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Publications in 2006

Journal Articles

1. Colinge, J., Masselot, A., Carbonell, P., and Appel, R.D., InSilicoSpectro: an open-source proteomics library. J.Proteome.Res., 2006. 5(3): p. 619-624.

2. Coute, Y., Burgess, J.A., Diaz, J.J., Chichester, C., Lisacek, F., Greco, A., and Sanchez, J.C., Deciphering the human nucleolar proteome. Mass Spectrometry Reviews, 2006. 25(2): p. 215-234.

3. Hernandez, P., Muller, M., and Appel, R.D., Automated protein identification by tandem mass spectrometry: issues and strategies. Mass Spectrometry Reviews, 2006. 25(2): p. 235-254.

4. Lisacek, F., Web-based MS/MS Data Analysis. Proteomics, 2006. 6(S2): p. 22-32.

5. Lisacek, F., Cohen-Boulakia, S., and Appel, R.D., Proteome informatics II: Bioinformatics for comparative proteomics. Proteomics, 2006. 6(20): p. 5445-5466.

6. Palagi, P.M., Hernandez, P., Walther, D., and Appel, R.D., Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics, 2006. 6(20): p. 5435-5444.

7. Scherl, A., Francois, P., Charbonnier, Y., Deshusses, J.M., 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, C.G., Binz, P.A., Sanchez, J.C., Hochstrasser, D.F., and 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: p. 296.

8. Stephan, C., Reidegeld, K.A., Hamacher, M., van, H.A., Marcus, K., Taylor, C., Jones, P., Muller, M., Apweiler, R., Martens, L., Korting, G., Chamrad, D.C., Thiele, H., Bluggel, M., Parkinson, D., Binz, P.A., Lyall, A., and Meyer, H.E., Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics, 2006. 6(18): p. 5015-5029.

9. Tbahriti, I., Chichester, C., Lisacek, F., and 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(6): p. 488-495.

Journal Articles - non peer-reviewed

1. Orchard, S., Hermjakob, H., Taylor, C., Binz, P.A., Hoogland, C., Julian, R., Garavelli, J.S., Aebersold, R., and Apweiler, R., Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics, 2006. 6(3): p. 738-741.

2. Wilkins, M.R., Appel, R.D., Van Eyk, J.E., Chung, M.C., Gorg, A., Hecker, M., Huber, L.A., Langen, H., Link, A.J., Paik, Y.K., Patterson, S.D., Pennington, S.R., Rabilloud, T., Simpson, R.J., Weiss, W., and Dunn, M.J., Guidelines for the next 10 years of proteomics. Proteomics., 2006. 6(1): p. 4-8.

Guest Edition

1. Elia, G., Neri, D., Palagi, P.M., Sanchez, J.C., Stöcklin, R., and Hopfgartner, G., Special Issue on the Proceedings of the 5th Annual Congress of the Swiss Proteomics Society. 2006, J. Chromatography B vol. 840, n.1 7 August 2006.

Book Chapters

1. Palagi, P.M., Brunner, Y., Sanchez, J.C., and Appel, R.D., Proteomics: beyond cDNA, in Bioinformatics: from Genomes to Therapies, Lengauer, T., Editor. 2006, John Wiley & Sons.

2. Palagi, P.M., Walther, D., Bouchet, G., Voordijk, S., and Appel, R.D., Image analysis and quantitation, in Cell Biology: a laboratory handbook, Cellis, J.E., Editor. 2006, Academic Press. p. 207-215.

Abstracts & Posters

1. Appel, R.D. Making Protein Identification Reliable. in HUPO Human Liver Proteome Project workshop. 2006. Bilbao, Spain.

2. Appel, R.D., Binz, P.A., 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, P.M., Pelhatre, S., Quandt, A., Rossier, G., Sapsezian, C., Sonesson, K., Tuloup, M., Verbregue, L., Walther, D., and Zangger, N. Swiss-Prot and PIG: 20 years of fruitful collaboration. in In-Silico Analysis of Proteins - Celebrating the 20th anniversary of Swiss-Prot. 2006. Fortaleza, Brazil.

3. Appel, R.D., Hernandez, P., Walther, D., Lisacek, F., Palagi, P.M., Hoogland, C., Binz, P.A., Masselot, A., Nahas, N., Sanchez, J.C., and Hochstrasser, D.F. Analytical bioinformatics: from data to knowledge. in MILA 2006 - First Latin-American Medical Informatics Congress. 2006.

4. Appel, R.D., Hernandez, P., Walther, D., Lisacek, F., Palagi, P.M., Hoogland, C., Binz, P.A., Masselot, A., Sanchez, J.C., and Hochstrasser, D.F. MS Analysis: imaging and protein identification tools. in Joint Third AOHUPO and Fourth Structural Biology and Functional Genomics Conference. 2006. Singapore.

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

6. Colinge, J., Masselot, A., Pitzer, E., and Appel, R.D. InSilicoSpectro - Proteomics Open-Source Library. in 54th ASMS Conference on Mass Spectrometry. CY - Seattle, Washington. 2006.

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

8. Hernandez, P., Quandt, A., Hernandez, C., and Appel, R.D. swissPIT, une plateforme pour l'identification de protines partir de spectres de masses. in Grille Bioinformatique: expriences et perspectives, Vendredi 12 mai, IBCP, Lyon. 2006. Lyon.

9. Hernandez, P., Quandt, A., Hernandez, C., Müller, M., and Appel, R.D. swissPIT - A platform for knowledge extraction from mass spectrometry data. in 7th Siena meeting - From Genome to Proteome. 2006. Siena, Italy.

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

11. Palagi, P.M., Hernandez, P., Quandt, A., Hernandez, C., and Appel, R.D. swissPIT - swiss Protein Identification Toolbox : A pipeline for knowledge extraction from MS data. in Münster Proteomics Meeting. 2006. Münster, Germany.

12. Palagi, P.M., 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., and Appel, R.D. Bioinformatics to explore and integrate proteomics data. in PROTEOME ANALYSIS IN SYSTEMS BIOLOGY. 2006. Antwerp, Belgium.

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

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

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

16. Vaezzadeh, A., Zimmermann-Ivol, C.G., Lassout, O., Francois, P., Hoogland, C., Appel, R.D., Schrenzel, J., and Hochstrasser, D.F. High-throughput profiling of bacterium proteome by Shotgun IEF. in 7th Siena Meeting - From Genome to Proteome - Back to the future. 2006. Siena, Italy.

17. Walther, D., Bouchet, G., Catherinet, S., Pelhatre, S., Tuloup, M., Palagi, P.M., and Appel, R.D. Analysis of liquid chromatography/mass spectrometry data with the MSight software. in 7th Siena meeting - From Genome to Proteome - Back to the future. 2006. Siena, Italy.

18. Walther, D., Bouchet, G., Catherinet, S., Pelhatre, S., Tuloup, M., Palagi, P.M., and Appel, R.D. Bioinformatics for proteome imaging: Melanie's example. in In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot. 2006. Fortaleza, Brazil.

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

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