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Publications in 2005

I. Articles in journals with editorial policy

  1. Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Binz PA, Hochstrasser DF, Appel RD. MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005; 5: 2381-2384.

  2. Ruch P, Baud R, Chichester C, Geissbuhler A, Lisacek F, Marty J, Rebholz-Schuhmann D, Tbahriti I, Veuthey AL. Extracting key sentences with latent argumentative structuring. Stud Health Technol Inform 2005; 116: 835-840.

  3. Scherl A, Francois P, Bento M, Deshusses JM, Charbonnier Y, Converset V, Huyghe A, Walter N, Hoogland C, Appel RD, Sanchez JC, Zimmermann-Ivol CG, Corthals GL, Hochstrasser DF, Schrenzel J. Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth. J Microbiol Methods 2005; 60: 247-257.

  4. Scherl A, Zimmermann-Ivol CG, Di DJ, Vaezzadeh AR, Binz PA, mez-Droz M, Cochard R, Sanchez JC, Gluckmann M, Hochstrasser DF. Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect. Rapid Commun Mass Spectrom 2005; 19: 605-610.

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

II. Books, book chapters & guest edition

  1. Aebersold R, Affolter M, Agurri A, Elia G, Gruissem W, Neri D, Palagi PM, Sanchez JC, Schlapbach R, Rossier JS, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2005 Congress, Expanding proteomics (Editors). Zurich, Switzerland: 2005.

  2. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server. In: Walker JM, ed. The Proteomics Protocols Handbook. Humana Press; 2005: 571-607.

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

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

  5. Hoogland C, Sanchez JC, Hochstrasser DF, Appel RD. 2-D PAGE databases for proteins in human body fluids. PROTEOMICS OF HUMAN BODY FLUIDS: Principles, Methods, and Applications. Humana Press; 2005. Submitted.

  6. Hoogland C, Mostaguir K, Appel RD. 2-DE Databases on the World-Wide Web. In: Walker JM, ed. The Proteomics Protocols Handbook. Humana Press; 2005: 259-266.

  7. Palagi PM, Walther D, Bouchet G, Voordijk S, Appel RD. Computer Analysis of 2D Images. In: Walker JM, ed. The Proteomics Protocols Handbook. Humana Press; 2005: 267-277.

  8. Palagi PM, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 4th Annual Congress of the Swiss Proteomics Society (Guest Editors). Proteomics vol. 45, n.12; 2005.

III. Articles in journals without editorial policy

  1. Orchard S, Hermjakob H, Binz PA, Hoogland C, Taylor CF, Zhu W, Julian RK, Jr., 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: 337-339.

IV. Conference proceedings

  1. Lisacek F, Chichester C, Kaplan A, Sandor A. Discovering paradigm shift patterns in biomedical abstracts: Application to neurodegenerative diseases. First International Symposium on Semantic Mining in Biomedicine (SMBM). 2005.

  2. Nikitin F, Lisacek F, Appel RD. Modular analysis of bacterial proteins in specific pathways. ECCB 05, 4th European Conference on Computational Biology. Madrid, Spain: Sept. 2005.

  3. Scherl A, Francois P, Bento M, Masselot A, Binz PA, Hoogland C, Appel RD, Zimmermann-Ivol CG, Sanchez JC, Stahl-Zeng J, Schrenzel J, Hochstrasser DF. Exploring antibiotic resistance with isobaric tags. 53rd ASMS Conference on Mass Spectrometry. San Antonio, Texas: June 2005.

  4. Zangger N, Cerutti L, Pagni M, Lisacek F, Appel RD. Clustering protein sequences based on motif content. ECCB 05, 4th European Conference on Computational Biology. Madrid, Spain: Sept. 2005.

V. Abstracts and posters

  1. Appel RD. Current and future challenges in proteome informatics. BC2, Basel Computational Biology Conference 2005. Basel: Mar. 2005.

  2. Appel RD, Masselot A, Budin N, Evalet O, Cambria L, Binz PA. What’s in MS spectra? What’s in databases? Take the best to identify active proteins. HUPO 4th Annual Congress. Munich: Aug. 2005.

  3. Binz PA. Aspects de bioinformatique appliquée à l'étude du phosphoprotéome. Atelier phosphoprotéome. June 2005. Aug. 2005.

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

  5. Binz PA, Masselot A, Walther D, Appel RD. Interpretation of protein identification results: more questions than answers? The confidence and validation issue. BSPR/EBI Meeting – From Proteins to Systems. Cambridge: July 2005.

  6. Binz PA. Phenyx: understand and manage. Proteomics Methods Forum. Apr. 2005. Aug. 2005.

  7. Binz PA, Masselot A, Appel RD. Proteome Bioinformatics: critically evaluating MS data. Swiss Proteomics Society 2004 Congress: Expanding proteomics. Zurich, Swizerland: Dec. 2005.

  8. Hernandez P, Gras R, Hernandez C, Appel RD. Peptide identification and characterization using tandem mass spectrometry data: an open-modification search approach with Popitam. Swiss Proteomics Society 2005 Congress: Expanding proteomics. Dec. 2005: 187-190.

  9. Hochstrasser DF, Walther D, Quadroni M, Catherinet S, Tuloup M, Binz PA, Burgess J, Vaezzadeh A, Zimmermann-Ivol CG, Corthals GL, Appel RD, Sanchez JC, Appel RD. Clinical Proteomics and MS imaging. ASBMB 2005, American Society for Biochemistry and Molecular biology. San Diego, CA: Apr. 2005.

  10. Hochstrasser DF, Scherl A, Binz PA, Zimmerman C, Sanchez JC, Appel RD. Complex Specimen struggling to survive. BSPR/EBI Meeting – From Proteins to Systems. Cambridge: July 2005.

  11. Hochstrasser DF, Walther D, Quadroni M, Catherinet S, Tuloup M, Binz P-A, Burgess J, Vaezzadeh A, Zimmerman C, Corthals GL, Sanchez JC, Appel RD. MS imaging in Clinical Proteomics. Beyond Genome. San Francisco, CA: June 2005.

  12. Hochstrasser DF, Appel RD, Paesano S, Binz PA, Sanchez JC, Zimmermann C. Proteomics & Clinical Chemistry. Fourth HUPO annual meeting. Munich: Aug. 2005.

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

  14. Mostaguir K, Hoogland C, Appel RD. Evolution et interconnexion des bases de données protéomiques avec l'outil Make2D-DB II : un exemple appliqué aux bases de données de gels 2-DE. JOBIM. July 2005.

  15. Palagi PM, Walther D, Quadroni M, Catherinet S, Binz PA, Hochstrasser DF, Appel RD. MSight: an LC-MS image analysis software. ISMB 2005, 13th Annual International Conference on Intelligent Systems for Molecular Biology. Michigan: June 2005.

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

  17. Scherl A, Zimmermann-Ivol CG, Bento M, Francois P, Sanchez JC, Appel RD, Schrenzel J, Hochstrasser DF. Characterization of Staphylococcus aureus Proteins involved in glycopeptide tolerance with mass spectrometric based quantitative methods. Congress of the Swiss Proteomics Society. Dec. 2005: 26.

  18. Walther D, Quadroni M, Catherinet S, Hochstrasser DF, Palagi PM, Appel RD. MSight: an LC-MS image analysis software. Fourth HUPO annual meeting. Munich: Aug. 2005.

  19. Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Powered by Melanie: a general framework for proteome imaging. Swiss Proteomics Society 2005 Congress: Expanding proteomics. Dec. 2005. Zurich, Switzerland: 2005.

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