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List of Publications

Last updated 8.Jan.2006 by P.M.Palagi

I. Articles in journals with editorial policy

  1. Palagi PM, Hernandez P, Walther D, Appel RD. Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics 2006; 6: 5435-5444.

  2. 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.

  3. Binz PA, Müller M, Walther D, Bienvenut WV, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins MR, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Sanchez JC, Appel RD, Hochstrasser DF. A molecular scanner to automate proteomic research and to display proteome images. Anal Chem 1999; 71: 4981-4988.

  4. Appel RD, Vargas JR, Palagi PM, Walther D, Hochstrasser DF. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 1997; 18: 2735-2748.

  5. Appel RD, Palagi PM, Walther D, Vargas JR, Sanchez JC, Ravier F, Pasquali C, Hochstrasser DF. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface. Electrophoresis 1997; 18: 2724-2734.

II. Books, book chapters & guest edition

  1. Elia G, Neri D, Palagi PM, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 5th Annual Congress of the Swiss Proteomics Society (Guest Editors). In: Hopfgartner G, ed. J. Chromatography B vol. 840, n.1 7 August 2006; 2006.

  2. Palagi PM, Walther D, Bouchet G, Voordijk S, Appel RD. Image analysis and quantitation. In: Cellis JE, ed. Cell Biology: a laboratory handbook. 3rd Edition, Academic Press; 2006: 207-215.

  3. Palagi PM, Brunner Y, Sanchez JC, Appel RD. Proteomics: beyond cDNA. In: Lengauer T, ed. Bioinformatics: from Genomes to Therapies. John Wiley & Sons; 2006.

  4. Palagi PM, Walther D, Zimmermann-Ivol CG, Appel RD. Proteome Imaging. In: Wilkins MR, Williams KL, Appel RD, Hochstrasser DF, eds. Proteome research: new frontiers in functional genomics. Berlin Heidelberg: Springer Verlag; 2006. In press.

  5. 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.

  6. 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.

  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. Affolter M, Gadola S, Haeberli A, Heller M, Palagi PM, Sanchez JC, Solioz M, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2004 Congress, Proteomics for Health (Editors). Bern, Switzerland: 2004.

  9. Palagi PM, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 3rd Annual Congress of the Swiss Proteomics Society (Guest Editors). Proteomics vol. 4, n.8; 2004.

  10. 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.

  11. 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.

  12. Palagi PM, Quadroni M, Rossier J, Sanchez JC, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2002 Congress, Applied Proteomics (Editors). Lausanne, Switzerland: FontisMedia Publishers; 2002.

  13. Sanchez JC, Palagi PM, Stöcklin R. Special Issue on the Proceedings of the 1st Annual Conference of the Swiss Proteomics Society (Guest Editors). Proteomics vol.2, n°7; 2002.

  14. Bienvenut WV, Müller M, Palagi PM, Heller M, Gay S, Binz PA, Giron M, Gasteiger E, Jung E, Gras R, Sanchez JC, Appel RD, Hochstrasser DF. Proteomics and mass spectrometry: some aspects and recent developments. In: Housby N, ed. Mass Spectrometry and Genomic Analysis. The Netherland: Kluwer Academic Publishers; 2001: 1-53.

  15. Palagi PM, Sanchez JC, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2001 Congress, Functional Proteomics (Editors). Lausanne, Switzerland: FontisMedia Publishers; 2001.

III. Abstracts and posters

  1. Appel RD, Binz PA, Bouchet G, Catherinet S, Dornevil D, Hernandez C, Hernandez P, Hoogland C, Ivanyi I, Lisacek F, Mostaguir K, Mangold V, Nikitin F, Paesano S, Palagi PM, Pelhatre S, Quandt A, Rossier G, Sapsezian C, Sonesson K, Tuloup M, Verbregue L, Walther D, Zangger N. Swiss-Prot and PIG: 20 years of fruitful collaboration. In-Silico Analysis of Proteins - Celebrating the 20th anniversary of Swiss-Prot. July 2006. Feb. 2006.

  2. Appel RD, Hernandez P, Walther D, Lisacek F, Palagi PM, Hoogland C, Binz P-A, Masselot A, Sanchez JC, Hochstrasser DF. MS analysis: imaging and protein identification tools. AOHUPO'06. Dec. 2006. 2006.

  3. Appel RD, Hernandez P, Walther D, Lisacek F, Palagi PM, Hoogland C, Binz P-A, Masselot A, Nahas N, Sanchez JC, Hochstrasser DF. Analytical bioinformatics: from data to knowledge. MILA 2006 - First Latin-American Medical Informatics Congress. Dec. 6 A.D. 2006.

  4. Palagi PM, Hernandez P, Quandt A, Hernandez C, Appel RD. swissPIT - swiss Protein Identification Toolbox : A pipeline for knowledge extraction from MS data. May 2006.

  5. Palagi PM, Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Hernandez P, Hernandez C, Quandt A, Lisacek F, Hoogland C, Binz P-A, Rossier G, Mostaguir K, Nikitin F, Zangger N, Appel RD. Bioinformatics to explore and integrate proteomics data. PROTEOME ANALYSIS IN SYSTEMS BIOLOGY. Dec. 2006. Antwerp, Belgium: Sept. 2006.

  6. Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Bioinformatics for proteome imaging: Melanie's example. In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot. July 6 A.D. Fortaleza, Brazil: 2006: 227.

  7. Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Analysis of liquid chromatography/mass spectrometry data with the MSight software. 7th Siena meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: 2006: 227.

  8. Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Imaging in proteomics: 2-DE vs. LC/MS data analysis. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 77.

  9. 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.

  10. 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.

  11. 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.

  12. Appel RD, Binz PA, 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, Zangger N. Current developments at the Proteome Informatics Group, Swiss Institute of Bioformatics, Geneva. Quelle informatique et bioinformatique pour la protéomique ? Journée Rhône-Alpes Genopole. INRIA Rhône-Alpes, Montbonnot (Grenoble): June 2004.

  13. Hoogland C, Lion N, Palagi PM, Rossier J, Sanchez JC, Stocklin R, Tissot JD, Voshol H. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. Swiss Proteomics Society 2004 Congress: Proteomics for Health. Aug. 2004. Bern, Switzerland: Dec. 2004: 230.

  14. Hoogland C, Lion N, Palagi PM, Sanchez JC, Tissot JD. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. 6th Siena Meeting From genome to proteome: Biomarker discovery & Proteome imaging. Siena, Italy: 2004: 230.

  15. Palagi PM, Bucher P, Notredame C, Schwede T, Galisson G, Appel RD. Evolution of bioinformatics education in Switzerland and the role of the Swiss Institute of Bioinformatics. WEB'04 - Workshop on Education in Bioinformatics 2004, ISMB2004. Glasgow, Scotland: July 2004.

  16. Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Binz PA, Hochstrasser DF, Appel RD. Proteome imaging: a prerequisite for any MS-related proteomic study? Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 61-63.

  17. 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.

  18. Gras R, Müller M, Hernandez D, Hernandez P, Zangger N, Palagi P, Binz PA, Appel RD. Cooperative metaheuristic for proteomics. Bioinformatics Workshop ISMIS. Lyon: 2002.

  19. Gras R, Müller M, Hernandez D, Hernandez P, Zangger N, Palagi P, Binz PA, Lisacek F, Appel RD. New approaches of computational proteomics. JOBIM 2002. 2002: 143-147.

  20. Palagi PM, Appel RD, Bairoch A, Bittar.G., Bucher P, Chopard B, Goudet J, Guex N, Jongeneel V, Peitsch MC, Pellegrini C. A Masters Degree in Bioinformatics in Switzerland. Workshop on Education in Bioinformatics 2001, ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology. Tivoli Gardens, Copenhagen, Denmark: July 2001.

  21. Appel RD, Walther D, Bouchet G, Voordijk S, Sontot C, Palagi PM, Sanchez JC, Hochstrasser DF. Future trends in 2-DE computer analysis. 4th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2000.

  22. Appel RD, Walther D, Binz PA, Hoogland C, Fabbretti R, Palagi P, Bouchet G, Gras R, Müller M, Gay S, Gasteiger E, Bairoch A, Sanchez JC, Hochstrasser DF. High-throughput proteomics: the need for high-performance computing. 27th SPEEDUP Workshop. Lugano: Mar. 2000.

  23. Hochstrasser DF, Binz PA, Müller M, Walther D, Bienvenut W, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins M, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Sanchez JC, Appel RD. MALDI-TOF “Imaging”: a Molecular Scanner for Proteomic Research. ABRF. 2000.

  24. Palagi PM, Hoogland C, Gras R, Mueller M, Binz PA, Fabbretti R, Bouchet G, Walther D, Gay S, Gasteiger E, Bairoch A, Sanchez JC, Hochstrasser DF, Appel RD. Human proteomics and bioinformatics tools. The first draft of the human genome : an academic and industrial perspective. Berlin, Germany: Oct. 2000.

  25. Palagi PM, Binz PA, Bairoch A, Hochstrasser DF, Appel RD. Bioinformatics in Proteomics. CCP11 GPCVI Conference "Bioinformatics and the Molecular Biologist". Chester, England: Apr. 2000.

  26. Palagi PM, Binz PA, Bairoch A, Hochstrasser DF, Appel RD. Bioinformatics challenges in proteomics. Symposium " Bioinformatics and proteomics ". Seoul, Korea: June 2000.

  27. Appel RD, Bairoch A, Walther D, Binz PA, Hoogland C, Fabbretti R, Palagi P, Bouchet G, Gras R, Müller M, Gay S, Gasteiger E, Sanchez JC, Hochstrasser DF. Improving, accelerating and automating proteomics discovery with bioinformatics. Elektrophorese Forum’99. Munich: Oct. 1999.

  28. Appel RD, Bairoch A, Walther D, Binz PA, Hoogland C, Fabbretti R, Palagi P, Bouchet G, Gras R, Müller M, Gay S, Gasteiger E, Sanchez JC, Hochstrasser DF. Improving Proteomics Discovery with Bioinformatics. Swiss Electrophoresis Society (CHEL) meeting. Montreux Palace: Dec. 1999.

  29. Hochstrasser DF, Binz PA, Bienvenut W, Müller M, Walther D, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins M, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Appel RD, Sanchez JC. Proteomics Technology Development in Geneva. Elektrophorese Forum’99. Munich: Oct. 1999.

  30. Palagi PM, Walther D, Bologna G, Vargas JR, Sanchez JC, Cremona O, Hochstrasser DF, Appel RD. 2-DE classification using heuristic clustering and neural nets. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.

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