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Publications in 2004

I. Articles in journals with editorial policy

  1. Binz PA, Müller M, Hoogland C, Zimmermann C, Pasquarello C, Corthals G, Sanchez JC, Hochstrasser DF, Appel RD. The molecular scanner: concept and developments. Curr Opin Biotechnol 2004; 15: 17-23.

  2. Bologna G, Yvon C, Duvaud S, Veuthey AL. N-Terminal myristoylation predictions by ensembles of neural networks. Proteomics 2004; 4: 1626-1632.

  3. Frey J, Gras R, Hernandez P, Appel R. A Hierarchical Model of Parallel Genetic Programming Applied to Bioinformatic Problems. Lecture Notes in Computer Science 2004; 3019: 1146-1153.

  4. Hernandez D, Gras R, Appel R. MoDEL: an efficient strategy for ungapped local multiple alignment. Comput Biol Chem 2004; 28: 119-128.

  5. Hoogland C, Mostaguir K, Sanchez JC, Hochstrasser DF, Appel RD. SWISS-2DPAGE, ten years later. Proteomics 2004; 4: 2352-2356.

  6. Lisacek F, Chichester C, Gonnet P, Jaillet O, Kappus S, Nikitin F, Roland P, Rossier G, Truong L, Appel R. Shaping biological knowledge: applications in proteomics. Comp Funct Genom 2004; 5: 190-195.

II. Books, book chapters & guest edition

  1. 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.

  2. Appel RD, Bairoch A. Special issue on Tools and Databases for Post-Translational Modifications (Guest Edition). Proteomics, Vol.4, No. 6; 2004.

  3. Boyer C, Appel RD. Steps towards Reliable Consumer Health Information. In: Nelson R, Ball MJ, eds. Consumer Informatics: Applications and Strategies in Cyber Health Care (Health Informatics). Springer Verlag; 2004: 80-89.

  4. Gras R, Hernandez D, Hernandez P, Zangger N, Mescam Y, Frey J, Martin O, Nicolas J, Appel RD. Cooperative Metaheuristics for Exploring Proteomic Data. In: Dubitzsky W, Azuaje F, eds. Artificial Intelligence Methods and Tools for Systems Biology. 2004: 87-106.

  5. Hochstrasser DF, Corthals G, Zimmerman C, Scherl A, Bougueleret L, Collinge J, Masselot A, Binz PA, Müller M, Bairoch A, Appel RD, Sanchez JC, Rose K. Proteomics & Mass Spectrometry in Medicine. In: Ashcroft AE, Brenton G, Monhagan JJ, eds. Advances in Mass Spectrometry. Elsevier B.V.; 2004: 19-32.

  6. 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.

V. Abstracts and posters

  1. 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.

  2. Binz PA, Masselot A, Cambria L, Müller M, Tuloup M, Hernandez C, Walther D, Catherinet S, Appel RD. Bioinformatics and relevance in proteomics. Société française d'électrophorèse et d'analyse protéomique. Bordeaux: Oct. 2004.

  3. Binz PA, Masselot A, Cambria L, Müller M, Tuloup M, Hernandez C, Appel RD. Phenyx: about compatibility of high-throughput and pertinence in protein identification. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 84.

  4. Gras R, Hernandez D, Hernandez P, Mescam Y, Appel RD. Cooperation in Metaheuristics and Application in Bioinformatics. European Conference on Combinatorial Optimisation - ECCO XVII 2004. Beirut, Lebanon: June 2004.

  5. Hernandez D, Gras R, Appel RD. Stratégies d’exploration de l’espace des alignements locaux multiples sans indels. Quatrièmes journées francophones de recherche opérationnelle (FRANCORO IV). Fribourg, Suisse: Aug. 2004.

  6. Hernandez P, Gras R, Appel RD. Popitam loves being fed on modified MS/MS spectra. Peptide Fragmentation and identification Workshop, NIST. Gaithersburg, Maryland: May 2004.

  7. Hernandez P, Gras R, Appel RD. Popitam squints to better identify ms/ms spectra of modified peptides. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 227.

  8. Hochstrasser DF, Zimmermann-Ivol CG, Corthals GL, Appel RD, Sanchez JC. Clinical Proteomics. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 10.

  9. Hochstrasser DF, Corthals G, Sanchez JC, Appel RD, Bairoch A, Bougueleret L, Rose K. Clinical proteomics: a challenge for diagnostic laboratories and the pharma industry? AACC 2004 Annual meeting. Los Angeles, CA: July 2004.

  10. 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.

  11. 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.

  12. Masselot A, Binz PA, Cambria L, Appel RD. Phenyx: combining high-throughput and pertinence in protein identification. Third Annual HUPO Congress (proceedings in Molecular & Cell Proteomics). Beijing: Oct. 2004: 257.

  13. Masselot A, Binz PA, Cambria L, Appel RD. Phenyx: Manage Protein Identification With Flexibility and Pertinence. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 168.

  14. Mostaguir K, Hoogland C, Appel RD. The Make2D-DB II Tool: building a large federated 2-DE database network. ISMB/ECCB04. Glasgow: July 2004.

  15. Mostaguir K, Hoogland C, Appel RD. The Make2D-DB II Tool: building a large federated 2-DE gel databases network. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 294.

  16. 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.

  17. 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.

  18. Potts A, Walther D, Catherinet S, Bienvenut W, Appel RD, Quadroni M. The application of a software tool for the two-dimensional representation of LC-MS data to the analysis of post-translational modifications and the comparison of complex peptide mixtures. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 323.

  19. Quadroni M, Walther D, Appel R, Bienvenut W, Potts A. Comparative mass spectrometric analysis of complex peptide mixtures using a novel software tool for two-dimensional data visualization. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 150.

  20. 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. Exploring the proteome and transcriptome of Staphylococcus aureus. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 352.

  21. Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Hochstrasser DF, Appel RD. Why not exploit ms data to its fullest? Using data-redundancy in mass spectra. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 41.

  22. Zimmermann-Ivol CG, Vaezzadeh A, Converset V, Hoogland C, Walther D, Catherinet S, Tuloup M, Hernandez C, Müller M, Moll S, Corthals GL, Pasquarello C, Appel RD, Hochstrasser DF. Distribution and visualisation of urine protein profile with the Molecular Scanner. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 411.

  23. Zimmermann-Ivol CG, Vaezzadeh A, Demalte I, Converset V, Di Dio J, Scherl A, Corthals GL, Appel RD, Hochstrasser DF. The Molecular Scanner. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 136.

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