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Complete list of publications

Thesis

1. Gay, S., Datamining in proteomics: extracting knowledge from peptide mass fingerprinting spectra. 2002, Thèse de doctorat ès sciences, mention interdisciplinaire (Universitè de Genève).

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

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

4. Mostaguir, K., Managing and Publishing Proteomics Data - The Make2D-DB II Tool, an Integrative Environment Applied to 2-DE Datasets. 2008, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

5. Müller, M., Molecular Scanner Data Analysis. 2003, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

6. Quandt, A., swissPIT: A Grid-based analysis platform for workflow oriented mining of mass spectra. 2008, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

7. Zangger, N., Development and Validation of a Novel Method for Clustering Protein Sequences and Detecting Diagnostic Motifs. 2007, Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).

Journal Articles

1. Ahrné, E., Masselot, A., Binz, P.A., Mueller, M., and Lisacek, F., A simple workflow to increase MS2 identification rate by subsequent spectral library search. Proteomics, 2009. 9(6): p. 1731-1736.

2. Appel, R., Hochstrasser, D., Roch, C., Funk, M., Muller, A.F., and Pellegrini, C., Automatic classification of two-dimensional gel electrophoresis pictures by heuristic clustering analysis: a step toward machine learning, in Electrophoresis. 1988. p. 136-142.

3. Appel, R.D., Bairoch, A., and Hochstrasser, D.F., A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends in Biochemical Sciences, 1994. 19(6): p. 258-260.

4. Appel, R.D., Bairoch, A., Sanchez, J.C., Vargas, J.R., Golaz, O., Pasquali, C., and Hochstrasser, D.F., Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data. Electrophoresis, 1996. 17(3): p. 540-546.

5. Appel, R.D., Hochstrasser, D.F., Funk, M., Vargas, J.R., Pellegrini, C., Muller, A.F., and Scherrer, J.R., The MELANIE project: from a biopsy to automatic protein map interpretation by computer. Electrophoresis, 1991. 12(10): p. 722-735.

6. Appel, R.D., Palagi, P.M., Walther, D., Vargas, J.R., Sanchez, J.C., Ravier, F., Pasquali, C., and Hochstrasser, D.F., Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface. Electrophoresis, 1997. 18(15): p. 2724-2734.

7. Appel, R.D., Sanchez, J.C., Bairoch, A., Golaz, O., Miu, M., Vargas, J.R., and Hochstrasser, D.F., SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images. Electrophoresis, 1993. 14(11): p. 1232-1238.

8. Appel, R.D., Sanchez, J.C., Bairoch, A., Golaz, O., Ravier, F., Pasquali, C., Hughes, G.J., and Hochstrasser, D.F., The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis. Nucleic Acids Research, 1994. 22(17): p. 3581-3582.

9. Appel, R.D., Sanchez, J.C., Bairoch, A., Golaz, O., Ravier, F., Pasquali, C., Hughes, G.J., and Hochstrasser, D.F., The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995. Nucleic Acids Research, 1996. 24(1): p. 180-181.

10. Appel, R.D., Vargas, J.R., Palagi, P.M., Walther, D., and Hochstrasser, D.F., Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis, 1997. 18(15): p. 2735-2748.

11. Baujard, O., Baujard, V., Aurel, S., Boyer, C., and Appel, R.D., MARVIN, multi-agent softbot to retrieve multilingual medical information on the Web. Med.Inform.(Lond), 1998. 23(3): p. 187-191.

12. Baujard, O., Baujard, V., Aurel, S., Boyer, C., and Appel, R.D., Trends in medical information retrieval on Internet. Computers in Biology and Medicine, 1998. 28(5): p. 589-601.

13. Bienvenut, W.V., Hoogland, C., Greco, A., Heller, M., Gasteiger, E., Appel, R.D., Diaz, J.J., Sanchez, J.C., and Hochstrasser, D.F., Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting. Rapid Communications in Mass Spectrometry, 2002. 16(6): p. 616-626.

14. Bienvenut, W.V., Sanchez, J.C., Karmime, A., Rouge, V., Rose, K., Binz, P.A., and Hochstrasser, D.F., Toward a clinical molecular scanner for proteome research: parallel protein chemical processing before and during western blot. Analytical Chemistry, 1999. 71(21): p. 4800-4807.

15. Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Mass spectrometry-based proteomics: current status and potential use in clinical chemistry. Clin.Chem.Lab Med., 2003. 41(12): p. 1540-1551.

16. Binz, P.A., Müller, M., Hoogland, C., Zimmermann, C., Pasquarello, C., Corthals, G., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., The molecular scanner: concept and developments. Current Opinion in Biotechnology, 2004. 15(1): p. 17-23.

17. Binz, P.A., Müller, M., Walther, D., Bienvenut, W.V., Gras, R., Hoogland, C., Bouchet, G., Gasteiger, E., Fabbretti, R., Gay, S., Palagi, P., Wilkins, M.R., Rouge, V., Tonella, L., Paesano, S., Rossellat, G., Karmime, A., Bairoch, A., Sanchez, J.C., Appel, R.D., and Hochstrasser, D.F., A molecular scanner to automate proteomic research and to display proteome images. Analytical Chemistry, 1999. 71(21): p. 4981-4988.

18. Bologna, G., A model for single and multiple knowledge based networks. Artificial Intelligence in Medicine, 2003. 28(2): p. 141-163.

19. Bologna, G., Yvon, C., Duvaud, S., and Veuthey, A.L., N-Terminal myristoylation predictions by ensembles of neural networks. Proteomics, 2004. 4(6): p. 1626-1632.

20. Borst, F., Appel, R., Baud, R., Ligier, Y., and Scherrer, J.R., Happy birthday DIOGENE: a hospital information system born 20 years ago. Int.J.Med.Inform., 1999. 54(3): p. 157-167.

21. Boyer, C., Baujard, O., Baujard, V., Aurel, S., Selby, M., and Appel, R.D., Health On the Net automated database of health and medical information. Int.J.Med.Inform., 1997. 47(1-2): p. 27-29.

22. Boyer, C., Selby, M., Scherrer, J.R., and Appel, R.D., The Health On the Net Code of Conduct for medical and health Websites. Computers in Biology and Medicine, 1998. 28(5): p. 603-610.

23. 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.

24. 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.

25. Coute, Y., Hernandez, C., Appel, R.D., Sanchez, J.C., and Margolles, A., Labeling of Bifidobacterium longum cells with 13C-substituted leucine for quantitative proteomic analyses. Applied and Environmental Microbiology, 2007. 73(17): p. 5653-5656.

26. Cremona, O., Muda, M., Appel, R.D., Frutiger, S., Hughes, G.J., Hochstrasser, D.F., Geinoz, A., and Gabbiani, G., Differential protein expression in aortic smooth muscle cells cultured from newborn and aged rats. Experimental Cell Research, 1995. 217(2): p. 280-287.

27. Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D., and Bairoch, A., ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 2003. 31(13): p. 3784-3788.

28. Gay, S., Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis, 1999. 20(18): p. 3527-3534.

29. Gay, S., Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics., 2002. 2(10): p. 1374-1391.

30. Geissbuhler, A., Lovis, C., Spahni, S., Appel, R.D., Ratib, O., Boyer, C., Hochstrasser, D.F., and Baud, R., A humanist's legacy in medical informatics: visions and accomplishments of Professor Jean-Raoul Scherrer. Methods of Information in Medicine, 2002. 41(3): p. 237-242.

31. Golaz, O., Hughes, G.J., Frutiger, S., Paquet, N., Bairoch, A., Pasquali, C., Sanchez, J.C., Tissot, J.D., Appel, R.D., and Walzer, C., Plasma and red blood cell protein maps: update 1993. Electrophoresis, 1993. 14(11): p. 1223-1231.

32. Golaz, O., Wilkins, M.R., Sanchez, J.C., Appel, R.D., Hochstrasser, D.F., and Williams, K.L., Identification of proteins by their amino acid composition: an evaluation of the method. Electrophoresis, 1996. 17(3): p. 573-579.

33. Gras, R., Hernandez, D., Hernandez, P., Zangger, N., Mescam, Y., Frey, J., Martin, O., Nicolas, J., and Appel, R.D., Cooperative Metaheuristics for Exploring Proteomic Data. Artificial Intelligence Review, 2003. 20(1-2): p. 95-120.

34. Gras, R. and Muller, M., Computational aspects of protein identification by mass spectrometry. Curr.Opin.Mol.Ther., 2001. 3(6): p. 526-532.

35. Gras, R., Müller, M., Gasteiger, E., Gay, S., Binz, P.A., Bienvenut, W., Hoogland, C., Sanchez, J.C., Bairoch, A., Hochstrasser, D.F., and Appel, R.D., Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis, 1999. 20(18): p. 3535-3550.

36. Hernandez, D., Gras, R., and Appel, R., MoDEL: an efficient strategy for ungapped local multiple alignment. Comput.Biol.Chem., 2004. 28(2): p. 119-128.

37. Hernandez, P., Gras, R., Frey, J., and Appel, R.D., Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics., 2003. 3(6): p. 870-878.

38. 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.

39. Hochstrasser, D., Augsburger, V., Funk, M., Appel, R., Pellegrini, C., and Muller, A.F., Immobilized pH gradients in capillary tubes and two-dimensional gel electrophoresis. Electrophoresis, 1986. 7(11): p. 505-511.

40. Hochstrasser, D., Roux, P., Dayer, J.M., Cruchaud, A., Appel, R., Funk, M., Pellegrini, C., and Muller, A.F., Cartographies protéiques de cellules circulantes normales: lymphocytes et monocytes. Schweizerische Medizinische Wochenschrift.Journal Suisse de Medecine, 1986. 116(50): p. 1773-1775.

41. Hochstrasser, D.F., Appel, R.D., Golaz, O., Pasquali, C., Sanchez, J.C., and Bairoch, A., Sharing of worldwide spread knowledge using hypermedia facilities & fast communication protocols (Mosaic and World Wide Web): the example of ExPASy. Methods of Information in Medicine, 1995. 34(1-2): p. 75-78.

42. Hochstrasser, D.F., Appel, R.D., Vargas, R., Perrier, R., Vurlod, J.F., Ravier, F., Pasquali, C., Funk, M., Pellegrini, C., and Muller, A.F., A clinical molecular scanner: the Melanie project. MD Computing, 1991. 8(2): p. 85-91.

43. Hochstrasser, D.F., Frutiger, S., Paquet, N., Bairoch, A., Ravier, F., Pasquali, C., Sanchez, J.C., Tissot, J.D., Bjellqvist, B., Vargas, R., Appel, R.D., and Hughes, G.J., Human liver protein map: A reference database established by microsequencing and gel comparison. Electrophoresis, 1992. 13(1): p. 992-1001.

44. Hochstrasser, D.F., Funk, M., Appel, R.D., Pun, T., James, R.W., Hochstrasser, A.C., Scherrer, J.R., Pellegrini, C., and Muller, A.F., From biopsy to automatic diagnosis. Schweizerische Medizinische Wochenschrift.Journal Suisse de Medecine, 1990. 120(49): p. 1862-1866.

45. Hochstrasser, D.F., Sanchez, J.C., and Appel, R.D., Proteomics and its trends facing nature's complexity. Proteomics., 2002. 2(7): p. 807-812.

46. Hoogland, C., Baujard, V., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., Make2ddb: a simple package to set up a two-dimensional electrophoresis database for the World Wide Web. Electrophoresis, 1997. 18(15): p. 2755-2758.

47. Hoogland, C., Lion, N., Palagi, P.M., Sanchez, J.C., and Tissot, J.D., SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. Proteomics, 2005. 5(12): p. 3045-3047.

48. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F., The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server. Journal of Proteomics, 2008. 71(2): p. 245-248.

49. Hoogland, C., Mostaguir, K., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., SWISS-2DPAGE, ten years later. Proteomics., 2004. 4(8): p. 2352-2356.

50. Hoogland, C., Sanchez, J.C., Tonella, L., Bairoch, A., Hochstrasser, D.F., and Appel, R.D., Current status of the SWISS-2DPAGE database. Nucleic Acids Research, 1998. 26(1): p. 332-333.

51. Hoogland, C., Sanchez, J.C., Tonella, L., Bairoch, A., Hochstrasser, D.F., and Appel, R.D., The SWISS-2DPAGE database: what has changed during the last year. Nucleic Acids Research, 1999. 27(1): p. 289-291.

52. Hoogland, C., Sanchez, J.C., Tonella, L., Binz, P.A., Bairoch, A., Hochstrasser, D.F., and Appel, R.D., The 1999 SWISS-2DPAGE database update. Nucleic Acids Research, 2000. 28(1): p. 286-288.

53. Hoogland, C., Sanchez, J.C., Walther, D., Baujard, V., Baujard, O., Tonella, L., Hochstrasser, D.F., and Appel, R.D., Two-dimensional electrophoresis resources available from ExPASy. Electrophoresis, 1999. 20(18): p. 3568-3571.

54. Hoogland, C., Walther, D., Palagi, P.M., Bouchet, G., Mostaguir, K., Robin, X., Appel, R.D., and Lisacek, F., A suite of tools to analyse and publish 2-DE data. Proteomics., 2008. 8(23-24): p. 4907-4909.

55. Hughes, G.J., Frutiger, S., Paquet, N., Pasquali, C., Sanchez, J.C., Tissot, J.D., Bairoch, A., Appel, R.D., and Hochstrasser, D.F., Human liver protein map: update 1993. Electrophoresis, 1993. 14(11): p. 1216-1222.

56. Jaconi, M.E., Theler, J.M., Schlegel, W., Appel, R.D., Wright, S.D., and Lew, P.D., Multiple elevations of cytosolic-free Ca2+ in human neutrophils: initiation by adherence receptors of the integrin family. Journal of Cell Biology, 1991. 112(6): p. 1249-1257.

57. James, R.W., Hochstrasser, D., Tissot, J.D., Funk, M., Appel, R., Barja, F., Pellegrini, C., Muller, A.F., and Pometta, D., Protein heterogeneity of lipoprotein particles containing apolipoprotein A-I without apolipoprotein A-II and apolipoprotein A-I with apolipoprotein A-II isolated from human plasma. Journal of Lipid Research, 1988. 29(12): p. 1557-1571.

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

59. Lisacek, F., Chichester, C., Gonnet, P., Jaillet, O., Kappus, S., Nikitin, F., Roland, P., Rossier, G., Truong, L., and Appel, R., Shaping biological knowledge: applications in proteomics. Comparative and Functional Genomics, 2004. 5: p. 190-195.

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

61. Lisacek, F., Hoogland, C., Lescuyer, P., Hochstrasser, D.F., and Appel, R.D., Using bioinformatic resources in the proteomic analysis of biological fluids. Proteomics - Clinical Applications, 2007. 1(8): p. 900-915.

62. Mascarini, C., Ratib, O., Trayser, G., Ligier, Y., and Appel, R.D., In-house access to PACS images and related data through World Wide Web. European Journal of Radiology, 1996. 22(3): p. 218-220.

63. Mostaguir, K., Hoogland, C., Binz, P.A., and Appel, R.D., The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases. Proteomics., 2003. 3(8): p. 1441-1444.

64. Müller, M., Gras, R., Appel, R.D., Bienvenut, W.V., and Hochstrasser, D.F., Visualization and analysis of molecular scanner peptide mass spectra. Journal of the American Society for Mass Spectrometry, 2002. 13(3): p. 221-231.

65. Müller, M., Gras, R., Binz, P.A., Hochstrasser, D.F., and Appel, R.D., Molecular scanner experiment with human plasma: improving protein identification by using intensity distributions of matching peptide masses. Proteomics., 2002. 2(10): p. 1413-1425.

66. Nikitin, F., Rance, B., Itoh, M., Kanehisa, M., and Lisacek, F., Using protein motif combinations to update KEGG pathway maps and orthologue tables. Genome Inform., 2004. 15(2): p. 266-275.

67. 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.

68. Palagi, P.M., Walther, D., Quadroni, M., Catherinet, S., Burgess, J., Zimmermann-Ivol, C.G., Sanchez, J.C., Binz, P.A., Hochstrasser, D.F., and Appel, R.D., MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics., 2005. 5(9): p. 2381-2384.

69. Pasquali, C., Frutiger, S., Wilkins, M.R., Hughes, G.J., Appel, R.D., Bairoch, A., Schaller, D., Sanchez, J.C., and Hochstrasser, D.F., Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis, 1996. 17(3): p. 547-555.

70. Peitsch, M.C., Wilkins, M.R., Tonella, L., Sanchez, J.C., Appel, R.D., and Hochstrasser, D.F., Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: the example of Escherichia coli. Electrophoresis, 1997. 18(3-4): p. 498-501.

71. Pun, T., Hochstrasser, D.F., Appel, R.D., Funk, M., Villars-Augsburger, V., and Pellegrini, C., Computerized classification of two-dimensional gel electrophoretograms by correspondence analysis and ascendant hierarchical clustering. Applied and Theoretical Electrophoresis, 1988. 1(1): p. 3-9.

72. Quandt, A., Hernandez, P., Masselot, A., Hernandez, C., Maffioletti, S., Pautasso, C., Appel, R.D., and Lisacek, F., swissPIT: A novel approach for pipelined analysis of mass spectrometry data. Bioinformatics, 2008. 24(11): p. 1416-1417.

73. Quandt, A., Hernandez, P., Masselot, A., Hernandez, C., Maffioletti, S., Pautasso, C., Appel, R.D., and Lisacek, F., swissPIT: A workflow-based platform for analyzing Tandem-MS spectra using the Grid. Proteomics, 2009. In press.

74. Rance, B., Lisacek, F., and Froidevaux, C., SNK: a new method for extracting sequential nuggets of knowledge from protein families. BMC Bioinformatics, 2009. Submitted.

75. Robin, X., Hoogland, C., Appel, R.D., and Lisacek, F., MIAPEGelDB, a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. Journal of Proteomics, 2008. 71(2): p. 249-251.

76. Ruch, P., Baud, R., Chichester, C., Geissbuhler, A., Lisacek, F., Marty, J., Rebholz-Schuhmann, D., Tbahriti, I., and Veuthey, A.L., Extracting key sentences with latent argumentative structuring. Studies in Health Technology and Informatics, 2005. 116: p. 835-840.

77. Ruch, P., Geissbuhler, A., Gobeill, J., Lisacek, F., Tbahriti, I., Veuthey, A.L., and Aronson, A.R., Using Discourse Analysis to Improve Text Categorization in MEDLINE. Studies in Health Technology and Informatics, 2007. 129: p. 710-715.

78. Sanchez, J.C., Appel, R.D., Golaz, O., Pasquali, C., Ravier, F., Bairoch, A., and Hochstrasser, D.F., Inside SWISS-2DPAGE database. Electrophoresis, 1995. 16(7): p. 1131-1151.

79. Sanchez, J.C., Chiappe, D., Converset, V., Hoogland, C., Binz, P.A., Paesano, S., Appel, R.D., Wang, S., Sennitt, M., Nolan, A., Cawthorne, M.A., and Hochstrasser, D.F., The mouse SWISS-2D PAGE database: a tool for proteomics study of diabetes and obesity. Proteomics., 2001. 1(1): p. 136-163.

80. Sanchez, J.C., Golaz, O., Frutiger, S., Schaller, D., Appel, R.D., Bairoch, A., Hughes, G.J., and Hochstrasser, D.F., The yeast SWISS-2DPAGE database. Electrophoresis, 1996. 17(3): p. 556-565.

81. Sanchez, J.C., Wirth, P., Jaccoud, S., Appel, R.D., Sarto, C., Wilkins, M.R., and Hochstrasser, D.F., Simultaneous analysis of cyclin and oncogene expression using multiple monoclonal antibody immunoblots. Electrophoresis, 1997. 18(3-4): p. 638-641.

82. Sarto, C., Binz, P.A., and Mocarelli, P., Heat shock proteins in human cancer. Electrophoresis, 2000. 21(6): p. 1218-1226.

83. Scherl, A., Francois, P., Bento, M., Deshusses, J.M., Charbonnier, Y., Converset, V., Huyghe, A., Walter, N., Hoogland, C., Appel, R.D., Sanchez, J.C., Zimmermann-Ivol, C.G., Corthals, G.L., Hochstrasser, D.F., and Schrenzel, J., Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth. Journal of Microbiological Methods, 2005. 60(2): p. 247-257.

84. 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.

85. Scherl, A., Shaffer, S.A., Taylor, G.K., Hernandez, P., Appel, R.D., Binz, P.A., and Goodlett, D.R., On the benefits of acquiring peptide fragment ions at high measured mass accuracy. J Am Soc Mass Spectrom., 2008. 19(6): p. 891-901.

86. Scherl, A., Zimmermann-Ivol, C.G., Di, D.J., Vaezzadeh, A.R., Binz, P.A., mez-Droz, M., Cochard, R., Sanchez, J.C., Gluckmann, M., and Hochstrasser, D.F., Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect. Rapid Communications in Mass Spectrometry, 2005. 19(5): p. 605-610.

87. Schuemie, M., Chichester, C., Lisacek, F., Coute, Y., Roes, P.J., Sanchez, J.C., Kors, J., and Mons, B., Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE. Proteomics, 2007. 7(6): p. 921-931.

88. Stephan, C., Hamacher, M., Bluggel, M., Korting, G., Chamrad, D., Scheer, C., Marcus, K., Reidegeld, K.A., Lohaus, C., Schafer, H., Martens, L., Jones, P., Muller, M., Auyeung, K., Taylor, C., Binz, P.A., Thiele, H., Parkinson, D., Meyer, H.E., and Apweiler, R., 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame. Proteomics, 2005. 5(14): p. 3560-3562.

89. 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.

90. Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian, R.K., Jr., Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E.W., Dunn, M.J., Heck, A.J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T.A., Patterson, S.D., Ping, P., Seymour, S.L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T.M., Whitelegge, J.P., Wilkins, M.R., Xenarios, I., Yates, J.R., III, and Hermjakob, H., The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol., 2007. 25(8): p. 887-893.

91. 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.

92. Tonella, L., Hoogland, C., Binz, P.A., Appel, R.D., Hochstrasser, D.F., and Sanchez, J.C., New perspectives in the Escherichia coli proteome investigation. Proteomics., 2001. 1(3): p. 409-423.

93. Tonella, L., Walsh, B.J., Sanchez, J.C., Ou, K., Wilkins, M.R., Tyler, M., Frutiger, S., Gooley, A.A., Pescaru, I., Appel, R.D., Yan, J.X., Bairoch, A., Hoogland, C., Morch, F.S., Hughes, G.J., Williams, K.L., and Hochstrasser, D.F., '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis, 1998. 19(11): p. 1960-1971.

94. Tsiknakis, M., Grangeat, P., Binz, P.A., Potamias, G., Lisacek, F., Gerfault, L., Paulus, C., Manakanatas, D., Kritsotakis, V., Kondylakis, H., Perez, M., Plexousakis, D., Kaforou, S., and Kafetzopoulos, D., Functional specifications of an integrated proteomics information management and analysis platform. Conf.Proc.IEEE Eng Med.Biol.Soc, 2007. 1: p. 6064-6068.

95. Vaezzadeh, A.R., Hernandez, C., Vadas, O., Deshusses, J.J., Lescuyer, P., Lisacek, F., and Hochstrasser, D.F., PICarver: a software tool and strategy for peptides isoelectric focusing. J Proteome.Res, 2008. 7(10): p. 4336-4345.

96. Wilkins, M.R., Gasteiger, E., Gooley, A.A., Herbert, B.R., Molloy, M.P., Binz, P.A., Ou, K., Sanchez, J.C., Bairoch, A., Williams, K.L., and Hochstrasser, D.F., High-throughput mass spectrometric discovery of protein post-translational modifications. Journal of Molecular Biology, 1999. 289(3): p. 645-657.

97. Wilkins, M.R., Gasteiger, E., Sanchez, J.C., Appel, R.D., and Hochstrasser, D.F., Protein identification with sequence tags. Current Biology, 1996. 6(12): p. 1543-1544.

98. Wilkins, M.R., Gasteiger, E., Tonella, L., Ou, K., Tyler, M., Sanchez, J.C., Gooley, A.A., Walsh, B.J., Bairoch, A., Appel, R.D., Williams, K.L., and Hochstrasser, D.F., Protein identification with N and C-terminal sequence tags in proteome projects. Journal of Molecular Biology, 1998. 278(3): p. 599-608.

99. Wilkins, M.R., Gasteiger, E., Wheeler, C.H., Lindskog, I., Sanchez, J.C., Bairoch, A., Appel, R.D., Dunn, M.J., and Hochstrasser, D.F., Multiple parameter cross-species protein identification using MultiIdent--a world-wide web accessible tool. Electrophoresis, 1998. 19(18): p. 3199-3206.

100. Wilkins, M.R., Hochstrasser, D.F., Sanchez, J.C., Bairoch, A., and Appel, R.D., Integrating two-dimensional gel databases using the Melanie II software. Trends in Biochemical Sciences, 1996. 21(12): p. 496-497.

101. Wilkins, M.R., Lindskog, I., Gasteiger, E., Bairoch, A., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., Detailed peptide characterization using PEPTIDEMASS--a World-Wide-Web-accessible tool. Electrophoresis, 1997. 18(3-4): p. 403-408.

102. Wilkins, M.R., Ou, K., Appel, R.D., Sanchez, J.C., Yan, J.X., Golaz, O., Farnsworth, V., Cartier, P., Hochstrasser, D.F., Williams, K.L., and Gooley, A.A., Rapid protein identification using N-terminal "sequence tag" and amino acid analysis. Biochemical and Biophysical Research Communications, 1996. 221(3): p. 609-613.

103. Wilkins, M.R., Pasquali, C., Appel, R.D., Ou, K., Golaz, O., Sanchez, J.C., Yan, J.X., Gooley, A.A., Hughes, G., Humphery-Smith, I., Williams, K.L., and Hochstrasser, D.F., From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N.Y.), 1996. 14(1): p. 61-65.

104. Wilkins, M.R., Sanchez, J.C., Gooley, A.A., Appel, R.D., Humphery-Smith, I., Hochstrasser, D.F., and Williams, K.L., Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol.Genet.Eng Rev., 1996. 13: p. 19-50.

105. Yan, J.X., Sanchez, J.C., Binz, P.A., Williams, K.L., and Hochstrasser, D.F., Method for identification and quantitative analysis of protein lysine methylation using matrix-assisted laser desorption/ionization--time-of-flight mass spectrometry and amino acid analysis. Electrophoresis, 1999. 20(4-5): p. 749-754.

Journal Articles - non peer-reviewed

1. Albar, J.P., Corthals, G.L., Gil, C., James, P., Jensen, O.N., Palagi, P.M., and Penque, D., Promoting Proteomics Knowledge in Europe: report on the Activities of the EuPA Education Committee. Proteomics, 2007. 7(S1): p. 90-94.

2. Appel, R.D., Hochstrasser, D.F., and Bairoch, A., Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical? Labolife, 1993. 4: p. 7-8.

3. Appel, R.D., Hochstrasser, D.F., and Pellegrini, C., Le projet Melanie. Cahier spécial de la Faculté des Sciences, 1993.

4. Bairoch, A., Appel, R.D., and Peitsch, M.C., The ExPASy WWW Server - a Tool for Proteome Research. Protein Data Bank Quaterly Newsletter, 1997. 81: p. 5-7.

5. Bairoch, A., Gasteiger, E., Gattiker, A., Hoogland, C., Lachaize, C., Mostaguir, K., Ivanyi, I., and Appel, R.D. The ExPASy proteome WWW server in 2003. 2003; Available from: http://www.expasy.org/doc/expasy.pdf.

6. Binz, P.A., Barkovich, R., Beavis, R.C., Creasy, D., Horn, D.M., Julian, R.K., Jr., Seymour, S.L., Taylor, C.F., and Vandenbrouck, Y., Guidelines for reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol., 2008. 26(8): p. 862.

7. Boyer, C., Appel, R.D., Griesser, V., and Scherrer, J.R., Internet pour les m‚decins: un outil d'aujourd'hui et de demain. Revue Médicale de la Suisse Romande, 1999. 119: p. 137-144.

8. Boyer, C., Appel, R.D., and Scherrer, J.R., Internet et la m‚decine: solutions propos‚es par la Fondation Health On the Net. Cahiers Psychiatriques, 1998. 24: p. 137-144.

9. Dunn, M.J., Gil, C., Kleinhammer, C., Lottspeich, F., Pennington, S., Sanchez, J.C., Albar, J.P., Bini, L., Corrales, F., Corthals, G., Fountoulakis, M.M., Hoogland, C., James, P., Jensen, O.N., Jimenez, C., Jorrin-Novo, J., Kraus, H.J., Meyer, H., Noukakis, D., Palagi, P.M., Penque, D., Quinn, A., and Rabilloud, T., EuPA achieves visibility - An activity report on the first three years. Journal of Proteomics, 2008. 71(1): p. 11-18.

10. Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P.A., Borthwick, A., Cash, P., Day, B.W., Friedman, D.B., Garland, D., Gutstein, H.B., Hoogland, C., Jones, N.A., Khan, A., Klose, J., Lamond, A.I., Lemkin, P.F., Lilley, K.S., Minden, J., Morris, N.J., Paton, N.W., Pisano, M.R., Prime, J.E., Rabilloud, T., Stead, D.A., Taylor, C.F., Voshol, H., Wipat, A., and Jones, A.R., Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol., 2008. 26(8): p. 863-864.

11. Hochstrasser, D., Funk, M., Appel, R., James, R., Hochstrasser, A.C., Scherrer, J.R., Pellegrini, C., and Muller, A.F., Applications Cliniques de l'Electrophorèse Bidimensionnelle. Spectra Biologie, 1990. 90/1: p. 45-46.

12. Hochstrasser, D.F., Sanchez, J.C., Golaz, O., Tissot, J.D., and Appel, R.D., Cartographie protéique du sérum et du plasma. Médicine & Hygiène, 1995. 53: p. 988-992.

13. Montecchi-Palazzi, L., Beavis, R., Binz, P.A., Chalkley, R.J., Cottrell, J., Creasy, D., Shofstahl, J., Seymour, S.L., and Garavelli, J.S., The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol., 2008. 26(8): p. 864-866.

14. Orchard, S., Albar, J.P., Deutsch, E.W., Binz, P.A., Jones, A.R., Creasy, D., and Hermjakob, H., Annual Spring Meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain. Proteomics., 2008. 8(20): p. 4168-4172.

15. Orchard, S., Hermjakob, H., Binz, P.A., Hoogland, C., Taylor, C.F., Zhu, W., Julian, R.K., Jr., and 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(2): p. 337-339.

16. 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.

17. Orchard, S., Hoogland, C., Bairoch, A., Eisenacher, M., Kraus, H.J., and Binz, P.A., Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands. Proteomics, 2009. 9(3): p. 499-501.

18. Orchard, S., Martens, L., Tasman, J., Binz, P.A., Albar, J.P., and Hermjakob, H., 6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea. Proteomics., 2008. 8(7): p. 1331-1333.

19. Pellegrini, C., Funk, M., and Appel, R.D., Le traitement de l'image. Cahiers de la faculté des sciences, 1985. p. 3-14.

20. Pellegrini, C., Hochstrasser, D., Appel, R., and Funk, M., Informatique et électrophorèse : de l'image d'une biopsie tissulaire au diagnostic automatique. Fonds National Suisse de la Recherche Scientifique, 1987.

21. Sanchez, J.C., Appel, R., and Hochstrasser, D.F., L'électrophorèse bidimensionnelle des protéines. Laboratoire et Médecine, 1998. 25.

22. Taylor, C.F., Binz, P.A., Aebersold, R., Affolter, M., Barkovich, R., Deutsch, E.W., Horn, D.M., Huhmer, A., Kussmann, M., Lilley, K., Macht, M., Mann, M., Muller, D., Neubert, T.A., Nickson, J., Patterson, S.D., Raso, R., Resing, K., Seymour, S.L., Tsugita, A., Xenarios, I., Zeng, R., and Julian, R.K., Jr., Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol., 2008. 26(8): p. 860-861.

23. Taylor, C.F., Field, D., Sansone, S.A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C.A., Binz, P.A., Bogue, M., Booth, T., Brazma, A., Brinkman, R.R., Michael, C.A., Deutsch, E.W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J.M., Hardy, N.W., Hermjakob, H., Julian, R.K., Jr., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Novere, N.L., Leebens-Mack, J., Lewis, S.E., Lord, P., Mallon, A.M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J.M., Robertson, D.G., Rocca-Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo-Lopez, J., Scheuermann, R.H., Schober, D., Smith, B., Snape, J., Stoeckert, C.J., Jr., Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J., and Wiemann, S., Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol., 2008. 26(8): p. 889-896.

24. Vargas, A.R., Balderrama, J.R., Hoogland, C., Gasteiger, E., Ivanyi, I., Bairoch, A., Appel, R.D., and Hochstrasser, D.F., El nuovo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org. Acta Nova, 2002. 2: p. 72-81.

25. 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.

Conference Proceedings

1. Appel, R., Funk, M., Hochstrasser, D., Muller, A.F., and Pellegrini, C. Un systéme expert d'aide à l'analyse et l'interprétation d'images médicales. in Cognitiva. 1985. Paris.

2. Appel, R., Funk, M., Hochstrasser, D., Muller, A.F., Pellegrini, C., Galteau, and Siest, Mélanie, un système expert d'aide à l'analyse et à l'interprétation d'électrophorèses bidimensionnelles, in Progrès Récents en Electrophorèse Bidimensionnelle. 1986, Presses Universitaires de Nancy. p. 107-116.

3. Appel, R., Funk, M., Hochstrasser, D., Pellegrini, C., and Muller, A.F. A computerized system for spot detection and analysis of two-dimensional electrophoresis images. in Computer-generated images (the state of the art) (Proceedings of Graphics Interface, Toronto 1985). 1985. Tokyo: Springer-Verlag.

4. Appel, R.D., Bologna, G., and Hochstrasser, D.F., Classification tools for Diagnostic Rule Formation from Protein Maps, in Proceedings of MIE 93, Jerusalem, April 18-22, 1993, Reichert, A., Editor. 1993, Freund Publishing House, Ltd. p. 40-44.

5. Appel, R.D., Brunet, D., Funk, M., and Hochstrasser, D.F. Improving automatic matching of 2D-PAGE images. in 2D-PAGE' 1991, Proc. Int. Meeting on Two-Dimensional Electrophoresis. 1991. London.

6. Boyer, C., Selby, M., and Appel, R.D., The Health On the Net Code of Conduct for medical and health web sites. Medinfo., 1998. 9 Pt 2: p. 1163-1166.

7. Burke, P., Appel, R.D., Funk, M., Hochstrasser, D.F., and Scherrer, J.R. Can AI Help the Physician ? in Third Annual Meeting of the Swiss Group for Artificial Intelligence and Cognitive Science SGAICO'91. 1992.

8. Burke, P., Appel, R.D., Funk, M., Vargas, R., Hochstrasser, D., and Scherrer, J.R., The Application of Distributed Articificial Intelligence to Medical Diagnosis, in AIME 91, Proc. 3rd Conference on AI in Medicine, Maastricht, Netherlands, June 1991. 1991, Springer Verlag. p. 160-172.

9. Burke, P., Appel, R.D., Vargas, J.R., Alpay, L.L., Pellegrini, C., Scherrer, J.R., and Hochstrasser, D.F. Computer Assisted Analysis of Two-Dimensional Polyacrylamide Gel Electrophoresis. in MEDINFO 92. 1992. Geneva.

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

11. Froidevaux, C., Lisacek, F., and Rance, B., Extracting Sequential Nuggets of Knowledge. Lecture Notes in Computer Science, 2007. 4653: p. 740-750.

12. Funk, M., Appel, R., Roch, C., Hochstrasser, D., Pellegrini, C., Muller, A.F., Fox, J., Fieschi, M., and Engelbrecht, R., Knowledge acquisition in expert system assisted diagnosis : a machine learning approach, in Lecture Notes in Medical Informatics (proceedings AIME, Marseille 1987). 1987, Springer-Verlag.

13. Goodman, A.M., Burke, P., Funk, M., Vargas, R.J., Snydr-Michal, J.T., Appel, R.D., and Hochstrasser, D.F. A model for a distributed database to manage large 2D-PAGE collaborative experiments. in 2D-PAGE' 1991, Proc. Int. Meeting on Two-Dimensional Electrophoresis. 1991. London.

14. Gras, R., Gasteiger, E., Binz, P.A., Müller, M., Chopard, B., and Appel, R.D. Classification automatique par algorithme génétique dans le cadre de l'identification par empreinte de masse peptidique. in Journées Fouille dans les données par la méthode d'analyse statistique implicative. 2000. Caen.

15. Hochstrasser, D., Augsburger, V., Funk, M., Appel, R., Pellegrini, C., Muller, A.F., and Dunn, M., Immobilized pH gradients in capillary tubes : effect of immobilines dilution on 2 dimensional gel pictures, in Electrophoresis '86. 1986, VCH Publishers. p. 566-568.

16. Hochstrasser, D., Funk, M., Appel, R., Pellegrini, C., Muller, A.F., Galteau, and Siest, Clinical application of automatic computer comparison of 2 D. gel electrophoresis images: diagnosis of Waldenstrom macroglobulinemia ?, in Progrès Récents en Electrophorèse Bidimensionnelle. 1986, Presses Universitaires de Nancy. p. 117-120.

17. Hochstrasser, D., Maignan, M.F., Dumont, J.M., Funk, M., Appel, R., Pellegrini, C., Muller, A.F., and Dunn, M., CCL4 induced cirrhosis of the liver: 2 dimensional gel electrophoretic analysis; biochemical and histological correlation, in Electrophoresis '86. 1986, VCH Publishers. p. 598-602.

18. Hochstrasser, D.F., Appel, R.D., Vargas, R., Perrier, R., Ravier, F., Funk, M., Pellegrini, C., Muller, A.F., and Scherrer, J.R., Clinical molecular scanner : The Melanie project, in Proceedings of HICSS-24. 1991: Hawaii. p. 626-635.

19. Lisacek, F., Chichester, C., Kaplan, A., and Sandor, A. Discovering paradigm shift patterns in biomedical abstracts: Application to neurodegenerative diseases. in CEUR Workshop Proceedings. 2005.

20. Martin, O., Gras, R., Hernandez, D., and Appel, R.D. Optimizing Genetic Algorithms Using Self-Adaptation And Explored Space Modelization. in The Fifth International Workshop on Frontiers in Evolutionary Algorithms (FEA 2003). 2003. Cary, North Carolina, USA.

21. Quandt, A., Hernandez, P., Kunzst, P., Pautasso, C., Tuloup, M., Hernandez, C., and Appel, R.D., Grid-based analysis of tandem mass spectrometry data in clinical proteomics. Studies in Health Technology and Informatics, 2007. 126: p. 13-22.

22. Vargas, A.R., Argote, G.G., Appel, R.D., Hochstrasser, D., and Pellegrini, C. Classificacion automatica de imagenes de geles de electroferesis bidimensionales mediante la classificacion heuristica. in Simposio de ciencias y tecnologia. 1998. Cochabamba, Bolivia.

23. Vargas, J.R., Appel, R.D., Hochstrasser, D.F., and Pellegrini, C., Modeling and Quantification of Protein Maps by Gaussian Fitting, in Proc. CAIP'93, 5th International Conference on Computer Analysis of Images and Patterns, Budapest, September 13-15, 1993. 1993, Springer Verlag. p. 627-633.

Books

1. Appel, R.D., MELANIE - un système d'analyse et d'interprétation automatique d'images de gels d'électrophorèse bidimensionnelle; systèmes experts et apprentissage automatique. 1988, Thèse de doctorat ès sciences, mention informatique (Université de Genève). Le concept moderne/Editions.

2. Wilkins, M.R., Appel, R.D., Williams, K.L., and Hochstrasser, D.F., Proteome Research: concepts, technology and application. 2007, Berlin Heidelberg: Springer Verlag.

3. Wilkins, M.R., Williams, K.L., Appel, R.D., and Hochstrasser, D.F., Proteome research: new frontiers in functional genomics. 1997, Berlin Heidelberg: Springer Verlag.

Book Chapters

1. Appel, R.D., Interfacing and Integrating Databases, in Proteome research: new frontiers in functional genomics, Appel, R.D., Wilkins, M.R., Williams, K.L., and Hochstrasser, D.F., Editors. 1997, Springer Verlag: Berlin Heidelberg. p. 149-175.

2. Appel, R.D., Bairoch, A., and Hochstrasser, D.F., 2-D Databases on the World Wide Web, in 2-D Proteome Analysis Protocols, Link, A.J., Editor. 1998, Humana Press: Totowa NJ. p. 383-391.

3. Appel, R.D. and Hochstrasser, D.F., Computer Analysis of 2-D Images, in 2-D Proteome Analysis Protocols, Link, A.J., Editor. 1998, Humana Press: Totowa NJ. p. 363-381.

4. Appel, R.D., Hoogland, C., Bairoch, A., and Hochstrasser, D.F., Constructing a 2-D Database for the World Wide Web, in 2-D Proteome Analysis Protocols, Link, A.J., Editor. 1999, Humana Press: Totowa NJ. p. 411-416.

5. Bienvenut, W.V., Müller, M., Palagi, P.M., Heller, M., Gay, S., Binz, P.A., Giron, M., Gasteiger, E., Jung, E., Gras, R., Sanchez, J.C., Appel, R.D., and Hochstrasser, D.F., Proteomics and mass spectrometry: some aspects and recent developments, in Mass Spectrometry and Genomic Analysis, Housby, N., Editor. 2001, Kluwer Academic Publishers: The Netherland. p. 1-53.

6. Binz, P.A., Gasteiger, E., Sanchez, J.C., Bairoch, A., Hochstrasser, D.F., and Appel, R.D., Proteome Analysis, in Bioinformatics: from Genomes to Drugs, Vol. II: applications, Lengauer, T., Editor. 2001, John Wiley & Sons. p. 69-118.

7. Binz, P.A., Wilkins, M.R., Gasteiger, E., Bairoch, A., Appel, R.D., and Hochstrasser, D.F., Internet Resources for Protein Identification and Characterization, in Microcharacterization of Proteins, Kellner, R., Lottspeich, F., and Meyer, H.E., Editors. 1999, Wiley-VCH, 2nd ed. p. 277-300.

8. Boyer, C. and Appel, R.D., Steps towards Reliable Consumer Health Information, in Consumer Informatics: Applications and Strategies in Cyber Health Care (Health Informatics), Nelson, R. and Ball, M.J., Editors. 2004, Springer Verlag. p. 80-89.

9. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A., Protein Identification and Analysis Tools on the ExPASy Server, in The Proteomics Protocols Handbook, Walker, J.M., Editor. 2005, Humana Press. p. 571-607.

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

11. Gras, R., Hernandez, P., Müller, M., and Appel, R.D., Scoring functions for mass spectrometric protein identification, in Handbook of Proteomic Methods, Conn, P.M., Editor. 2003, Humana Press. p. 477-486.

12. Hernandez, P., Binz, P.A., and Wilkins, M.R., Protein Identification in Proteome Projects, in Proteome Research: concepts, technology and application, Wilkins, M.R., Appel, R.D., Williams, K.L., and Hochstrasser, D.F., Editors. 2007, Springer Verlag: Berlin Heidelberg.

13. Hochstrasser, D.F., Corthals, G., Zimmerman, C., Scherl, A., Bougueleret, L., Collinge, J., Masselot, A., Binz, P.A., Müller, M., Bairoch, A., Appel, R.D., Sanchez, J.C., and Rose, K., Proteomics & Mass Spectrometry in Medicine, in Advances in Mass Spectrometry, Ashcroft, A.E., Brenton, G., and Monhagan, J.J., Editors. 2004, Elsevier B.V. p. 19-32.

14. Hoogland, C., Mostaguir, K., and Appel, R.D., 2-DE Databases on the World-Wide Web, in The Proteomics Protocols Handbook, Walker, J.M., Editor. 2005, Humana Press. p. 259-266.

15. Hoogland, C., Mostaguir, K., and Appel, R.D., Creating 2-DE Databases for the World Wide Web, in Methods in Molecular Biology - Two Dimensional Electrophoresis Protocols, Sheehan, D., Editor. 2009, Humana Press. p. 533-539.

16. Hoogland, C., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D., 2-D PAGE databases for proteins in human body fluids, in PROTEOMICS OF HUMAN BODY FLUIDS: Principles, Methods, and Applications, Thongboonkerd, V., Editor. 2007, Humana Press. p. 137-145.

17. Lisacek, F., Hoogland, C., Bougueleret, L., and Bairoch, A., Data Integration in Proteomics, in Proteome Research: concepts, technology and application, Wilkins, M.R., Appel, R.D., Williams, K.L., and Hochstrasser, D.F., Editors. 2007, Springer Verlag: Berlin Heidelberg. p. 145-168.

18. 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.

19. Palagi, P.M. and Lisacek, F., Analytical bioinformatics for proteomics, in Bioinformatics: A Swiss Perspective, Appel, R.D. and Feytmans, E., Editors. 2009, World Scientific: Singapore.

20. Palagi, P.M., Lisacek, F., and Appel, R.D., Database interrogation algorithms for identification of proteins in proteomic separations, in Methods in Molecular Biology - Two Dimensional Electrophoresis Protocols, Sheehan, D., Editor. 2009, Humana Press. p. 515-531.

21. Palagi, P.M., Walther, D., Bouchet, G., Voordijk, S., and Appel, R.D., Computer Analysis of 2D Images, in The Proteomics Protocols Handbook, Walker, J.M., Editor. 2005, Humana Press. p. 267-277.

22. 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.

23. Palagi, P.M., Walther, D., Zimmermann-Ivol, C.G., and Appel, R.D., Proteome Imaging, in Proteome research: concepts, technology and application, Wilkins, M.R., Appel, R.D., Williams, K.L., and Hochstrasser, D.F., Editors. 2007, Springer Verlag: Berlin Heidelberg.

24. Sanchez, J.C., Wilkins, M., Appel, R.D., and Hochstrasser, D.F., Identifying Proteins for Proteome Studies, in Protein Function: a practical approach (second edition), Creighton, E.T., Editor. 1997, IRL Press. p. 1-27.

25. Voordijk, S., Walther, D., Bouchet, G., and Appel, R.D., Image Analysis Tools in Proteomics, in Encyclopedia of the human genome. 2003, Macmillian Publishers Ltd, Nature Publishing Group. p. 404-410.

26. Wilkins, M.R., Gasteiger, E., Bairoch, A., Sanchez, J.C., Williams, K.L., Appel, R.D., and Hochstrasser, D.F., Protein Identification and Analysis Tools in the ExPASy Server, in 2-D Proteome Analysis Protocols, Link, A.J., Editor. 1998, Humana Press: Totowa NJ. p. 531-552.

Guest Edition

1. Aebersold, R., Affolter, M., Agurri, A., Elia, G., Gruissem, W., Neri, D., Palagi, P.M., Sanchez, J.C., Schlapbach, R., Rossier, J.S., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2005 Congress, Expanding proteomics 2005: Zurich, Switzerland.

2. Affolter, M., Gadola, S., Haeberli, A., Heller, M., Palagi, P.M., Sanchez, J.C., Solioz, M., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2004 Congress, Proteomics for Health 2004: Bern, Switzerland.

3. Affolter, M., Lashuel, H., Lion, N., Moniatte, M., Palagi, P.M., Quadroni, M., and Sanchez, J.C., Proceedings of the Swiss Proteomics Society, 2007 Congress, Proteomics - pushing the limits 2007: Lausanne, Switzerland.

4. Appel, R.D. and Bairoch, A., Special issue on Applications of Bioinformatics to Mass Spectrometry 2002, Proteomics, Vol.2, No. 10.

5. Appel, R.D. and Bairoch, A., Special issue on Tools and Databases for Post-Translational Modifications 2004, Proteomics, Vol.4, No. 6.

6. Appel, R.D., Dunn, M.J., and Hochstrasser, D.F., Special issue on Biomedicine and Biocomputing 1997, Electrophoresis, Vol.18, No. 15.

7. Appel, R.D., Dunn, M.J., and Hochstrasser, D.F., Special issue on Biomedicine and Biocomputing 1999, Electrophoresis, Vol.20, No. 18.

8. Appel, R.D. and Scherrer, J.R., Special Issue on Internet for Medicine and Health Care 1998, Computers in Biology and Medicine, Volume 28, Number 5.

9. Ducret, A., Eberle, A.N., Faupel, M.D., Hofsteenge, J., Jen”, P., Langen, H., Palagi, P.M., Rossier, J., Sanchez, J.C., Stöcklin, R., van Oostrum, J., and Voshol, J., Proceedings of the Swiss Proteomics Proceedings of the Swiss Proteomics Society, 2003 Congress, Understanding biological systems 2003, FontisMedia Publishers: Lausanne, Switzerland.

10. 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.

11. Lisacek, F. and Appel, R.D., Special issue on Systems Biology 2007, Proteomics, Vol.7, No. 6.

12. Palagi, P.M., Quadroni, M., Rossier, J., Sanchez, J.C., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2002 Congress, Applied Proteomics 2002, FontisMedia Publishers: Lausanne, Switzerland.

13. Palagi, P.M., Quadroni, M., Rossier, J., Sanchez, J.C., and Stöcklin, R., Special Issue on the Proceedings of the 2nd Annual Conference of the Swiss Proteomics Society. 2003, Proteomics vol.3, nø8.

14. Palagi, P.M. and Sanchez, J.C., Editorial. J Proteomics., 2008. 71(2): p. 210.

15. Palagi, P.M., Sanchez, J.C., and Stöcklin, R., Proceedings of the Swiss Proteomics Society, 2001 Congress, Functional Proteomics 2001, FontisMedia Publishers: Lausanne, Switzerland.

16. Palagi, P.M., Sanchez, J.C., and Stöcklin, R., Special Issue on the Proceedings of the 3rd Annual Congress of the Swiss Proteomics Society. 2004, Proteomics vol. 4, n.8.

17. Palagi, P.M., Sanchez, J.C., and Stöcklin, R., Special Issue on the Proceedings of the 4th Annual Congress of the Swiss Proteomics Society. 2005, Proteomics vol. 45, n.12.

18. Sanchez, J.C., Palagi, P.M., and Stöcklin, R., Special Issue on the Proceedings of the 1st Annual Conference of the Swiss Proteomics Society. 2002, Proteomics vol.2, nø7.

Abstracts & Posters

1. Ahrné, E., Masselot, A., Mueller, M., Mauron, Y., Mylonas, R., Vaezzadeh, A., Binz, P.A., Appel, R.D., and Lisacek, F. More (and faster) MS/MS identifications: combining on-the-fly spectral library search (spectraST) and sequence database search (Phenyx). in SPS'07. 2007. Lausanne, Switzerland.

2. Ahrné, E., Masselot, A., Mueller, M., Mauron, Y., Mylonas, R., Vaezzadeh, A., Binz, P.A., Appel, R.D., and Lisacek, F. More (and faster) MS/MS identifications: combining on-the-fly spectral library search (spectraST) and sequence database search (Phenyx). in HUPO 2007. 2007. Seoul, South Korea.

3. Ahrné, E., Müller, M., Binz, P.A., Masselot, A., and Lisacek, F. Increase Identification Rate by Combining On-the-fly Spectral Library and Sequence Searches. in HUPO 2008. 2008. Amsterdam, Nederlands.

4. Alpay, L.L., Appel, R.D., and Hochstrasser, D.F. Building an Expert System for Obtaining Diagnoses from Protein Maps. in MEDINFO 92. 1992. Geneva.

5. Appel, R., Funk, M., Hochstrasser, D., Muller, A.F., and Pellegrini, C. Un systéme interactif de traitement d'images d'électrophorèse bidimensionnelle. in International Electronic Image Week. 1986. Nice.

6. Appel, R.D. Current and future challenges in proteome informatics. in BC2, Basel Computational Biology Conference 2005. 2005. Basel.

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

8. Appel, R.D. Proteomics in the 3rd Millennium: Is It Possible without HPC? in Teraflop. 2001.

9. Appel, R.D. and Bairoch, A. Proteomics: back to the future. in Congress of the Swiss Proteomics Society. 2001. Geneva.

10. Appel, R.D., Bairoch, A., Miu, M., Sanchez, J.C., Golaz, O., and Hochstrasser, D.F. SWISS-2DPAGE: A 2D-PAGE Image Database. in Annual Symposium of the American Electrophoresis Society. 1993. Charleston.

11. Appel, R.D., Bairoch, A., Peitsch, M., and Hochstrasser, D.F. Browsing through Molecular Biology Data on Internet : the ExPASy World-Wide Web Server. in ACM Workshop on Information Retrieval and Genomics. 1994. Bethesda, MD.

12. Appel, R.D., Bairoch, A., Sanchez, J.C., Pasquali, C., Golaz, O., and Hochstrasser, D.F. World-Wide Web and the ExPASy Server. in Siena Meeting on 2D Electrophoresis. 1994. Siena.

13. Appel, R.D., Bairoch, A., Walther, D., Binz, P.A., Hoogland, C., Fabbretti, R., Palagi, P., Bouchet, G., Gras, R., Müller, M., Gay, S., Gasteiger, E., Sanchez, J.C., and Hochstrasser, D.F. Improving Proteomics Discovery with Bioinformatics. in Swiss Electrophoresis Society (CHEL) meeting. 1999. Montreux Palace.

14. Appel, R.D., Bairoch, A., Walther, D., Binz, P.A., Hoogland, C., Fabbretti, R., Palagi, P., Bouchet, G., Gras, R., Müller, M., Gay, S., Gasteiger, E., Sanchez, J.C., and Hochstrasser, D.F. Improving, accelerating and automating proteomics discovery with bioinformatics. in Elektrophorese Forum'99. 1999. Munich.

15. 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.

16. Appel, R.D., Binz, P.A., 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., and Zangger, N. Current developments at the Proteome Informatics Group, Swiss Institute of Bioformatics, Geneva. in Quelle informatique et bioinformatique pour la prot‚omique ? Journ‚e Rh“ne-Alpes Genopole. 2004. INRIA Rh“ne-Alpes, Montbonnot (Grenoble).

17. Appel, R.D., Hernandez, P., Tuloup, M., Walther, D., Gras, R., Müller, M., Hoogland, C., Binz, P.A., Corthals, G.L., Sanchez, J.C., and Hochstrasser, D.F. New developments in proteomatics at the Swiss Institute of Bioinformatics. in First Annual HUPO Congress. 2002. Versailles, France.

18. 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.

19. 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.

20. Appel, R.D., Hochstrasser, D.F., Funk, M., Roch, C., Pun, T., and Pellegrini, C. Automatic classification of 2 dimensional gel electrophoresis pictures by heuristic clustering. in Electrophoresis '88. 1988. Copenhagen, Denmark.

21. Appel, R.D., Hochstrasser, D.F., Vargas, R., Funk, M., Pellegrini, C., Muller, A.F., and Scherrer, J.R. New Developments Toward Automatic Medical Diagnosis in the MELANIE Project. in International Meeting of the Electrophoresis Societies. 1991. Washington DC.

22. Appel, R.D., Komorowski, H.J., Barr, C.E., and Greenes, R.A. Intelligent Focusing in Knowledge Indexing and Retrieval - The Relatedness Tool. in Symposium on Computer Applications in Medical Care. 1981. Washington.

23. Appel, R.D., Masselot, A., Budin, N., Evalet, O., Cambria, L., and Binz, P.A. What's in MS spectra? What's in databases? Take the best to identify active proteins. in HUPO 4th Annual Congress. 2005. Munich.

24. Appel, R.D., Quandt, A., Walther, D., Masselot, A., Ahrné, E., Palagi, P.M., Binz, P.A., Hernandez, P., Hochstrasser, D.F., and Lisacek, F. Has the proteome informatics bottleneck been sufficiently widened? in HUPO 6th Annual World Congress. 2007. Seoul, Korea.

25. Appel, R.D., Ratib, O., and Scherrer, J.R. Champolion : an Image File Format Translator. in Picture Archiving and Communication Systems (PACS) in Medicine. 1990. Evian, France.

26. Appel, R.D., Ratib, O., and Scherrer, J.R. The Use of a File Format Description Language for easy Handling of Images from Multiple Sources. in EuroPACS meeting. 1990. Trieste.

27. Appel, R.D., Sanchez, J.C., Bairoch, A., and Hochstrasser, D.F. Federation of two-dimensional electrophoresis databases and integration with interactive data analysis programs. in BIOINFORMATICS<-->STRUCTURE (reprinted in Folding & Design, vol. 1, supplement, 1996, p. S2). 1996. Jerusalem, Israel.

28. Appel, R.D., Sanchez, J.C., Golaz, O., and Hochstrasser, D.F. World Wide Federation of 2D gel data bases. in 2nd Siena 2D electrophoresis meeting. 1996. Siena, Italy.

29. Appel, R.D., Vargas, J.R., Bjellqvist, B., Corre, J.Y., Snydr-Michal, J., Burke, P., and Hochstrasser, D.F. Improving quantitative and qualitative analysis of 2D-PAGE images. in Annual Meeting of the Electrophoresis Society. 1992. Research Triangle Park, NC.

30. Appel, R.D., Walther, D., Binz, P.A., Hoogland, C., Fabbretti, R., Palagi, P., Bouchet, G., Gras, R., Müller, M., Gay, S., Gasteiger, E., Bairoch, A., Sanchez, J.C., and Hochstrasser, D.F. High-throughput proteomics: the need for high-performance computing. in 27th SPEEDUP Workshop. 2000. Lugano.

31. Appel, R.D., Walther, D., Binz, P.A., Hoogland, C., Gras, R., and Hochstrasser, D.F. Le rôle de la bioinformatique en protéomique. in Atelier de formation - Proteomics: new experimental approaches to unravel biological processes. 2000. Le Vésinet.

32. Appel, R.D., Walther, D., Bouchet, G., Voordijk, S., Sontot, C., Palagi, P.M., Sanchez, J.C., and Hochstrasser, D.F. Future trends in 2-DE computer analysis. in 4th Siena 2D electrophoresis meeting. 2000. Siena, Italy.

33. Bairoch, A., Appel, R.D., Offord, R.E., and Hochstrasser, D.F. Bioinformatics for Proteome Analysis in Switzerland. in 3rd Siena 2D electrophoresis meeting. 1998. Siena, Italy.

34. Baujard, O., Baujard, V., Aurel, S., Boyer, C., and Appel, R.D. MARVIN - A multi-agent softbot to retrieve multilingual medical information on the Internet. in MEDNET97 - European Congress on the Internet in Medicine. 1997. Brighton, U.K.

35. Baujard, O., Baujard, V., Aurel, S., Boyer, C., and Appel, R.D., A multi-agent softbot to retrieve medical information on Internet. Medinfo., 1998. 9 Pt 1: p. 150-154.

36. Bienvenut, W., Binz, P.A., Appel, R.D., Sanchez, J.C., Rose, K., Veuthey, J.L., and Hochstrasser, D.F. Parallel protein chemical processing during transblot. in 3rd Siena 2D electrophoresis meeting. 1998. Siena, Italy.

37. Bienvenut, W., Binz, P.A., Appel, R.D., Sanchez, J.C., Veuthey, J.L., and Hochstrasser, D.F. Towards a molecular scanner for proteome research : parallel protein chemical processing during transblot. in Journ‚e des Soci‚t‚s Suisse et Fran‡aise d'ElectrophorŠse. 1998. Bƒle.

38. Bienvenut, W.V., Heller, M., Müller, M., Paesano, S., Converset, V., Gras, R., Binz, P.A., Sanchez, J.C., Appel, R.D., and Hochstrasser, D.F. Comprehensive one step analysis by the molecular scanner: quantitative evaluation. in 4th Siena 2D electrophoresis meeting. 2000. Siena, Italy.

39. Bienvenut, W.V., Müller, M., Paesano, S., Gras, R., Binz, P.A., Converset, V., D‚on, C., Appel, R.D., Sanchez, J.C., and Hochstrasser, D.F. Comprehensive proteome analysis: the molecular scanner. in CongrŠs commun des soci‚t‚s de biochimie fran‡aise et italienne. 2000. Sienne.

40. Binz, P.A. Aspects de bioinformatique appliqu‚e … l'‚tude du phosphoprot‚ome. in Atelier phosphoprot‚ome. 2005. Cap d'Agde, France.

41. Binz, P.A. The GeneBio-SIB collaborations: where Convergence and Divergence merge into successful bioinformatics. in European Bioalpine Convention. 2008. Geneva, Switzerland.

42. Binz, P.A. Phenyx: understand and manage. in Proteomics Methods Forum. 2005. York, UK.

43. Binz, P.A. Protein Identification - Tools and Algorithms. in Joint BSPR/EBI Workshop - Bioinformatics for Proteomics. 2008. Hinxton, United Kingdom.

44. Binz, P.A. Strategies for protein identification: What data is in my data? in FinnProt meeting. 2008. Takho, Finland.

45. Binz, P.A. Validation approaches in protein identification: use cases with Penyx. in Proteomics Methods Forum. 2008. Dundee, United Kingdom.

46. Binz, P.A., Bairoch, A., Hochstrasser, D.F., and Appel, R.D. Bioinformatics in proteomics. in Proteomics Workshop. 2000. Korea.

47. Binz, P.A., Bairoch, A., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D. Bioinformatics challenges in proteomics. in MipTec-ICAR. 2000.

48. Binz, P.A., Bienvenut, W., Fabbretti, R., Gasteiger, E., Bairoch, A., Appel, R.D., Sanchez, J.C., and Hochstrasser, D.F. The "molecular scanner": an highly automated methos for protein identification and 2-D PAGE annotation. in 3rd Siena 2D electrophoresis meeting. 1998. Siena, Italy.

49. Binz, P.A., Bienvenut, W., Müller, M., Gras, R., Gasteiger, E., Hoogland, C., Fabbretti, R., Karmime, A., Paesano, S., Rossellat, G., Rouge, V., Tonella, L., Bairoch, A., Appel, R., Sanchez, J.C., and Hochstrasser, D.F. Automation in Proteomics: the molecular scanner and the robotization of protein identification by peptide mass fingerprinting. in 3Šme Journ‚e d'Interaction des Groupes de Recherche des Facult‚s de M‚decine de GenŠve et Lausanne. 1999. Changins, Switzerland.

50. Binz, P.A., Bologna, G., Gay, S., Hernandez, C., Hoogland, C., Mostaguir, K., Tuloup, M., and Appel, R.D. Bioinformatics tools in proteomics: issues and perspectives. in Functional Genomics and Disease, ESF Workshop. 2003. Prague.

51. Binz, P.A., Budin, N., Sankar, M., Müller, M., Lisacek, F., and Masselot, A. Proteomics: Data explosion under control? in 8th Siena Meeting from genome to proteome 2008. 2008. Siena, Italy.

52. Binz, P.A., Gasteiger, E., Gras, R., Hoogland, C., Müller, M., Walther, D., Bienvenut, W., Zimmermann, C., Sanchez, J.C., Bairoch, A., Appel, R.D., and Hochstrasser, D.F. Informatics of Proteomics and Possible Use in Laboratory Sciences. in Computation in Clinical Laboratory 2000 Third Millenium CCL. 2000. Milano.

53. Binz, P.A., Gay, S., Hochstrasser, D.F., and Appel, R.D. Knowledge Discovery to understand and predict peptide mass fingerprinting spectra. in First Annual HUPO Congress. 2002. Versailles, France.

54. Binz, P.A., Kapp, E.A., Shofstahl, J., Creasy, D., UniProt, C., Falkner, J.A., Andrews, P.C., and Seymour, S.L. A Common Sequence Database Format in Proteomics. in HUPO 8th Annual World Congress. 2008. Amsterdam, Netherlands.

55. Binz, P.A., Masselot, A., and Appel, R.D. Proteome Bioinformatics: critically evaluating MS data. in Swiss Proteomics Society 2004 Congress: Expanding proteomics. 2005. Zurich, Swizerland.

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

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

58. Binz, P.A., Masselot, A., Cambria, L., Müller, M., Tuloup, M., Hernandez, C., Walther, D., Catherinet, S., and Appel, R.D. Bioinformatics and relevance in proteomics. in Soci‚t‚ fran‡aise d'‚lectrophorŠse et d'analyse prot‚omique. 2004. Bordeaux.

59. Binz, P.A., Masselot, A., Mylonas, R., BouyssiŠ, 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.

60. Binz, P.A., Masselot, A., Walther, D., and Appel, R.D. Interpretation of protein identification results: more questions than answers? The confidence and validation issue. in BSPR/EBI Meeting - From Proteins to Systems. 2005. Cambridge.

61. Binz, P.A., Müller, M., Bouyssié, D., and Lisacek, F. How Stable are Peptide Identifications with Regards to Variations in MS/MS Spectra? in ASMS 2008. 2008. Denver, Colorado, USA.

62. Binz, P.A., Müller, M., Hoogland, C., Walther, D., Gay, S., Gras, R., Bienvenut, W.V., Pasquarello, C., Paesano, S., Corthals, G., Sanchez, J.C., Bairoch, A., Hochstrasser, D.F., and Appel, R.D. The Synergy between Bioinformatics and Proteomics Research. in Danish Society for Biochemistry and Molecular Biology. 2002.

63. Binz, P.A., Niknejad, A., Budin, N., Evalet, O., and Masselot, A. Validation approaches in Protein Identification with Phenyx: not only FDR. in SFEAP 2008. 2008. Tours, France.

64. Binz, P.A., Paesano, S., Zanini, P., Scherl, A., Hoogland, C., Allard, L., Zimmermann, C., Carrette, O., Sanchez, J.C., Borella, S., Castelnovo, R., Appel, R.D., and Hochstrasser, D.F. Why and How? A LIMS in a proteomics research environment. in Congress of the Swiss Proteomics Society. 2003. Basel.

65. Binz, P.A., Tuloup, M., Hernandez, C., Fabretti, R., Hernandez, P., Bologna, G., Hoogland, C., Mostaguir, K., Walther, D., Bouchet, G., Palagi, P.M., and Appel, R.D. Bioinformatics and Proteome Analysis in MS dominated workflows. in Jahrestagung Chemie 2003 der Gesellschaft Deutscher Chemiker. 2003. Mnchen.

66. Bologna, G. On the validation of the DIMLP Neural Network. in FLAIRS'02. 2002. Florida.

67. Bologna, G. and Appel, R.D. A comparaison study on protein fold recognition. in 9th International Conference on Neural Information Processing. 2002. Singapore.

68. Bologna, G., Appel, R.D., and Hochstrasser, D.F. Automatic Classification of 2-D PAGE Images. in Siena Meeting on 2D Electrophoresis. 1994. Siena.

69. Bologna, G., Veuthey, A.L., and Appel, R.D. N-terminal myristoylation predictions by neural network ensembles. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

70. Boyer, C., Baujard, O., Baujard, V., and Appel, R.D. New developments of MedHunt medical search engine. in MEDNET98 - World Congress on the Internet in Medicine. 1998. Brighton, U.K.

71. Boyer, C., Baujard, O., Baujard, V., Aurel, S., Selby, M., and Appel, R.D. HON automated database of health and medical information. in MEDNET96 - European Congress on the Internet in Medicine. 1996. Brighton, U.K.

72. Boyer, C., Baujard, V., Nater, T., Scherrer, J.R., and Appel, R. HON's Fourth survey on the usage of the Internet for medical & health Internet purposes. in MEDNET'99 - 4th World congress on the internet in medicine. 1999. Heidelberg, Germany.

73. Boyer, C., Baujard, V., Nater, T., Scherrer, J.R., and Appel, R.D. The Health On the Net Code of Conduct for medical and health-related Web sites: Three years on. in MEDNET'99 - 4th World congress on the internet in medicine. 1999. Heidelberg, Germany.

74. Boyer, C., Baujard, V., Nater, T., Scherrer, J.R., and Appel, R.D. HONselect: A new assisted-search facility for health information and resources integrating heterogeneous databases. in MEDNET'99 - 4th World congress on the internet in medicine. 1999. Heidelberg, Germany.

75. Boyer, C., Baujard, V., Scherrer, J.R., and Appel, R.D. HON's Third survey on the usage of the Internet for medical/health Internet purposes. in MEDNET98 - World Congress on the Internet in Medicine. 1998. Brighton, U.K.

76. Boyer, C., Selby, M., and Appel, R.D. The Health On the Net code of conduct for medical and health web sites. in MEDINFO 98. 1998. Seoul.

77. Boyer, C., Selby, M., and Appel, R.D. The Health On the Net Code of Conduct for medical and health Web sites; its status in 1997. in MEDNET97 - European Congress on the Internet in Medicine. 1997. Brighton, U.K.

78. Boyer, C., Selby, M., Baujard, V., and Appel, R.D. Medical Information on the Internet: Who wants what? in MEDNET97 - European Congress on the Internet in Medicine. 1997. Brighton, U.K.

79. Burke, P., Appel, R.D., Funk, M., Hochstrasser, D.F., and Scherrer, J.R. Can AI Help The Physician ? in SCAICO 1991. 1991. Biel.

80. Chauvet, A., Binz, P.A., Vaezzadeh, A., Zimmermann-Ivol, C.G., Palagi, P.M., Appel, R.D., Thiele, H., and Hochstrasser, D.F. High-throughput data management of Shotgun IEF results by ProteinScape. in ASMS Conference on Mass Spectrometry. 2007. Indianapolis, Indiana.

81. 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.

82. 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.

83. Corthals, G., Pasquarello, C., Scherl, A., Burgess, J., Allard, L., Deshusses, J., Walter, N., Paesano, S., Carrette, O., Bienvenut, W., Hoogland, C., Binz, P.A., Müller, M., Appel, R.D., Hochstrasser, D.F., and Sanchez, J.C. Tools and technologies in proteome analysis. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

84. Corthals, G., Pasquarello, C., Scherl, A., Burgess, J., Vaezzadeh, A., Deshusses, J., Hochstrasser, D.F., Sanchez, J.C., Binz, P.A., and Appel, R.D. Controlling data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry. in MipTec. 2003. Basel.

85. Corthals, G., Schmidt, G., Scherl, A., Pasquarello, C., Bienvenut, W., Binz, P.A., Walther, D., Voordijk, S., Appel, R.D., Hochstrasser, D.F., and Sanchez, J.C. Proteomics: tools and applications. in Association of Clinical Biochemists (UK), Pharmacogenomics Meeting. 2002. Cambridge, UK.

86. Corthals, G.L., Pasquarello, C., Scherl, A., Burgess, J., Vaezzadeh, A., Binz, P.A., Deshusses, J., Appel, R.D., Sanchez, J.C., and Hochstrasser, D.F. Guiding data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry (NRMS). in 16th International Mass Spectrometry Conference. 2003. Edinburgh.

87. Deutsch, E., Souda, P., Montecchi-Palazzi, L., Tasman, J., Binz, P.A., Hermjakob, H., and Martens, L. Design and implementations of the new Proteomics Standards Initiative's mass spectrometer output file standard format : mzML 1.0. in ASMS 2008. 2008. Denver, Colorado, USA.

88. Deutsch, E.W., Binz, P.A., Kessner, D., Chambers, M., Montecchi-Palazzi, L., Shofstahl, J., Tasman, J., Julian Jr, R.K., Levander, F., Souda, P., and Martens, L. Design and implementations of the new PSI mass spectrometer output file standard : mzML. in 8th Siena Meeting from genome to proteome 2008. 2008. Siena, Italy.

89. Deutsch, E.W., Martens, L., Tasman, J., Shofstahl, J., Kessner, D., Chambers, M., Levander, F., Souda, P., Montecchi-Palazzi, L., Hermjakob, H., and Binz, P.A. Design and implementations of the new PSI mass spectrometer output file standard: mzML 1.0. in HUPO 2008. 2008. Amsterdam, Nederlands.

90. Fabbretti, R., Binz, P.A., Bienvenut, W., Gasteiger, E., Bairoch, A., Wilkins, M.R., Sanchez, J.C., Walther, D., Hochstrasser, D.F., and Appel, R.D. Towards fully automated identification of proteins on 2-D PAGE gels. in 3rd Siena 2D electrophoresis meeting. 1998. Siena, Italy.

91. Frey, J., Gras, R., Hernandez, P., and Appel, R.D. A Hierarchical Model of Coarse-Grained Parallel Genetic Programming. in PPAM 2003 - Fifth International Conference on Parallel Processing and Applied Mathematics. 2003. Czestochowa, Poland.

92. Friha, L., Baujard, O., Berry, P., and Appel, R.D. DISA: an interactive scheduler using abstractions. in 14th Workshop of the UK Planning and Scheduling SIG, University of Essex. 1995. Colchester, U.K.

93. Funk, M., Appel, R.D., Bost, J.M., Hochstrasser, D.F., Muller, A.F., and Pellegrini, C. A graphical Interface for the knowledge acquisition in the MELANIE expert system. in Two-dimensional Electrophoresis. 1988. Vienna, Austria.

94. Golaz, O., Gravel, P., Walzer, C., Sanchez, J.C., Pasquali, C., Appel, R.D., and Hochstrasser, D.F. Sugar detection at the picomole level using lectins and chemiluminescence. in Siena Meeting on 2D Electrophoresis. 1994. Siena.

95. Golaz, O., Hughes, G., Frutiger, S., Paquet, N., Sanchez, J.C., Pasquali, C., Bairoch, A., Appel, R.D., and Hochstrasser, D.F. Plasma and red blood cell 2-D PAGE databases. in Siena Meeting on 2D Electrophoresis. 1994. Siena.

96. Golaz, O., Sanchez, J.C., Heenan, R., Ravier, F., Rouge, V., Tonella, L., Wilkins, M.R., Appel, R.D., and Hochstrasser, D.F. SWISS-2DISEASE: a 2-D database of samples in disease states. in 2nd Siena 2D electrophoresis meeting. 1996. Siena, Italy.

97. Gras, R., Frey, J., Hernandez, P., and Appel, R.D. Un modéle hiérarchique "coarse-grained" de parallélisation d'algorithme de programmation génétique appliqué à des problèmes de bioinformatique. in Workshop: Résolution Parallèle des Problémes NP-complets. 2003. Nice.

98. Gras, R., Gasteiger, E., Chopard, B., Müller, M., and Appel, R.D. New learning method to improving protein identification from peptide mass fingerprinting. in 4th Siena 2D electrophoresis meeting. 2000. Siena, Italy.

99. Gras, R., Gasteiger, E., Müller, M., and Appel, R.D. New learning method to improve protein identification from peptide mass fingerprinting. in The eighth International Conference on Computational Biology Intelligent Systems for Molecular Biology (ISMB). 2000. La Jolla, California.

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

101. Gras, R., Hernandez, D., Hernandez, P., Zangger, N., Mescam, Y., Frey, J., Martin, O., Nicolas, J., and Appel, R.D. Cooperative metaheuristics to solve complex bioinformatics problem. in International Summer School on Metaheuristics. 2003. Tenerife.

102. Gras, R., Müller, M., Hernandez, D., Hernandez, P., Zangger, N., Palagi, P., Binz, P.A., and Appel, R.D. Cooperative metaheuristic for proteomics. in Bioinformatics Workshop ISMIS. 2002. Lyon.

103. Gras, R., Müller, M., Hernandez, D., Hernandez, P., Zangger, N., Palagi, P., Binz, P.A., Lisacek, F., and Appel, R.D. New approaches of computational proteomics. in JOBIM 2002. 2002. St-Malo, France.

104. Hernandez, D., Gras, R., and Appel, R. Automated learning of unknown length motifs in unaligned DNA sequences with genetic algorithms. in ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology. 2001. Tivoli Gardens, Copenhagen, Denmark.

105. Hernandez, D., Gras, R., and Appel, R.D. Automated learning of unknown lenght motifs in unaligned biological sequences with genetic algorithm. in Congress of the Swiss Proteomics Society. 2001. Geneva.

106. Hernandez, D., Gras, R., and Appel, R.D. Stratégies d'exploration de l'espace des alignements locaux multiples sans indels. in Quatrièmes journées francophones de recherche opérationnelle (FRANCORO IV). 2004. Fribourg, Suisse.

107. Hernandez, D., Gras, R., Lisacek, F., and Appel, R.D. MoDEL: Inférence de motifs avec un algorithme évolutionniste. in JOBIM. 2002.

108. Hernandez, P., Gras, R., and Appel, R.D. Ant Colony Optimization Metaheuristic Applied to Automated Protein Identification from Tandem Mass Spectrometric Data. in Second International Workshop on "AGENTS IN BIOINFORMATICS". 2002. Bologna, Italy.

109. Hernandez, P., Gras, R., and Appel, R.D. Automated Protein Identification from Tandem Mass Spectrometric Data Using Bio-Inspired Algorithms. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

110. Hernandez, P., Gras, R., and Appel, R.D. Popitam loves being fed on modified MS/MS spectra. in Peptide Fragmentation and identification Workshop, NIST. 2004. Gaithersburg, Maryland.

111. Hernandez, P., Gras, R., and Appel, R.D. Popitam squints to better identify ms/ms spectra of modified peptides. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

112. Hernandez, P., Gras, R., Frey, J.P., and Appel, R.D. Automated Protein Identification from Tandem Mass Spectrometric Data Using Bio-Inspired Algorithms. in Congress of the Swiss Proteomics Society. 2002. Lausanne.

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

114. Hernandez, P., Quandt, A., Hernandez, C., and Appel, R.D. swissPIT, une plateforme pour l'identification de prot‚ines … partir de spectres de masses. in Grille Bioinformatique: exp‚riences et perspectives, Vendredi 12 mai, IBCP, Lyon. 2006. Lyon.

115. 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.

116. Hochstrasser, D., Appel, R., Bienvenut, W., Binz, P.A., Chiappe, D., Demalte, I., Jung, E., and Sanchez, J.C. Proteomic complexity and computational aspects in oncology. in Tenth Symposium of the Division of Experimental Cancer Research (AEK) of the German Cancer Society; Journal of Cancer Research and clinical Oncology, supplement to vol. 125, Scientific Proceeding (abstracts). 1999. Heidelberg, Germany.

117. Hochstrasser, D., Bjellqvist, B., Bairoch, A., Sanchez, J.C., Appel, R., and Hughes, G.J. From the genome to 2D-PAGE or predicting the position of a polypeptide on protein maps. in ICES-ELPHO 93. 1993. Oslo.

118. Hochstrasser, D., Funk, M., Appel, R., Pellegrini, C., and Muller, A.F. Electrophorèses bidimensionnelles : analyse et comparaison automatique par ordinateur. in Société Suisse de chimie clinique. 1985. Zurich.

119. Hochstrasser, D., Funk, M., Appel, R.D., James, R., Hochstrasser, A.C., Scherrer, J.R., Pellegrini, C., and Muller, A.F. Clinical applications of two-dimensional polyacrylamide gel electrophoresis. in Electrophoresis forum '89. 1989.

120. Hochstrasser, D., Maignan, M.F., Dumont, J.M., Funk, M., Appel, R., Aellig, A., Grandjean, E.M., Pellegrini, C., and Muller, A.F. 2-dimensional gel electrophoresis : a new tool for the evaluation of a therapeutic agent. in 18th Congress of the International Union of Therapeutics. 1987. Geneva.

121. Hochstrasser, D., Ratib, O., Funk, M., Appel, R., and Scherrer, J.R. Images en Médecine Clinique et en Médecine Fondamentale. in Journées Francophones d'Informatique Médicale. 1990. Nimes.

122. Hochstrasser, D., Sanchez, J.C., Binz, P.A., Bienvenut, W., and Appel, R.D. A clinical molecular scanner to study human proteome complexity. in Novartis.Found.Symp. 2000.

123. Hochstrasser, D., Sanchez, J.C., Fabretti, R., Müller, M., Gasteiger, E., Bienvenut, W., Rosselat, G., Binz, P.A., Bairoch, A., and Appel, R. Proteome research and its impact on laboratory medicine. in WorldLab 99. 1999. Florence.

124. Hochstrasser, D., Siegenthaler, G., De Moerloose, P., Funk, M., Appel, R., Pellegrini, C., Saurat, J.H., and Muller, A.F. Elévation de la protéine sérique liant le rétinol et de l'antithrombine III. in Société Suisse de Médecine Interne. 1987.

125. Hochstrasser, D., Wilkins, M., Sanchez, J.C., Gasteiger, E., and Appel, R. Proteome Research: State of the art. in Electrophorese Forum '97. 1997. Strasbourg.

126. Hochstrasser, D.F., Appel, R.D., Bairoch, A., Golaz, O., Pasquali, C., and Sanchez, J.C. Expert Protein Analysis Server (ExPASy). in IMIA WG6 Working Conference. 1994. Vevey.

127. Hochstrasser, D.F., Appel, R.D., Bienvenut, W., Binz, P.A., Müller, M., Rouge, V., Tonella, L., and Sanchez, J.C. Present status of proteomics. in Biochemical society transactions. 1999. Glasgow.

128. Hochstrasser, D.F., Appel, R.D., Burke, P., Goodman, A., Snydr-Michal, J., Vargas, J.R., Ratib, O., Pellegrini, C., and Scherrer, J.R. L'Imagerie dans le diagnostic médical - l'exemple du système Melanie. in Journées Francophones d'Informatique. 1992. Genève.

129. Hochstrasser, D.F., Appel, R.D., Golaz, O., Pasquali, C., and Sanchez, J.C. De la cartographie prot‚ique au g‚nome. in R‚union annuelle de la Soci‚t‚ Fran‡aise d'ElectrophorŠse. 1993. Chamb‚ry.

130. Hochstrasser, D.F., Appel, R.D., Paesano, S., Binz, P.A., Sanchez, J.C., and Zimmermann, C. Proteomics & Clinical Chemistry. in Fourth HUPO annual meeting. 2005. Munich.

131. Hochstrasser, D.F., Appel, R.D., and Sanchez, J.C. Clinical Applications of 2D-PAGE. in ATB'93. 1993. Milan.

132. Hochstrasser, D.F., Appel, R.D., Wiederkehr, F., Funk, M., Vonderschmidt, D., Scherrer, J.R., and Muller, A.F. Electrophoréses Bidimensionnelles en Chimie Clinique. in Schweizerische Medizinische Wochenschrift, 121: suppl. 38, 59ème Assemblée Générale de la Société Suisse de Médecine. 1991. Lugano.

133. Hochstrasser, D.F., Bienvenut, W., Müller, M., Gras, R., Binz, P.A., Appel, R.D., and Sanchez, J.C. From Genome to Proteome: the development of a molecular scanner. in Colloque AcM/MdA - Acquisition conduite par le ModŠle - Model driven Acquisition. 2000. Grenoble.

134. Hochstrasser, D.F., Binz, P.A., Bairoch, A., Appel, R.D., and Sanchez, J.C. From genome to proteome: a new look at Nature complexity. in Miami conference. 1999.

135. Hochstrasser, D.F., Binz, P.A., Bairoch, A., Appel, R.D., and Sanchez, J.C. From Genome to Proteome: a New Look at Nature Complexity. in Elektrophorese Forum'99. 1999. Munich.

136. Hochstrasser, D.F., Binz, P.A., 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, R.D., and Sanchez, J.C. Proteomics Technology Development in Geneva. in Elektrophorese Forum'99. 1999. Munich.

137. Hochstrasser, D.F., Binz, P.A., 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, J.C., and Appel, R.D. MALDI-TOF "Imaging": a Molecular Scanner for Proteomic Research. in ABRF. 2000.

138. Hochstrasser, D.F., Corthals, G., Appel, R.D., and Sanchez, J.C. Large scale proteomics in medecine. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

139. Hochstrasser, D.F., Corthals, G., Appel, R.D., and Sanchez, J.C. Proteomics in medecine. in Barnett Lecture, Barnett Institute. 2003. Boston.

140. Hochstrasser, D.F., Corthals, G., Rose, K., Bougueleret, L., Appel, R.D., Bairoch, A., and Sanchez, J.C. The five dimensions of diseases. in Second Annual HUPO Congress. 2003. Montreal.

141. Hochstrasser, D.F., Corthals, G., Sanchez, J.C., Appel, R.D., Bairoch, A., Bougueleret, L., and Rose, K. Clinical proteomics: a challenge for diagnostic laboratories and the pharma industry? in AACC 2004 Annual meeting. 2004. Los Angeles, CA.

142. Hochstrasser, D.F., Corthals, G., Zimmerman, C., Scherl, A., Bougueleret, L., Collinge, J., Masselot, A., Binz, P.A., Müller, M., Bairoch, A., Appel, R.D., Sanchez, J.C., and Rose, K. Proteomics & Mass Spectrometry in Medicine. in International Mass Spectrometry Conference. 2003. Edinburgh.

143. Hochstrasser, D.F., Funk, M., Appel, R.D., Scherrer, J.R., Pellegrini, C., and Muller, A.F. Les techniques d'intelligence artificielle dans l'analyse des électrophorèses bidimensionnelles. in Journées Franc. d'IA. 1988. Montpelier.

144. Hochstrasser, D.F., Hochstrasser, A.C., Villars, V., Funk, M., Appel, R.D., Pellegrini, C., and Muller, A.F. Storable precast IEF gels with urea. in Two-dimensional Electrophoresis. 1988. Vienna, Austria.

145. Hochstrasser, D.F., Huber, O., Kaelin, K., Touss, A., Pavlovic, A., Funk, M., Appel, R.D., Pasquali, C., Ravier, F., Tissot, J.D., Goodman, A., and Muller, A.F. Clinical Application of Two Dimensional Polyacrylamide Gel Electrophoresis: Its Future. in 2D-PAGE' 1991, Proc. Int. Meeting on Two-Dimensional Electrophoresis. 1991. London.

146. Hochstrasser, D.F., Lescuyer, P., Moll, S., Vaezzadeh, A., Sanchez, J.C., Zimmerman, C., and Appel, R.D. Clinical Proteomics & Biomarker Discovery. in Congress on Proteomic & Pathology. 2007. Valencia, Spain.

147. Hochstrasser, D.F., Lescuyer, P., Moll, S., Vaezzadeh, A., Sanchez, J.C., Zimmerman, C., and Appel, R.D. Clinical Proteomics & Biomarker Discovery. in International Symposium on High Performance Proteomics. 2007. Dortmund.

148. Hochstrasser, D.F., Sanchez, J.C., and Appel, R.D. Proteomics (and its trends facing nature complexity). in Congress of the Swiss Proteomics Society. 2001. Geneva.

149. Hochstrasser, D.F., Sanchez, J.C., Binz, P.A., Bienvenut, W., and Appel, R.D. Analytical techniques for proteome research. in PBA 2000. 2000.

150. Hochstrasser, D.F., Sanchez, J.C., Binz, P.A., Bienvenut, W., Gasteiger, E., Müller, M., Gras, R., Fabretti, R., and Appel, R.D. The role of the virtual or computer "dry" laboratory in proteomics. in 31st Annual Meeting of USGEB 99. 1999.

151. Hochstrasser, D.F., Sanchez, J.C., Corthals, G., Binz, P.A., Müller, M., Appel, R.D., Bougueleret, L., and Rose, K. Proteomics in laboratory medicine. in EUROMEDLAB Barcelona 2003, 15th IFCC - FESCC European Congress of Clinical Chemistry and Laboratory Medicine. 2003. Barcelona.

152. Hochstrasser, D.F., Sanchez, J.C., Corthals, G., Binz, P.A., Müller, M., Walther, D., and Appel, R.D. Bioinformatics in proteomics. in International Conference "Genomics, Proteomics and Bioinformatics for Medicine". 2002. Moscow.

153. Hochstrasser, D.F., Sanchez, J.C., Corthals, G., Scherl, A., Rose, K., Bougueleret, L., Colinge, J., Bairoch, A., and Appel, R.D. Proteomics & Mass Spectrometry in Medicine. in 16th International Mass Spectrometry Conference. 2003. Edinburgh.

154. Hochstrasser, D.F., Sanchez, J.C., James, R., and Appel, R.D. The use of proteomics in plasma investigation. in Clinical Chemistry Society Conference. 2000. Rabat.

155. Hochstrasser, D.F., Sanchez, J.C., Rose, K., Bougueleret, L., Appel, R.D., Bairoch, A., and Corthals, G. Clinical Proteomics. in Proteomic Forum '03. 2003. Mnich.

156. Hochstrasser, D.F., Sanchez, J.C., Scherl, A., Corthals, G., and Appel, R.D. Proteomics: three approaches. in Endoderm. 2002. Arolla, Switzerland.

157. Hochstrasser, D.F., Scherl, A., Binz, P.A., Zimmerman, C., Sanchez, J.C., and Appel, R.D. Complex Specimen struggling to survive. in BSPR/EBI Meeting - From Proteins to Systems. 2005. Cambridge.

158. Hochstrasser, D.F., Viette, V., Geiser, L., Farina, A., Dumonceau, J.M., Frossard, J.L., Hadengue, A., Mauron, Y., Mylonas, R., Masselot, A., Binz, P.A., Lisacek, F., Fathi, M., and Lescuyer, P. Proteomics & Clinical Chemistry. in IFCC-WorldLab 2008. 2008. Fortaleza, Brasil.

159. Hochstrasser, D.F., Walther, D., Quadroni, M., Catherinet, S., Tuloup, M., Binz, P.A., Burgess, J., Vaezzadeh, A., Zimmerman, C., Corthals, G.L., Sanchez, J.C., and Appel, R.D. MS imaging in Clinical Proteomics. in Beyond Genome. 2005. San Francisco, CA.

160. Hochstrasser, D.F., Walther, D., Quadroni, M., Catherinet, S., Tuloup, M., Binz, P.A., Burgess, J., Vaezzadeh, A., Zimmermann-Ivol, C.G., Corthals, G.L., Appel, R.D., and Sanchez, J.C. Clinical Proteomics and MS imaging. in ASBMB 2005, American Society for Biochemistry and Molecular biology. 2005. San Diego, CA.

161. Hochstrasser, D.F., Wilkins, M., Appel, R., Bairoch, A., Sanchez, J.C., and Williams, K. From Genomes to "Proteomes": EXPASY & SWISS-2DPAGE. in The Protein Society First European Symposium. 1995. Davos, Switzerland.

162. Hochstrasser, D.F., Zimmermann-Ivol, C.G., Corthals, G.L., Appel, R.D., and Sanchez, J.C. Clinical Proteomics. in Congress of the Swiss Proteomics Society. 2004. Bern.

163. Hoogland, C., Ehrler, F., Palagi, P.M., Sanchez, J.C., Lisacek, F., and Ruch, P. Turning a set of binary classifiers into a single ranker to help digestion of proteomics literature. in 3rd EuPA Congress. 2009. Stockholm, Sweden.

164. Hoogland, C., Lion, N., Palagi, P.M., Rossier, J., Sanchez, J.C., Stocklin, R., Tissot, J.D., and Voshol, H. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. in Swiss Proteomics Society 2004 Congress: Proteomics for Health. 2004. Bern, Switzerland.

165. Hoogland, C., Lion, N., Palagi, P.M., Sanchez, J.C., and Tissot, J.D. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. in 6th Siena Meeting From genome to proteome: Biomarker discovery & Proteome imaging. 2004. Siena, Italy.

166. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F. World-2DPAGE Repository: your contribution to a large proteomics data network. in 8th Siena meeting "From genome to proteome: Integration and proteome completion". 2008. Siena, Italy.

167. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F. World-2DPAGE Repository: your contribution to a large proteomics data network. in HUPO 8th Annual World Congress. 2008. Amsterdam, Netherlands.

168. Hoogland, C., Mostaguir, K., Appel, R.D., and Lisacek, F. World-2DPAGE: your proteomics data publicly available from the ExPASy server. in Swiss Proteomics Society 2007 Congress: Pushing the limits. 2007. Lausanne, Switzerland.

169. Hoogland, C., Mostaguir, K., Hochstrasser, D.F., Sanchez, J.C., and Appel, R.D. SWISS-2DPAGE, 10 years later. in Congress of the Swiss Proteomics Society. 2003. Basel.

170. Hoogland, C., Sanchez, J.C., Tonella, L., Hochstrasser, D.F., and Appel, R.D. SWISS-2DPAGE, My-2DPAGE, Your-2DPAGE...: how to publish 2-DE data on the Web. in 3rd Siena 2D electrophoresis meeting. 1998. Siena, Italy.

171. Jaconi, M., Theler, J.M., Schlegel, W., Appel, R.D., Wright, S.D., and Lew, P.D. Repetitive cytosolic free CA2+ elevations in human neutrophils are initiated by adherence receptors of the integrin family. in European Society for Clinical Investigation. 1991. Pisa.

172. Jaconi, M.E.E., Theler, J.M., Schlegel, W., Appel, R.D., Wright, S.D., and Lew, P.D. Fluctuations of cytosolic free Ca2+ in human neutrophils: initiation by adherence receptors of the integrin family. in American Society for Cell Biology. 1990.

173. Langevin, E., Bairoch, A., Appel, R.D., Rialle, V., Scherrer, J.R., and Hochstrasser, D.F. ExPASy: Un système expert pour l'analyse de séquences protéiques. in 4èmes Journées Francophones d'Informatique Médicale. 1993. Bruxelles.

174. Mascarini, C., Ratib, O., Trayser, G., Ligier, Y., and Appel, R.D. In-house Access to PACS Images and Related Data Through World Wide Web. in SPIE International Symposium - Medical Imaging. 1996. Newport Beach, CA.

175. Mascarini, C., Ratib, O., Trayser, G., Ligier, Y., and Appel, R.D. In-house access to PACS images and related data through World Wide Web. in SGMR, 83. Jahresversammlung. 1996. Lausanne.

176. Masselot, A., Binz, P.A., Cambria, L., and Appel, R.D. Phenyx: combining high-throughput and pertinence in protein identification. in Third Annual HUPO Congress (proceedings in Molecular & Cell Proteomics). 2004. Beijing.

177. Masselot, A., Binz, P.A., Cambria, L., and Appel, R.D. Phenyx: Manage Protein Identification With Flexibility and Pertinence. in Congress of the Swiss Proteomics Society. 2004. Bern.

178. Mauron, Y., Mylonas, R., Masselot, A., Binz, P.A., Hochstrasser, D.F., and Lisacek, F. SmileMS; A New Mass Spectrometry Based Identification Platform for Small Molecules. in Swiss MedLab 2008. 2008. Montreux, Switzerland.

179. Mench, M., Vangronsveld, J., Herzig, R., Renella, G., Kolbas, A., Bes, C., Bedon, F., Plomion, C., Jaunatre, R., Gasté, H., Aulen, M., Garcia, S., Kechit, F., François, J., Guinberteau, J., Nehnevajova, E., Gawronski, S., Kidd, P., Becerra-Castro, C., Song, J., Carrier, O., Loppinet-Serani, A., Aymonier, C., Kumpiene, J., Palagi, P.M., Chaumeil, P., Barre, A., Claverol, S., Dupuy, J.W., Bonneu, M., and Van der Lelie, D. Aggregation of COST 859 phytoremediation knowledge from genes to field trials at the BIOGECO phytoremediation platform. in COST Action 859 - Phyto 2009. Final International Conference on: " Phytotechnologies to promote sustainable land use and improve food safety ". 2009. Ascona, Switzerland.

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

181. Mostaguir, K., Hoogland, C., and Appel, R.D. Evolution et interconnexion des bases de donn‚es prot‚omiques avec l'outil Make2D-DB II : un exemple appliqu‚ aux bases de donn‚es de gels 2-DE. in JOBIM. 2005.

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185. Mostaguir, K., Hoogland, C., Binz, P.A., and Appel, R.D. The Make 2D-DB II Package - Conversion of federated 2-DE gel databases into a relational format and interconnection of distributed databases. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

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188. Müller, M., Gras, R., and Appel, R. Vizualization and Interpretation of the Molecular Scanner Data. in ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology. 2001. Tivoli Gardens, Copenhagen, Denmark.

189. Müller, M., Gras, R., Bienvenut, W.V., Binz, P.A., Pasquarello, C., Hochstrasser, D.F., and Appel, R.D. Using Peptide Signal Intensity Distributions for a Better Interpretation of Molecular Scanner Data. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

190. Müller, M., Gras, R., Bienvenut, W.V., Hochstrasser, D.F., and Appel, R.D. Visualisation and Analysis of Molecular Scanner Peptide Mass Spectra. in Congress of the Swiss Proteomics Society. 2001. Geneva.

191. 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.

192. Nadler, T., Huang, Y., Wagenfeld, B., Parker, B., Lotti, R., Vella, G.J., Binz, P.A., Müller, M., Gras, R., Hochstrasser, D.F., Bienvenut, W., Sanchez, J.C., Corthals, G., and Appel, R.D. Proteome Analysis by Multi-Dimensional Liquid Chromatography Gel-Electrophoresis and the Molecular Scanner. in 5th Siena 2D electrophoresis meeting. 2002. Siena, Italy.

193. Nikitin, F., Lisacek, F., and Appel, R.D. Modular analysis of bacterial proteins in specific pathways. in ECCB 05, 4th European Conference on Computational Biology. 2005. Madrid, Spain.

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196. Palagi, P.M., Binz, P.A., Bairoch, A., Hochstrasser, D.F., and Appel, R.D. Bioinformatics challenges in proteomics. in Symposium " Bioinformatics and proteomics ". 2000. Seoul, Korea.

197. Palagi, P.M., Binz, P.A., Bairoch, A., Hochstrasser, D.F., and Appel, R.D. Bioinformatics in Proteomics. in CCP11 GPCVI Conference "Bioinformatics and the Molecular Biologist". 2000. Chester, England.

198. Palagi, P.M., Bucher, P., Notredame, C., Schwede, T., Galisson, G., and Appel, R.D. Evolution of bioinformatics education in Switzerland and the role of the Swiss Institute of Bioinformatics. in WEB'04 - Workshop on Education in Bioinformatics 2004, ISMB2004. 2004. Glasgow, Scotland.

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208. Peitsch, M.C., Tonella, L., Sanchez, J.C., Wilkins, M.R., Appel, R.D., and Hochstrasser, D.F. Automated comparative protein modelling and its integration with the SWISS-2DPAGE database. in 2nd Siena 2D electrophoresis meeting. 1996. Siena, Italy.

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217. Ratib, O., Mascarini, C., Ligier, Y., Appel, R.D., and Trayser, G. The World Wide Web for Intra- and Extra-Hospital Communication of Images and Patient Records. in 3rd INCIS Workshop. 1996. Mainz.

218. Ratib, O., Mascarini, C., Trayser, G., Revillard, C., Ligier, Y., and Appel, R.D. The "INTRANET" concept applied for convenient access to PACS image data and computerized patient record. in 14TH International EuroPACS Meeting. 1996. Heraklion, Crete, Hellas.

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228. Scherl, A., Francois, P., Bento, M., Deshusses, J.M., Charbonnier, Y., Converset, V., Huyghe, A., Walter, N., Hoogland, C., Appel, R.D., Sanchez, J.C., Zimmermann-Ivol, C.G., Corthals, G.L., Hochstrasser, D.F., and Schrenzel, J. Exploring the proteome and transcriptome of Staphylococcus aureus. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

229. Scherl, A., Francois, P., Bento, M., Masselot, A., Binz, P.A., Hoogland, C., Appel, R.D., Zimmermann-Ivol, C.G., Sanchez, J.C., Stahl-Zeng, J., Schrenzel, J., and Hochstrasser, D.F. Exploring antibiotic resistance with isobaric tags. in 53rd ASMS Conference on Mass Spectrometry. 2005. San Antonio, Texas.

230. 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.

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232. Selby, M., Boyer, C., Jenefski, D.A., and Appel, R.D. Health On the Net Foundation Code of Conduct for Medical and Health Websites. in MEDNET96 - European Congress on the Internet in Medicine. 1996. Brighton, U.K.

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240. Vaezzadeh, A., Deshusses, J., Lescuyer, P., Zimmermann-Ivol, C.G., Chauvet, A., Hernandez, C., Walther, D., Appel, R.D., and Hochstrasser, D.F. Towards High-Throughput Shotgun IEF. in ASMS Conference on Mass Spectrometry. 2007. Indianapolis, Indiana.

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243. Vargas, J.R., Bologna, G., Appel, R.D., Hochstrasser, D.F., and Pellegrini, C. Classification of Protein Patterns using Neural Networks: Pixel based versus Feature based Approach. in Proc. AIME'93, 5th Conference on AI in Medicine. 1993. Munich, Germany.

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245. Voordijk, S., Rossier, G., Walther, D., Bouchet, G., and Appel, R.D. New features in the Melanie 2D gel analysis software. in Congress of the Swiss Proteomics Society. 2003. Lausanne.

246. 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.

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249. Walther, D., Bouchet, G., Catherinet, S., Pelhatre, S., Tuloup, M., Palagi, P.M., and Appel, R.D. Powered by Melanie: a general framework for proteome imaging. in Swiss Proteomics Society 2005 Congress: Expanding proteomics. 2005. Zurich, Switzerland.

250. Walther, D., Quadroni, M., Catherinet, S., Burgess, J., Zimmermann-Ivol, C.G., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D. Why not exploit ms data to its fullest? Using data-redundancy in mass spectra. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

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252. Wilkins, M., Gooley, A., Williams, K., Humpherey-Smith, I., Cordwell, S., Appel, R.D., Sanchez, J.C., Golaz, O., Pasquali, C., and Hochstrasser, D.F. Towards the Protein Genome: Rapid Identification of 2D Spots by Amino Acid Analysis. in Siena Meeting on 2D Electrophoresis. 1994. Siena.

253. Wilkins, M.R., Gasteiger, E., Bairoch, A., Sanchez, J.C., Hochstrasser, D.F., and Appel, R.D. Software tools for mass spectrometric data analysis of proteins separated by 2-D gel electrophoresis. in ICES'97. 1997. Seattle, Washington.

254. Wilkins, M.R., Gasteiger, E., Sexton, D.K., Herbert, B.R., Molloy, M.P., Ou, K., Binz, P.A., Bairoch, A., Appel, R.D., Gooley, A.A., Hochstrasser, D.F., and Williams, K.L. Protein modifications, processing and identification in proteomics projects. in 3rd Siena 2D electrophoresis meeting. 1998. Siena, Italy.

255. Wilkins, M.R., Lindskog, I., Ou, K., Wheeler, C., Sanchez, J.C., Yan, J., Cartier, P., Farnsworth, V., Frutiger, S., Hughes, G., Ravier, F., Tonella, L., Gooley, A.A., Appel, R.D., Dunn, M.J., Williams, K.L., and Hochstrasser, D.F. Rapid protein identification for proteome projects. in 2nd Siena 2D electrophoresis meeting. 1996. Siena, Italy.

256. Wilkins, M.R., Sanchez, J.C., Ravier, F., Tonella, L., Appel, R.D., and Hochstrasser, D.F. Vector maps in two-dimensional polyacrylamide gel electrophoresis - a means of predicting protein post-translational modification. in 2nd Siena 2D electrophoresis meeting. 1996. Siena, Italy.

257. Zangger, N., Cerutti, L., Pagni, M., Lisacek, F., and Appel, R.D. Clustering protein sequences based on motif content. in ECCB 05, 4th European Conference on Computational Biology. 2005. Madrid, Spain.

258. Zangger, N., Gras, R., and Appel, R.D. Biological Sequence Clustering by Cooperative Agents. in Congress of the Swiss Proteomics Society. 2002. Lausanne.

259. Zangger, N., Gras, R., and Appel, R.D. A Symmetric Cooperative Metaheuristic for Biological Sequence Clustering Using Local Entropy as Similarity Criterion. in Second International Workshop on "AGENTS IN BIOINFORMATICS". 2002. Bologna, Italy.

260. Zimmermann-Ivol, C.G., Vaezzadeh, A., Converset, V., Hoogland, C., Walther, D., Catherinet, S., Tuloup, M., Hernandez, C., Müller, M., Moll, S., Corthals, G.L., Pasquarello, C., Appel, R.D., and Hochstrasser, D.F. Distribution and visualisation of urine protein profile with the Molecular Scanner. in 6th Siena meeting - From Genome to Proteome. 2004. Siena, Italy.

261. Zimmermann-Ivol, C.G., Vaezzadeh, A., Demalte, I., Converset, V., Di Dio, J., Scherl, A., Corthals, G.L., Appel, R.D., and Hochstrasser, D.F. The Molecular Scanner. in Congress of the Swiss Proteomics Society. 2004. Bern.

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