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Publications in 2006

I. Articles in journals with editorial policy

  1. Colinge J, Masselot A, Carbonell P, Appel RD. InSilicoSpectro: an open-source proteomics library. J Proteome Res 2006; 5: 619-624.

  2. Coute Y, Burgess JA, Diaz JJ, Chichester C, Lisacek F, Greco A, Sanchez JC. Deciphering the human nucleolar proteome. Mass Spectrom Rev 2006; 25: 215-234.

  3. Hernandez P, Muller M, Appel RD. Automated protein identification by tandem mass spectrometry: issues and strategies. Mass Spectrom Rev 2006; 25: 235-254.

  4. Lisacek F, Cohen-Boulakia S, Appel RD. Proteome informatics II: Bioinformatics for comparative proteomics. Proteomics 2006; 6: 5445-5466.

  5. Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R. Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics 2006; 6: 738-741.

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

  7. Scherl A, Francois P, Charbonnier Y, Deshusses JM, Koessler T, Huyghe A, Bento M, Stahl-Zeng J, Fischer A, Masselot A, Vaezzadeh A, Galle F, Renzoni A, Vaudaux P, Lew D, Zimmermann-Ivol CG, Binz PA, Sanchez JC, Hochstrasser DF, Schrenzel J. Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers. BMC Genomics 2006; 7: 296.

  8. Stephan C, Reidegeld KA, Hamacher M, van HA, Marcus K, Taylor C, Jones P, Muller M, Apweiler R, Martens L, Korting G, Chamrad DC, Thiele H, Bluggel M, Parkinson D, Binz PA, Lyall A, Meyer HE. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics 2006; 6: 5015-5029.

  9. Tbahriti I, Chichester C, Lisacek F, Ruch P. Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library. Int J Med Inform 2006; 75: 488-495.

  10. Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Gorg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ. Guidelines for the next 10 years of proteomics. Proteomics 2006; 6: 4-8.

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.

V. Abstracts and posters

  1. 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.

  2. Appel RD. Making Protein Identification Reliable. HUPO Human Liver Proteome Project workshop. May 6 A.D. 2006.

  3. 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.

  4. 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.

  5. Binz PA, Masselot A, Mylonas R, Bouyssiè D, Niknejad A, Budin N, Appel RD. "Garbage in – Garbage out": The peaklist issue in proteomics. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 106.

  6. Colinge J, Masselot A, Pitzer E, Appel RD. InSilicoSpectro - Proteomics Open-Source Library. 54th ASMS Conference on Mass Spectrometry. Jan. 2006. Seattle, Washington: Jan. 2006.

  7. Colinge J, Masselot A, Pitzer E, Mylonas R, Appel RD. Mass Spectrometry Data Mining supported by an open source initiative to develop new generic peak intensity models and evaluate peptide de novo sequencing algorithms. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 101.

  8. Hernandez P, Quandt A, Hernandez C, Müller M, Appel RD. swissPIT - A platform for knowledge extraction from mass spectrometry data. 7th Siena meeting - From Genome to Proteome. Siena, Italy: 2006: 43.

  9. Hernandez P, Quandt A, Hernandez C, Appel RD. swissPIT, une plateforme pour l'identification de protéines à partir de spectres de masses. Grille Bioinformatique: expériences et perspectives, Vendredi 12 mai, IBCP, Lyon. Lyon: 2006.

  10. Mylonas R, Masselot A, Binz PA, Appel RD. An opensource toolkit for quality assessment and filtering of peptide
    mass spectra    . HUPO 5th Annual World Congress. Oct. 2006. Long Beach, California: Oct. 2006.

  11. 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.

  12. 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.

  13. Quandt A, Hernandez P, Hernandez C, Müller M, Appel RD. swissPIT, a multi-tool protein identification platform. In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot. July 6 A.D. Fortaleza, Brazil: 2006: 227.

  14. Rossier G, Lisacek F, Appel RD. E-PROXEMIS: A BIOINFORMATICS LEARNING PORTAL
    FOR PROTEOMICS    . 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 334.

  15. Scherl A, Kulasekara H, Binz PA, Hernandez P, Schaffer S, Taylor G, Ryu S, Masselot A, Appel RD, Radulovic D, Miller SI, Goodlett DR. High measured mass accuracy on CID fragments: What do we gain, what do we lose? 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 40.

  16. Vaezzadeh A, Zimmermann-Ivol CG, Lassout O, Francois P, Hoogland C, Appel RD, Schrenzel J, Hochstrasser DF. High-throughput profiling of bacterium proteome by Shotgun IEF. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 67.

  17. 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.

  18. 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.

  19. 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.

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