Appel, R.D. MS imaging in Clinical Proteomics. in Beyond Genome. 2005. San Francisco, CA.

12. Hochstrasser, D.F., Walther, D., Quadroni, M., Catherinet, S., Tuloup, M., Binz, P.A., Burgess, J., Vaezzadeh, A., Zimmermann-Ivol, C.G., Corthals, G.L., Appel, R.D., and Sanchez, J.C. Clinical Proteomics and MS imaging. in ASBMB 2005, American Society for Biochemistry and Molecular biology. 2005. San Diego, CA.

13. Mostaguir, K., Hoogland, C., and Appel, R.D. Creation and interconnection of distributed proteomic databases: the Make2D-DB II tool, an example applied to 2-DE datasets. in Fourth HUPO annual meeting. 2005. Munich.

14. Mostaguir, K., Hoogland, C., and Appel, R.D. Evolution et interconnexion des bases de donnes protomiques avec l'outil Make2D-DB II : un exemple appliqu aux bases de donnes de gels 2-DE. in JOBIM. 2005.

15. Nikitin, F., Lisacek, F., and Appel, R.D. Modular analysis of bacterial proteins in specific pathways. in ECCB 05, 4th European Conference on Computational Biology. 2005. Madrid, Spain.

16. Palagi, P.M., Walther, D., Quadroni, M., Catherinet, S., Binz, P.A., Hochstrasser, D.F., and Appel, R.D. MSight: an LC-MS image analysis software. in ISMB 2005, 13th Annual International Conference on Intelligent Systems for Molecular Biology. 2005. Michigan.

17. Quadroni, M., Baruthio, F., Walther, D., Appel, R., Ruegg, C., and Mariotti, A. Label-free differential analysis of proteins in lipid rafts using LC-MS and the MSIGHT software tool. in 53rd ASMS Conference on Mass Spectrometry. 2005. San Antonio, Texas.

18. Scherl, A., Francois, P., Bento, M., Masselot, A., Binz, P.A., Hoogland, C., Appel, R.D., Zimmermann-Ivol, C.G., Sanchez, J.C., Stahl-Zeng, J., Schrenzel, J., and Hochstrasser, D.F. Exploring antibiotic resistance with isobaric tags. in 53rd ASMS Conference on Mass Spectrometry. 2005. San Antonio, Texas.

19. Scherl, A., Zimmermann-Ivol, C.G., Bento, M., Francois, P., Sanchez, J.C., Appel, R.D., Schrenzel, J., and Hochstrasser, D.F. Characterization of Staphylococcus aureus Proteins involved in glycopeptide tolerance with mass spectrometric based quantitative methods. in Congress of the Swiss Proteomics Society. 2005.

20. Walther, D., Bouchet, G., Catherinet, S., Pelhatre, S., Tuloup, M., Palagi, P.M., and Appel, R.D. Powered by Melanie: a general framework for proteome imaging. in Swiss Proteomics Society 2005 Congress: Expanding proteomics. 2005. Zurich, Switzerland.

21. Walther, D., Quadroni, M., Catherinet, S., Hochstrasser, D.F., Palagi, P.M., and Appel, R.D. MSight: an LC-MS image analysis software. in Fourth HUPO annual meeting. 2005. Munich.

22. Zangger, N., Cerutti, L., Pagni, M., Lisacek, F., and Appel, R.D. Clustering protein sequences based on motif content. in ECCB 05, 4th European Conference on Computational Biology. 2005. Madrid, Spain.

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