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Complete list of publications

I. Articles in journals with editorial policy

Albar JP, Corthals GL, Gil C, James P, Jensen ON, Palagi PM, Penque D. Promoting Proteomics Knowledge in Europe: report on the Activities of the EuPA Education Committee. Proteomics 2007; 7: 90-94.
Appel R, Hochstrasser D, Roch C, Funk M, Muller AF, Pellegrini C. Automatic classification of two-dimensional gel electrophoresis pictures by heuristic clustering analysis: a step toward machine learning. Electrophoresis 1988; 9: 136-142.
Appel RD, Hochstrasser DF, Funk M, Vargas JR, Pellegrini C, Muller AF, Scherrer JR. The MELANIE project: from a biopsy to automatic protein map interpretation by computer. Electrophoresis 1991; 12: 722-735.
Appel RD, Sanchez JC, Bairoch A, Golaz O, Miu M, Vargas JR, Hochstrasser DF. SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images. Electrophoresis 1993; 14: 1232-1238.
Appel RD, Sanchez JC, Bairoch A, Golaz O, Ravier F, Pasquali C, Hughes GJ, Hochstrasser DF. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis. Nucleic Acids Res 1994; 22: 3581-3582.
Appel RD, Bairoch A, Hochstrasser DF. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem Sci 1994; 19: 258-260.
Appel RD, Bairoch A, Sanchez JC, Vargas JR, Golaz O, Pasquali C, Hochstrasser DF. Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data. Electrophoresis 1996; 17: 540-546.
Appel RD, Sanchez JC, Bairoch A, Golaz O, Ravier F, Pasquali C, Hughes GJ, Hochstrasser DF. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995. Nucleic Acids Res 1996; 24: 180-181.
Appel RD, Vargas JR, Palagi PM, Walther D, Hochstrasser DF. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 1997; 18: 2735-2748.
Appel RD, Palagi PM, Walther D, Vargas JR, Sanchez JC, Ravier F, Pasquali C, Hochstrasser DF. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface. Electrophoresis 1997; 18: 2724-2734.
Baujard O, Baujard V, Aurel S, Boyer C, Appel RD. Trends in medical information retrieval on Internet. Comput Biol Med 1998; 28: 589-601.
Baujard O, Baujard V, Aurel S, Boyer C, Appel RD. MARVIN, multi-agent softbot to retrieve multilingual medical information on the Web. Med Inform (Lond) 1998; 23: 187-191.
Bienvenut WV, Hoogland C, Greco A, Heller M, Gasteiger E, Appel RD, Diaz JJ, Sanchez JC, Hochstrasser DF. Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprinting. Rapid Commun Mass Spectrom 2002; 16: 616-626.
Binz PA, Müller M, Walther D, Bienvenut WV, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins MR, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Sanchez JC, Appel RD, Hochstrasser DF. A molecular scanner to automate proteomic research and to display proteome images. Anal Chem 1999; 71: 4981-4988.
Binz PA, Hochstrasser DF, Appel RD. Mass spectrometry-based proteomics: current status and potential use in clinical chemistry. Clin Chem Lab Med 2003; 41: 1540-1551.
Binz PA, Müller M, Hoogland C, Zimmermann C, Pasquarello C, Corthals G, Sanchez JC, Hochstrasser DF, Appel RD. The molecular scanner: concept and developments. Curr Opin Biotechnol 2004; 15: 17-23.
Bologna G. A model for single and multiple knowledge based networks. Artif Intell Med 2003; 28: 141-163.
Bologna G, Yvon C, Duvaud S, Veuthey AL. N-Terminal myristoylation predictions by ensembles of neural networks. Proteomics 2004; 4: 1626-1632.
Borst F, Appel R, Baud R, Ligier Y, Scherrer JR. Happy birthday DIOGENE: a hospital information system born 20 years ago. Int J Med Inform 1999; 54: 157-167.
Boyer C, Baujard O, Baujard V, Aurel S, Selby M, Appel RD. Health On the Net automated database of health and medical information. Int J Med Inform 1997; 47: 27-29.
Boyer C, Selby M, Scherrer JR, Appel RD. The Health On the Net Code of Conduct for medical and health Websites. Comput Biol Med 1998; 28: 603-610.
Colinge J, Masselot A, Carbonell P, Appel RD. InSilicoSpectro: an open-source proteomics library. J Proteome Res 2006; 5: 619-624.
Coute Y, Burgess JA, Diaz JJ, Chichester C, Lisacek F, Greco A, Sanchez JC. Deciphering the human nucleolar proteome. Mass Spectrom Rev 2006; 25: 215-234.
Coute Y, Hernandez C, Appel RD, Sanchez JC, Margolles A. Labeling of Bifidobacterium longum cells with 13C-substituted leucine for quantitative proteomic analyses. Appl Environ Microbiol 2007; 73: 5653-5656.
Cremona O, Muda M, Appel RD, Frutiger S, Hughes GJ, Hochstrasser DF, Geinoz A, Gabbiani G. Differential protein expression in aortic smooth muscle cells cultured from newborn and aged rats. Exp Cell Res 1995; 217: 280-287.
Dunn MJ, Gil C, Kleinhammer C, Lottspeich F, Pennington S, Sanchez JC, Albar JP, Bini L, Corrales F, Corthals G, Fountoulakis MM, Hoogland C, James P, Jensen ON, Jimenez C, Jorrin-Novo J, Kraus HJ, Meyer H, Noukakis D, Palagi PM, Penque D, Quinn A, Rabilloud T. EuPA achieves visibility - An activity report on the first three years. Journal of Proteomics 2008; 71: 11-18.
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003; 31: 3784-3788.
Gay S, Binz PA, Hochstrasser DF, Appel RD. Modeling peptide mass fingerprinting data using the atomic composition of peptides. Electrophoresis 1999; 20: 3527-3534.
Gay S, Binz PA, Hochstrasser DF, Appel RD. Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics 2002; 2: 1374-1391.
Geissbuhler A, Lovis C, Spahni S, Appel RD, Ratib O, Boyer C, Hochstrasser DF, Baud R. A humanist's legacy in medical informatics: visions and accomplishments of Professor Jean-Raoul Scherrer. Methods Inf Med 2002; 41: 237-242.
Golaz O, Hughes GJ, Frutiger S, Paquet N, Bairoch A, Pasquali C, Sanchez JC, Tissot JD, Appel RD, Walzer C, . Plasma and red blood cell protein maps: update 1993. Electrophoresis 1993; 14: 1223-1231.
Golaz O, Wilkins MR, Sanchez JC, Appel RD, Hochstrasser DF, Williams KL. Identification of proteins by their amino acid composition: an evaluation of the method. Electrophoresis 1996; 17: 573-579.
Gras R, Müller M, Gasteiger E, Gay S, Binz PA, Bienvenut W, Hoogland C, Sanchez JC, Bairoch A, Hochstrasser DF, Appel RD. Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection. Electrophoresis 1999; 20: 3535-3550.
Gras R, Hernandez D, Hernandez P, Zangger N, Mescam Y, Frey J, Martin O, Nicolas J, Appel RD. Cooperative Metaheuristics for Exploring Proteomic Data. Artif Intell Rev 2003; 20: 95-120.
Hernandez D, Gras R, Appel R. MoDEL: an efficient strategy for ungapped local multiple alignment. Comput Biol Chem 2004; 28: 119-128.
Hernandez P, Gras R, Frey J, Appel RD. Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics 2003; 3: 870-878.
Hernandez P, Muller M, Appel RD. Automated protein identification by tandem mass spectrometry: issues and strategies. Mass Spectrom Rev 2006; 25: 235-254.
Hochstrasser D, Roux P, Dayer JM, Cruchaud A, Appel R, Funk M, Pellegrini C, Muller AF. Cartographies protéiques de cellules circulantes normales: lymphocytes et monocytes. Schweiz Med Wochenschr 1986; 116: 1773-1775.
Hochstrasser D, Augsburger V, Funk M, Appel R, Pellegrini C, Muller AF. Immobilized pH gradients in capillary tubes and two-dimensional gel electrophoresis. Electrophoresis 1986; 7: 505-511.
Hochstrasser DF, Funk M, Appel RD, Pun T, James RW, Hochstrasser AC, Scherrer JR, Pellegrini C, Muller AF. From biopsy to automatic diagnosis. Schweiz Med Wochenschr 1990; 120: 1862-1866.
Hochstrasser DF, Appel RD, Vargas R, Perrier R, Vurlod JF, Ravier F, Pasquali C, Funk M, Pellegrini C, Muller AF, . A clinical molecular scanner: the Melanie project. MD Comput 1991; 8: 85-91.
Hochstrasser DF, Frutiger S, Paquet N, Bairoch A, Ravier F, Pasquali C, Sanchez JC, Tissot JD, Bjellqvist B, Vargas R, Appel RD, Hughes GJ. Human liver protein map: A reference database established by microsequencing and gel comparison. Electrophoresis 1992; 13: 992-1001.
Hochstrasser DF, Appel RD, Golaz O, Pasquali C, Sanchez JC, Bairoch A. Sharing of worldwide spread knowledge using hypermedia facilities & fast communication protocols (Mosaic and World Wide Web): the example of ExPASy. Methods Inf Med 1995; 34: 75-78.
Hochstrasser DF, Sanchez JC, Appel RD. Proteomics and its trends facing nature's complexity. Proteomics 2002; 2: 807-812.
Hoogland C, Mostaguir K, Appel RD, Lisacek F. The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server. Journal of Proteomics 2008; 71: 245-248.
Hoogland C, Walther D, Palagi PM, Bouchet G, Mostaguir K, Robin X, Appel RD, Lisacek F. A suite of tools to analyse and publish 2-DE data. Proteomics 2008. in press.
Hoogland C, Baujard V, Sanchez JC, Hochstrasser DF, Appel RD. Make2ddb: a simple package to set up a two-dimensional electrophoresis database for the World Wide Web. Electrophoresis 1997; 18: 2755-2758.
Hoogland C, Sanchez JC, Tonella L, Bairoch A, Hochstrasser DF, Appel RD. Current status of the SWISS-2DPAGE database. Nucleic Acids Res 1998; 26: 332-333.
Hoogland C, Sanchez JC, Walther D, Baujard V, Baujard O, Tonella L, Hochstrasser DF, Appel RD. Two-dimensional electrophoresis resources available from ExPASy. Electrophoresis 1999; 20: 3568-3571.
Hoogland C, Sanchez JC, Tonella L, Bairoch A, Hochstrasser DF, Appel RD. The SWISS-2DPAGE database: what has changed during the last year. Nucleic Acids Res 1999; 27: 289-291.
Hoogland C, Sanchez JC, Tonella L, Binz PA, Bairoch A, Hochstrasser DF, Appel RD. The 1999 SWISS-2DPAGE database update. Nucleic Acids Res 2000; 28: 286-288.
Hoogland C, Mostaguir K, Sanchez JC, Hochstrasser DF, Appel RD. SWISS-2DPAGE, ten years later. Proteomics 2004; 4: 2352-2356.
Hughes GJ, Frutiger S, Paquet N, Pasquali C, Sanchez JC, Tissot JD, Bairoch A, Appel RD, Hochstrasser DF. Human liver protein map: update 1993. Electrophoresis 1993; 14: 1216-1222.
Jaconi ME, Theler JM, Schlegel W, Appel RD, Wright SD, Lew PD. Multiple elevations of cytosolic-free Ca2+ in human neutrophils: initiation by adherence receptors of the integrin family. J Cell Biol 1991; 112: 1249-1257.
James RW, Hochstrasser D, Tissot JD, Funk M, Appel R, Barja F, Pellegrini C, Muller AF, 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. J Lipid Res 1988; 29: 1557-1571.
Lisacek F, Chichester C, Gonnet P, Jaillet O, Kappus S, Nikitin F, Roland P, Rossier G, Truong L, Appel R. Shaping biological knowledge: applications in proteomics. Comp Funct Genom 2004; 5: 190-195.
Lisacek F, Cohen-Boulakia S, Appel RD. Proteome informatics II: Bioinformatics for comparative proteomics. Proteomics 2006; 6: 5445-5466.
Lisacek F, Hoogland C, Lescuyer P, Hochstrasser DF, Appel RD. Using bioinformatic resources in the proteomic analysis of biological fluids. Proteomics - Clinical Applications 2007; 1: 900-915.
Mascarini C, Ratib O, Trayser G, Ligier Y, Appel RD. In-house access to PACS images and related data through World Wide Web. Eur J Radiol 1996; 22: 218-220.
Mostaguir K, Hoogland C, Binz PA, Appel RD. 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: 1441-1444.
Müller M, Gras R, Binz PA, Hochstrasser DF, Appel RD. Molecular scanner experiment with human plasma: improving protein identification by using intensity distributions of matching peptide masses. Proteomics 2002; 2: 1413-1425.
Müller M, Gras R, Appel RD, Bienvenut WV, Hochstrasser DF. Visualization and analysis of molecular scanner peptide mass spectra. J Am Soc Mass Spectrom 2002; 13: 221-231.
Orchard S, Hermjakob H, Binz PA, Hoogland C, Taylor CF, Zhu W, Julian RK, Jr., 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: 337-339.
Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R. Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005. Proteomics 2006; 6: 738-741.
Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Binz PA, Hochstrasser DF, Appel RD. MSight: An image analysis software for liquid chromatography-mass spectrometry. Proteomics 2005; 5: 2381-2384.
Palagi PM, Hernandez P, Walther D, Appel RD. Proteome informatics I: Bioinformatics tools for processing experimental data. Proteomics 2006; 6: 5435-5444.
Pasquali C, Frutiger S, Wilkins MR, Hughes GJ, Appel RD, Bairoch A, Schaller D, Sanchez JC, Hochstrasser DF. Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 1996; 17: 547-555.
Peitsch MC, Wilkins MR, Tonella L, Sanchez JC, Appel RD, Hochstrasser DF. Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: the example of Escherichia coli. Electrophoresis 1997; 18: 498-501.
Pun T, Hochstrasser DF, Appel RD, Funk M, Villars-Augsburger V, Pellegrini C. Computerized classification of two-dimensional gel electrophoretograms by correspondence analysis and ascendant hierarchical clustering. Appl Theor Electrophor 1988; 1: 3-9.
Quandt A, Hernandez P, Masselot A, Hernandez C, Maffioletti S, Pautasso C, Appel RD, Lisacek F. swissPIT: A novel approach for pipelined analysis of mass spectrometry data. Bioinformatics 2008; 24: 1416-1417.
Quandt A, Hernandez P, Masselot A, Hernandez C, Maffioletti S, Pautasso C, Appel RD, Lisacek F. swissPIT: A workflow-based platform for analyzing Tandem-MS spectra using the Grid. Proteomics 2008. Submitted.
Rance B, Lisacek F, Froidevaux C. SNK: a new method for extracting sequential nuggets of knowledge from protein families. Nucleic Acids Res 2008. Submitted.
Robin X, Hoogland C, Appel RD, Lisacek F. MIAPEGelDB, a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. Journal of Proteomics 2008; 71: 249-251.
Ruch P, Baud R, Chichester C, Geissbuhler A, Lisacek F, Marty J, Rebholz-Schuhmann D, Tbahriti I, Veuthey AL. Extracting key sentences with latent argumentative structuring. Stud Health Technol Inform 2005; 116: 835-840.
Ruch P, Geissbuhler A, Gobeill J, Lisacek F, Tbahriti I, Veuthey AL, Aronson AR. Using Discourse Analysis to Improve Text Categorization in MEDLINE. Stud Health Technol Inform 2007; 129: 710-715.
Sanchez JC, Appel RD, Golaz O, Pasquali C, Ravier F, Bairoch A, Hochstrasser DF. Inside SWISS-2DPAGE database. Electrophoresis 1995; 16: 1131-1151.
Sanchez JC, Golaz O, Frutiger S, Schaller D, Appel RD, Bairoch A, Hughes GJ, Hochstrasser DF. The yeast SWISS-2DPAGE database. Electrophoresis 1996; 17: 556-565.
Sanchez JC, Wirth P, Jaccoud S, Appel RD, Sarto C, Wilkins MR, Hochstrasser DF. Simultaneous analysis of cyclin and oncogene expression using multiple monoclonal antibody immunoblots. Electrophoresis 1997; 18: 638-641.
Sanchez JC, Chiappe D, Converset V, Hoogland C, Binz PA, Paesano S, Appel RD, Wang S, Sennitt M, Nolan A, Cawthorne MA, Hochstrasser DF. The mouse SWISS-2D PAGE database: a tool for proteomics study of diabetes and obesity. Proteomics 2001; 1: 136-163.
Scherl A, Francois P, Bento M, Deshusses JM, Charbonnier Y, Converset V, Huyghe A, Walter N, Hoogland C, Appel RD, Sanchez JC, Zimmermann-Ivol CG, Corthals GL, Hochstrasser DF, Schrenzel J. Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth. J Microbiol Methods 2005; 60: 247-257.
Scherl A, Zimmermann-Ivol CG, Di DJ, Vaezzadeh AR, Binz PA, mez-Droz M, Cochard R, Sanchez JC, Gluckmann M, Hochstrasser DF. Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect. Rapid Commun Mass Spectrom 2005; 19: 605-610.
Scherl A, Francois P, Charbonnier Y, Deshusses JM, Koessler T, Huyghe A, Bento M, Stahl-Zeng J, Fischer A, Masselot A, Vaezzadeh A, Galle F, Renzoni A, Vaudaux P, Lew D, Zimmermann-Ivol CG, Binz PA, Sanchez JC, Hochstrasser DF, Schrenzel J. Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers. BMC Genomics 2006; 7: 296.
Schuemie M, Chichester C, Lisacek F, Coute Y, Roes PJ, Sanchez JC, Kors J, Mons B. Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE. Proteomics 2007; 7: 921-931.
Stephan C, Hamacher M, Bluggel M, Korting G, Chamrad D, Scheer C, Marcus K, Reidegeld KA, Lohaus C, Schafer H, Martens L, Jones P, Muller M, Auyeung K, Taylor C, Binz PA, Thiele H, Parkinson D, Meyer HE, Apweiler R. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame. Proteomics 2005; 5: 3560-3562.
Stephan C, Reidegeld KA, Hamacher M, van HA, Marcus K, Taylor C, Jones P, Muller M, Apweiler R, Martens L, Korting G, Chamrad DC, Thiele H, Bluggel M, Parkinson D, Binz PA, Lyall A, Meyer HE. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase. Proteomics 2006; 6: 5015-5029.
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jr., Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, III, Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 2007; 25: 887-893.
Tbahriti I, Chichester C, Lisacek F, Ruch P. Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library. Int J Med Inform 2006; 75: 488-495.
Tonella L, Walsh BJ, Sanchez JC, Ou K, Wilkins MR, Tyler M, Frutiger S, Gooley AA, Pescaru I, Appel RD, Yan JX, Bairoch A, Hoogland C, Morch FS, Hughes GJ, Williams KL, Hochstrasser DF. '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 1998; 19: 1960-1971.
Tonella L, Hoogland C, Binz PA, Appel RD, Hochstrasser DF, Sanchez JC. New perspectives in the Escherichia coli proteome investigation. Proteomics 2001; 1: 409-423.
Tsiknakis M, Grangeat P, Binz PA, Potamias G, Lisacek F, Gerfault L, Paulus C, Manakanatas D, Kritsotakis V, Kondylakis H, Perez M, Plexousakis D, Kaforou S, Kafetzopoulos D. Functional specifications of an integrated proteomics information management and analysis platform. Conf Proc IEEE Eng Med Biol Soc 2007; 1: 6064-6068.
Vaezzadeh A, Hernandez C, Vadas O, Deshusses JM, Lescuyer P, Lisacek F, Hochstrasser DF. pICarver: A software tool and strategy for peptides IEF. Journal of Proteomics 2008. In press.
Vargas AR, Balderrama JR, Hoogland C, Gasteiger E, Ivanyi I, Bairoch A, Appel RD, Hochstrasser DF. El nuovo servidor Latinoamericano de biologia molecular de la UCB: bo.expasy.org. Acta Nova 2002; 2: 72-81.
Wilkins MR, Pasquali C, Appel RD, Ou K, Golaz O, Sanchez JC, Yan JX, Gooley AA, Hughes G, Humphery-Smith I, Williams KL, Hochstrasser DF. From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y ) 1996; 14: 61-65.
Wilkins MR, Hochstrasser DF, Sanchez JC, Bairoch A, Appel RD. Integrating two-dimensional gel databases using the Melanie II software. Trends Biochem Sci 1996; 21: 496-497.
Wilkins MR, Ou K, Appel RD, Sanchez JC, Yan JX, Golaz O, Farnsworth V, Cartier P, Hochstrasser DF, Williams KL, Gooley AA. Rapid protein identification using N-terminal "sequence tag" and amino acid analysis. Biochem Biophys Res Commun 1996; 221: 609-613.
Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL. 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: 19-50.
Wilkins MR, Lindskog I, Gasteiger E, Bairoch A, Sanchez JC, Hochstrasser DF, Appel RD. Detailed peptide characterization using PEPTIDEMASS--a World-Wide-Web-accessible tool. Electrophoresis 1997; 18: 403-408.
Wilkins MR, Gasteiger E, Wheeler CH, Lindskog I, Sanchez JC, Bairoch A, Appel RD, Dunn MJ, Hochstrasser DF. Multiple parameter cross-species protein identification using MultiIdent--a world-wide web accessible tool. Electrophoresis 1998; 19: 3199-3206.
Wilkins MR, Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA, Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF. Protein identification with N and C-terminal sequence tags in proteome projects. J Mol Biol 1998; 278: 599-608.
Wilkins MR, Appel RD, Van Eyk JE, Chung MC, Gorg A, Hecker M, Huber LA, Langen H, Link AJ, Paik YK, Patterson SD, Pennington SR, Rabilloud T, Simpson RJ, Weiss W, Dunn MJ. Guidelines for the next 10 years of proteomics. Proteomics 2006; 6: 4-8.

II. Books, book chapters & guest edition

Aebersold R, Affolter M, Agurri A, Elia G, Gruissem W, Neri D, Palagi PM, Sanchez JC, Schlapbach R, Rossier JS, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2005 Congress, Expanding proteomics (Editors). Zurich, Switzerland: 2005.
Affolter M, Gadola S, Haeberli A, Heller M, Palagi PM, Sanchez JC, Solioz M, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2004 Congress, Proteomics for Health (Editors). Bern, Switzerland: 2004.
Affolter M, Lashuel H, Lion N, Moniatte M, Palagi PM, Quadroni M, Sanchez JC. Proceedings of the Swiss Proteomics Society, 2007 Congress, Proteomics - pushing the limits (Editors). Lausanne, Switzerland: 2007.
Appel RD. MELANIE - un système d'analyse et d'interprétation automatique d'images de gels d'électrophorèse bidimensionnelle; systèmes experts et apprentissage automatique. Thèse de doctorat ès sciences, mention informatique (Université de Genève). Le concept moderne/Editions; 1988; ISBN: 2-88242-003-X.
Appel RD. Interfacing and Integrating Databases. In: Wilkins MR, Williams KL, Appel RD, Hochstrasser DF, eds. Proteome research: new frontiers in functional genomics. Berlin Heidelberg: Springer Verlag; 1997: 149-175.
Appel RD, Dunn MJ, Hochstrasser DF. Special issue on Biomedicine and Biocomputing (Guest edition). Electrophoresis, Vol.18, No. 15; 1997.
Appel RD, Hochstrasser DF. Computer Analysis of 2-D Images. In: Link AJ, ed. 2-D Proteome Analysis Protocols. Totowa NJ: Humana Press; 1998: 363-381.
Appel RD, Bairoch A, Hochstrasser DF. 2-D Databases on the World Wide Web. In: Link AJ, ed. 2-D Proteome Analysis Protocols. Totowa NJ: Humana Press; 1998: 383-391.
Appel RD, Scherrer JR. Special Issue on Internet for Medicine and Health Care (Guest Edition). Computers in Biology and Medicine, Volume 28, Number 5; 1998.
Appel RD, Hoogland C, Bairoch A, Hochstrasser DF. Constructing a 2-D Database for the World Wide Web. In: Link AJ, ed. 2-D Proteome Analysis Protocols. Totowa NJ: Humana Press; 1999: 411-416.
Appel RD, Dunn MJ, Hochstrasser DF. Special issue on Biomedicine and Biocomputing (Guest Edition). Electrophoresis, Vol.20, No. 18; 1999.
Appel RD, Bairoch A. Special issue on Applications of Bioinformatics to Mass Spectrometry (Guest Edition). Proteomics, Vol.2, No. 10; 2002.
Appel RD, Bairoch A. Special issue on Tools and Databases for Post-Translational Modifications (Guest Edition). Proteomics, Vol.4, No. 6; 2004.
Bienvenut WV, Müller M, Palagi PM, Heller M, Gay S, Binz PA, Giron M, Gasteiger E, Jung E, Gras R, Sanchez JC, Appel RD, Hochstrasser DF. Proteomics and mass spectrometry: some aspects and recent developments. In: Housby N, ed. Mass Spectrometry and Genomic Analysis. The Netherland: Kluwer Academic Publishers; 2001: 1-53.
Binz PA, Wilkins MR, Gasteiger E, Bairoch A, Appel RD, Hochstrasser DF. Internet Resources for Protein Identification and Characterization. In: Kellner R, Lottspeich F, Meyer HE, eds. Microcharacterization of Proteins. Wiley-VCH, 2nd ed.; 1999: 277-300.
Binz PA, Gasteiger E, Sanchez JC, Bairoch A, Hochstrasser DF, Appel RD. Proteome Analysis. In: Lengauer T, ed. Bioinformatics: from Genomes to Drugs, Vol. II: applications. John Wiley & Sons; 2001: 69-118.
Boyer C, Appel RD. Steps towards Reliable Consumer Health Information. In: Nelson R, Ball MJ, eds. Consumer Informatics: Applications and Strategies in Cyber Health Care (Health Informatics). Springer Verlag; 2004: 80-89.
Ducret A, Eberle AN, Faupel MD, Hofsteenge J, Jenö P, Langen H, Palagi PM, Rossier J, Sanchez JC, Stöcklin R, van Oostrum J, Voshol J. Proceedings of the Swiss Proteomics Proceedings of the Swiss Proteomics Society, 2003 Congress, Understanding biological systems (Editors). Lausanne, Switzerland: FontisMedia Publishers; 2003.
Elia G, Neri D, Palagi PM, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 5th Annual Congress of the Swiss Proteomics Society (Guest Editors). In: Hopfgartner G, ed. J. Chromatography B vol. 840, n.1 7 August 2006; 2006.
Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server. In: Walker JM, ed. The Proteomics Protocols Handbook. Humana Press; 2005: 571-607.
Gay S. Datamining in proteomics: extracting knowledge from peptide mass fingerprinting spectra. Thèse de doctorat ès sciences, mention interdisciplinaire (Université de Genève).; 2002.
Gras R, Hernandez P, Müller M, Appel RD. Scoring functions for mass spectrometric protein identification. In: Conn PM, ed. Handbook of Proteomic Methods. Humana Press; 2003: 477-486.
Gras R, Hernandez D, Hernandez P, Zangger N, Mescam Y, Frey J, Martin O, Nicolas J, Appel RD. Cooperative Metaheuristics for Exploring Proteomic Data. In: Dubitzsky W, Azuaje F, eds. Artificial Intelligence Methods and Tools for Systems Biology. 2004: 87-106.
Hernandez D. Stratégies d'optimisation combinatoire pour le problème de l'alignement local multiple sans indels, et application aux séquences protéiques. Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).; 2005.
Hernandez P. Peptide Identification by Tandem Mass Spectrometry: A Tag-Oriented Open-Modification Search Method. Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).; 2005.
Hernandez P, Binz P-A, Wilkins MR. Protein Identification in Proteome Projects. In: Wilkins MR, Appel RD, Williams KL, Hochstrasser DF, eds. Proteome Research: concepts, technology and application. Berlin Heidelberg: Springer Verlag; 2007.
Hochstrasser DF, Corthals G, Zimmerman C, Scherl A, Bougueleret L, Collinge J, Masselot A, Binz PA, Müller M, Bairoch A, Appel RD, Sanchez JC, Rose K. Proteomics & Mass Spectrometry in Medicine. In: Ashcroft AE, Brenton G, Monhagan JJ, eds. Advances in Mass Spectrometry. Elsevier B.V.; 2004: 19-32.
Hoogland C, Mostaguir K, Appel RD. 2-DE Databases on the World-Wide Web. In: Walker JM, ed. The Proteomics Protocols Handbook. Humana Press; 2005: 259-266.
Hoogland C, Sanchez JC, Hochstrasser DF, Appel RD. 2-D PAGE databases for proteins in human body fluids. In: Thongboonkerd V, ed. PROTEOMICS OF HUMAN BODY FLUIDS: Principles, Methods, and Applications. Humana Press; 2007: 137-145.
Lisacek F, Hoogland C, Bougueleret L, Bairoch A. Data Integration in Proteomics. In: Wilkins MR, Appel RD, Williams KL, Hochstrasser DF, eds. Proteome Research: concepts, technology and application. 2nd, Berlin Heidelberg: Springer Verlag; 2007: 145-168.
Lisacek F, Appel RD. Special issue on Systems Biology (Guest Edition). Proteomics, Vol.7, No. 6. 2007.
Müller M. Molecular Scanner Data Analysis. Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève).; 2003.
Palagi PM, Sanchez JC, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2001 Congress, Functional Proteomics (Editors). Lausanne, Switzerland: FontisMedia Publishers; 2001.
Palagi PM, Quadroni M, Rossier J, Sanchez JC, Stöcklin R. Proceedings of the Swiss Proteomics Society, 2002 Congress, Applied Proteomics (Editors). Lausanne, Switzerland: FontisMedia Publishers; 2002.
Palagi PM, Quadroni M, Rossier J, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 2nd Annual Conference of the Swiss Proteomics Society (Guest Editors). Proteomics vol.3, n°8; 2003.
Palagi PM, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 3rd Annual Congress of the Swiss Proteomics Society (Guest Editors). Proteomics vol. 4, n.8; 2004.
Palagi PM, Walther D, Bouchet G, Voordijk S, Appel RD. Computer Analysis of 2D Images. In: Walker JM, ed. The Proteomics Protocols Handbook. Humana Press; 2005: 267-277.
Palagi PM, Sanchez JC, Stöcklin R. Special Issue on the Proceedings of the 4th Annual Congress of the Swiss Proteomics Society (Guest Editors). Proteomics vol. 45, n.12; 2005.
Palagi PM, Brunner Y, Sanchez JC, Appel RD. Proteomics: beyond cDNA. In: Lengauer T, ed. Bioinformatics: from Genomes to Therapies. John Wiley & Sons; 2006.
Palagi PM, Walther D, Bouchet G, Voordijk S, Appel RD. Image analysis and quantitation. In: Cellis JE, ed. Cell Biology: a laboratory handbook. 3rd Edition, Academic Press; 2006: 207-215.
Palagi PM, Walther D, Zimmermann-Ivol CG, Appel RD. Proteome Imaging. In: Wilkins MR, Appel RD, Williams KL, Hochstrasser DF, eds. Proteome research: concepts, technology and application. Berlin Heidelberg: Springer Verlag; 2007.
Palagi PM, Lisacek F. Analytical bioinformatics for proteomics. In: Feytmans E, ed. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2008. Submitted.
Palagi PM, Lisacek F, Appel RD. Database interrogation algorithms for identification of proteins in proteomic separations. In: David Sheehan, ed. Methods in Molecular Biology – Two Dimensional Electrophoresis Protocols. Humana Press; 2008. In press.
Sanchez JC, Wilkins M, Appel RD, Hochstrasser DF. Identifying Proteins for Proteome Studies. In: Creighton ET, ed. Protein Function: a practical approach (second edition). IRL Press; 1997: 1-27.
Sanchez JC, Palagi PM, Stöcklin R. Special Issue on the Proceedings of the 1st Annual Conference of the Swiss Proteomics Society (Guest Editors). Proteomics vol.2, n°7; 2002.
Voordijk S, Walther D, Bouchet G, Appel RD. Image Analysis Tools in Proteomics. Encyclopedia of the human genome. Macmillian Publishers Ltd, Nature Publishing Group; 2003: 404-410.
Wilkins MR, Williams KL, Appel RD, Hochstrasser DF. Proteome research: new frontiers in functional genomics. Berlin Heidelberg, Springer Verlag; 1997.
Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, Hochstrasser DF. Protein Identification and Analysis Tools in the ExPASy Server. In: Link AJ, ed. 2-D Proteome Analysis Protocols. Totowa NJ: Humana Press; 1998: 531-552.
Wilkins MR, Appel RD, Williams KL, Hochstrasser DF. Proteome Research: concepts, technology and application. Berlin Heidelberg, Springer Verlag; 2007.

III. Articles in journals without editorial policy

Appel RD, Hochstrasser DF, Bairoch A. Electrophorèse bidimensionnelle et informatique: un outil pour le diagnostic médical? Labolife 1993; 4: 7-8.
Appel RD, Hochstrasser DF, Pellegrini C. Le projet Melanie. Cahier spécial de la Faculté des Sciences 1993.
Bairoch A, Appel RD, Peitsch MC. The ExPASy WWW Server - a Tool for Proteome Research. Protein Data Bank Quaterly Newsletter 1997; 81: 5-7.
Bairoch A, Gasteiger E, Gattiker A, Hoogland C, Lachaize C, Mostaguir K, Ivanyi I, Appel RD. The ExPASy proteome WWW server in 2003. Swiss Institute of Bioinformatics. 2003; http://www.expasy.org/doc/expasy.pdf.
Boyer C, Appel RD, Scherrer JR. Internet et la médecine: solutions proposées par la Fondation Health On the Net. Cahiers Psychiatriques 1998; 24: 137-144.
Boyer C, Appel RD, Griesser V, Scherrer JR. Internet pour les médecins: un outil d’aujourd’hui et de demain. Revue Médicale de la Suisse Romande 1999; 119: 137-144.
Hochstrasser D, Funk M, Appel R, James R, Hochstrasser AC, Scherrer JR, Pellegrini C, Muller AF. Applications Cliniques de l'Electrophorèse Bidimensionnelle. Spectra Biologie 1990; 90/1: 45-46.
Hochstrasser DF, Sanchez JC, Golaz O, Tissot JD, Appel RD. Cartographie protéique du sérum et du plasma. Méd & Hyg 1995; 53: 988-992.
Pellegrini C, Funk M, Appel RD. Le traitement de l'image. Cahiers de la faculté des sciences 1985; 3-14.
Pellegrini C, Hochstrasser D, Appel R, Funk M. Informatique et électrophorèse : de l'image d'une biopsie tissulaire au diagnostic automatique. Fonds National Suisse de la Recherche Scientifique 1987.
Sanchez JC, Appel R, Hochstrasser DF. L’électrophorèse bidimensionnelle des protéines. Laboratoire et Médecine 1998; 25.

IV. Conference proceedings

Alpay LL, Appel RD, Hochstrasser DF. Building an Expert System for Obtaining Diagnoses from Protein Maps. MEDINFO 92. Geneva: Sept. 1992: 649-652.
Appel R, Funk M, Hochstrasser D, Pellegrini C, Muller AF. A computerized system for spot detection and analysis of two-dimensional electrophoresis images. In: Thalmann N, Thalmann D, eds. Computer-generated images (the state of the art) (Proceedings of Graphics Interface, Toronto 1985). Tokyo: Springer-Verlag; 1985: 118-124.
Appel R, Funk M, Hochstrasser D, Muller AF, Pellegrini C. Un système expert d'aide à l'analyse et l'interprétation d'images médicales. Cognitiva. Paris: 1985.
Appel R, Funk M, Hochstrasser D, Muller AF, Pellegrini C. Mélanie, un système expert d'aide à l'analyse et à l'interprétation d'électrophorèses bidimensionnelles. In: Galteau, Siest, eds. Progrès Récents en Electrophorèse Bidimensionnelle. Presses Universitaires de Nancy; 1986: 107-116.
Appel R, Funk M, Hochstrasser D, Muller AF, Pellegrini C. Un système interactif de traitement d'images d'électrophorèse bidimensionnelle. International Electronic Image Week. Nice: Apr. 1986.
Appel RD, Komorowski HJ, Barr CE, Greenes RA. Intelligent Focusing in Knowledge Indexing and Retrieval - The Relatedness Tool. Symposium on Computer Applications in Medical Care. Washington: Nov. 1988.
Appel RD, Ratib O, Scherrer JR. The Use of a File Format Description Language for easy Handling of Images from Multiple Sources. EuroPACS meeting. Trieste: 1990.
Appel RD, Ratib O, Scherrer JR. Champolion : an Image File Format Translator. Picture Archiving and Communication Systems (PACS) in Medicine. Evian, France: Oct. 1990.
Appel RD, Brunet D, Funk M, Hochstrasser DF. Improving automatic matching of 2D-PAGE images. 2D-PAGE' 1991, Proc. Int. Meeting on Two-Dimensional Electrophoresis. London: July 1991: 58-62.
Appel RD, Bologna G, Hochstrasser DF. Classification tools for Diagnostic Rule Formation from Protein Maps. Proceedings of MIE 93, Jerusalem, April 18-22, 1993. Freund Publishing House, Ltd; 1993: 40-44.
Baujard O, Baujard V, Aurel S, Boyer C, Appel RD. A multi-agent softbot to retrieve medical information on Internet. Medinfo 1998; 9 Pt 1: 150-154.
Bologna G, Appel RD. A comparaison study on protein fold recognition. 9th International Conference on Neural Information Processing. Singapore: Nov. 2002.
Bologna G. On the validation of the DIMLP Neural Network. FLAIRS'02. Florida: Nov. 2002.
Boyer C, Selby M, Appel RD. The Health On the Net Code of Conduct for medical and health web sites. Medinfo 1998; 9 Pt 2: 1163-1166.
Boyer C, Selby M, Appel RD. The Health On the Net code of conduct for medical and health web sites. MEDINFO 98. Seoul: Aug. 1998.
Burke P, Appel RD, Funk M, Vargas R, Hochstrasser D, Scherrer JR. The Application of Distributed Articificial Intelligence to Medical Diagnosis. AIME 91, Proc. 3rd Conference on AI in Medicine, Maastricht, Netherlands, June 1991. Springer Verlag; 1991: 160-172.
Burke P, Appel RD, Funk M, Hochstrasser DF, Scherrer JR. Can AI Help the Physician ? Third Annual Meeting of the Swiss Group for Artificial Intelligence and Cognitive Science SGAICO'91. Mar. 1992: 49-59.
Burke P, Appel RD, Vargas JR, Alpay LL, Pellegrini C, Scherrer JR, Hochstrasser DF. Computer Assisted Analysis of Two-Dimensional Polyacrylamide Gel Electrophoresis. MEDINFO 92. Geneva: Sept. 1992: 312-317.
Frey J, Gras R, Hernandez P, Appel RD. A Hierarchical Model of Coarse-Grained Parallel Genetic Programming. PPAM 2003 - Fifth International Conference on Parallel Processing and Applied Mathematics. Czestochowa, Poland: Sept. 2003.
Frey J, Gras R, Hernandez P, Appel R. A Hierarchical Model of Parallel Genetic Programming Applied to Bioinformatic Problems. Lecture Notes in Computer Science 2004; 3019: 1146-1153.
Friha L, Baujard O, Berry P, Appel RD. DISA: an interactive scheduler using abstractions. 14th Workshop of the UK Planning and Scheduling SIG, University of Essex. Colchester, U.K.: Nov. 1995.
Froidevaux C, Lisacek F, Rance B. Extracting Sequential Nuggets of Knowledge. Lecture Notes in Computer Science 2007; 4653: 740-750.
Funk M, Appel R, Roch C, Hochstrasser D, Pellegrini C, Muller AF. Knowledge acquisition in expert system assisted diagnosis : a machine learning approach. In: Fox J, Fieschi M, Engelbrecht R, eds. Lecture Notes in Medical Informatics (proceedings AIME, Marseille 1987). Springer-Verlag; 1987.
Goodman AM, Burke P, Funk M, Vargas RJ, Snydr-Michal JT, Appel RD, Hochstrasser DF. A model for a distributed database to manage large 2D-PAGE collaborative experiments. 2D-PAGE' 1991, Proc. Int. Meeting on Two-Dimensional Electrophoresis. London: July 1991: 73-77.
Gras R, Gras R, Gasteiger E, Binz PA, Müller M, Chopard B, Appel RD. Classification automatique par algorithme génétique dans le cadre de l'identification par empreinte de masse peptidique. Journées Fouille dans les données par la méthode d'analyse statistique implicative. Caen: 2000: 59-84.
Hochstrasser D, Funk M, Appel R, Pellegrini C, Muller AF. Clinical application of automatic computer comparison of 2 D. gel electrophoresis images: diagnosis of Waldenström macroglobulinemia ? In: Galteau, Siest, eds. Progrès Récents en Electrophorèse Bidimensionnelle. Presses Universitaires de Nancy; 1986: 117-120.
Hochstrasser D, Maignan MF, Dumont JM, Funk M, Appel R, Pellegrini C, Muller AF. CCL4 induced cirrhosis of the liver: 2 dimensional gel electrophoretic analysis; biochemical and histological correlation. In: Dunn M, ed. Electrophoresis '86. VCH Publishers; 1986: 598-602.
Hochstrasser D, Augsburger V, Funk M, Appel R, Pellegrini C, Muller AF. Immobilized pH gradients in capillary tubes : effect of immobilines dilution on 2 dimensional gel pictures. In: Dunn M, ed. Electrophoresis '86. VCH Publishers; 1986: 566-568.
Hochstrasser D, Funk M, Appel RD, James R, Hochstrasser AC, Scherrer JR, Pellegrini C, Muller AF. Clinical applications of two-dimensional polyacrylamide gel electrophoresis. Electrophoresis forum '89. 1989: 134-136.
Hochstrasser D, Ratib O, Funk M, Appel R, Scherrer JR. Images en Médecine Clinique et en Médecine Fondamentale. Journées Francophones d'Informatique Médicale. Nîmes: 1990: 231-234.
Hochstrasser D, Sanchez JC, Binz PA, Bienvenut W, Appel RD. A clinical molecular scanner to study human proteome complexity. 2000: 33-38.
Hochstrasser DF, Funk M, Appel RD, Scherrer JR, Pellegrini C, Muller AF. Les techniques d'intelligence artificielle dans l'analyse des électrophorèses bidimensionnelles. Journées Franc. d'IA. Montpelier: 1988.
Hochstrasser DF, Appel RD, Vargas R, Perrier R, Ravier F, Funk M, Pellegrini C, Muller AF, Scherrer JR. Clinical molecular scanner : The Melanie project. Proceedings of HICSS-24. Hawaii: 1991: 626-635.
Hochstrasser DF, Huber O, Kaelin K, Touss A, Pavlovic A, Funk M, Appel RD, Pasquali C, Ravier F, Tissot JD, Goodman A, Muller AF. Clinical Application of Two Dimensional Polyacrylamide Gel Electrophoresis: Its Future. 2D-PAGE' 1991, Proc. Int. Meeting on Two-Dimensional Electrophoresis. London: July 1991: 224-229.
Hochstrasser DF, Appel RD, Burke P, Goodman A, Snydr-Michal J, Vargas JR, Ratib O, Pellegrini C, Scherrer JR. L'Imagerie dans le diagnostic médical - l'exemple du système Melanie. Journées Francophones d'Informatique. Genève: Apr. 1992.
Hochstrasser DF, Appel RD, Bairoch A, Golaz O, Pasquali C, Sanchez JC. Expert Protein Analysis Server (ExPASy). IMIA WG6 Working Conference. Vevey: May 1994.
Hochstrasser DF, Corthals G, Zimmerman C, Scherl A, Bougueleret L, Collinge J, Masselot A, Binz PA, Müller M, Bairoch A, Appel RD, Sanchez JC, Rose K. Proteomics & Mass Spectrometry in Medicine. International Mass Spectrometry Conference. Edinburgh: Aug. 2003.
Langevin E, Bairoch A, Appel RD, Rialle V, Scherrer JR, Hochstrasser DF. ExPASy: Un système expert pour l'analyse de séquences protéiques. 4èmes Journées Francophones d'Informatique Médicale. Bruxelles: June 1993.
Lisacek F, Chichester C, Kaplan A, Sandor A. Discovering paradigm shift patterns in biomedical abstracts: Application to neurodegenerative diseases. First International Symposium on Semantic Mining in Biomedicine (SMBM). 2005.
Martin O, Gras R, Hernandez D, Appel RD. Optimizing Genetic Algorithms Using Self-Adaptation And Explored Space Modelization. The Fifth International Workshop on Frontiers in Evolutionary Algorithms (FEA 2003). Cary, North Carolina, USA: Sept. 2003: 291-294.
Mascarini C, Ratib O, Trayser G, Ligier Y, Appel RD. In-house Access to PACS Images and Related Data Through World Wide Web. SPIE International Symposium - Medical Imaging. Newport Beach, CA: Feb. 1996.
Nikitin F, Lisacek F, Appel RD. Modular analysis of bacterial proteins in specific pathways. ECCB 05, 4th European Conference on Computational Biology. Madrid, Spain: Sept. 2005.
Quandt A, Hernandez P, Kunzst P, Pautasso C, Tuloup M, Hernandez C, Appel RD. Grid-based analysis of tandem mass spectrometry data in clinical proteomics. Stud Health Technol Inform 2007; 126: 13-22.
Ratib O, Ligier Y, Appel R, Scherrer JR. Papyrus: a portable image file format. Picture Archiving and Communication Systems (PACS) in Medicine. Evian, France: Oct. 1990.
Ratib O, Mascarini C, Trayser G, Revillard C, Ligier Y, Appel RD. The “INTRANET” concept applied for convenient access to PACS image data and computerized patient record. 14TH International EuroPACS Meeting. Heraklion, Crete, Hellas: Oct. 1996.
Scherl A, Francois P, Bento M, Masselot A, Binz PA, Hoogland C, Appel RD, Zimmermann-Ivol CG, Sanchez JC, Stahl-Zeng J, Schrenzel J, Hochstrasser DF. Exploring antibiotic resistance with isobaric tags. 53rd ASMS Conference on Mass Spectrometry. San Antonio, Texas: June 2005.
Vargas AR, Argote GG, Appel RD, Hochstrasser D, Pellegrini C. Classificación automática de imágenes de geles de electrofóresis bidimensionales mediante la classificación heurística. Simposio de ciencias y tecnologia. Cochabamba, Bolivia: Sept. 1998: 263-286.
Vargas JR, Appel RD, Hochstrasser DF, Pellegrini C. Modeling and Quantification of Protein Maps by Gaussian Fitting. Proc. CAIP'93, 5th International Conference on Computer Analysis of Images and Patterns, Budapest, September 13-15, 1993. Springer Verlag; 1993: 627-633.
Vargas JR, Bologna G, Appel RD, Pellegrini C. Protein Maps Classification Using Neural Networks. Swiss Vision'93. Zurich: Sept. 1993.
Vargas JR, Bologna G, Appel RD, Hochstrasser DF, Pellegrini C. Classification of Protein Patterns using Neural Networks: Pixel based versus Feature based Approach. Proc. AIME'93, 5th Conference on AI in Medicine. Munich, Germany: Oct. 1993.
Zangger N, Cerutti L, Pagni M, Lisacek F, Appel RD. Clustering protein sequences based on motif content. ECCB 05, 4th European Conference on Computational Biology. Madrid, Spain: Sept. 2005.

V. Abstracts and posters

Ahrne E, Masselot A, Vaezzadeh A, Binz P-A, Appel RD. More (and faster) MS/MS identifications: combining on-the-fly spectral library search (spectraST) and sequence database search (Phenyx). HUPO 2007. Seoul, South Korea: Oct. 2007.
Ahrne E, Masselot A, Mueller M, Mauron Y, Mylonas R, Vaezzadeh A, Binz P-A, Appel RD, Lisacek F. More (and faster) MS/MS identifications: combining on-the-fly spectral library search (spectraST) and sequence database search (Phenyx). SPS'07. Lausanne, Switzerland: Dec. 2007.
Appel RD, Hochstrasser DF, Funk M, Roch C, Pun T, Pellegrini C. Automatic classification of 2 dimensional gel electrophoresis pictures by heuristic clustering. Electrophoresis '88. Copenhagen, Denmark: 1988.
Appel RD, Hochstrasser DF, Vargas R, Funk M, Pellegrini C, Muller AF, Scherrer JR. New Developments Toward Automatic Medical Diagnosis in the MELANIE Project. International Meeting of the Electrophoresis Societies. Washington DC: Mar. 1991.
Appel RD, Vargas JR, Bjellqvist B, Corre JY, Snydr-Michal J, Burke P, Hochstrasser DF. Improving quantitative and qualitative analysis of 2D-PAGE images. Annual Meeting of the Electrophoresis Society. Research Triangle Park, NC: June 1992.
Appel RD, Bairoch A, Miu M, Sanchez JC, Golaz O, Hochstrasser DF. SWISS-2DPAGE: A 2D-PAGE Image Database. Annual Symposium of the American Electrophoresis Society. Charleston: Nov. 1993.
Appel RD, Bairoch A, Peitsch M, Hochstrasser DF. Browsing through Molecular Biology Data on Internet : the ExPASy World-Wide Web Server. ACM Workshop on Information Retrieval and Genomics. Bethesda, MD: May 1994.
Appel RD, Bairoch A, Sanchez JC, Pasquali C, Golaz O, Hochstrasser DF. World-Wide Web and the ExPASy Server. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 50-51.
Appel RD, Sanchez JC, Golaz O, Hochstrasser DF. World Wide Federation of 2D gel data bases. 2nd Siena 2D electrophoresis meeting. Siena, Italy: Sept. 1996.
Appel RD, Sanchez JC, Bairoch A, Hochstrasser DF. Federation of two-dimensional electrophoresis databases and integration with interactive data analysis programs. BIOINFORMATICS<-->STRUCTURE (reprinted in Folding & Design, vol. 1, supplement, 1996, p. S2). Jerusalem, Israel: Nov. 1996.
Appel RD, Bairoch A, Walther D, Binz PA, Hoogland C, Fabbretti R, Palagi P, Bouchet G, Gras R, Müller M, Gay S, Gasteiger E, Sanchez JC, Hochstrasser DF. Improving, accelerating and automating proteomics discovery with bioinformatics. Elektrophorese Forum’99. Munich: Oct. 1999.
Appel RD, Bairoch A, Walther D, Binz PA, Hoogland C, Fabbretti R, Palagi P, Bouchet G, Gras R, Müller M, Gay S, Gasteiger E, Sanchez JC, Hochstrasser DF. Improving Proteomics Discovery with Bioinformatics. Swiss Electrophoresis Society (CHEL) meeting. Montreux Palace: Dec. 1999.
Appel RD, Walther D, Binz PA, Hoogland C, Fabbretti R, Palagi P, Bouchet G, Gras R, Müller M, Gay S, Gasteiger E, Bairoch A, Sanchez JC, Hochstrasser DF. High-throughput proteomics: the need for high-performance computing. 27th SPEEDUP Workshop. Lugano: Mar. 2000.
Appel RD, Walther D, Binz PA, Hoogland C, Gras R, Hochstrasser DF. Le rôle de la bioinformatique en protéomique. Atelier de formation - Proteomics: new experimental approaches to unravel biological processes. Le Vésinet: May 2000.
Appel RD, Walther D, Bouchet G, Voordijk S, Sontot C, Palagi PM, Sanchez JC, Hochstrasser DF. Future trends in 2-DE computer analysis. 4th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2000.
Appel RD. Proteomics in the 3rd Millennium: Is It Possible without HPC? Teraflop. Nov. 2001.
Appel RD, Bairoch A. Proteomics: back to the future. Congress of the Swiss Proteomics Society. Geneva: Nov. 2001: 6.
Appel RD, Hernandez P, Tuloup M, Walther D, Gras R, Müller M, Hoogland C, Binz PA, Corthals GL, Sanchez JC, Hochstrasser DF. New developments in proteomatics at the Swiss Institute of Bioinformatics. First Annual HUPO Congress. Versailles, France: Sept. 2002.
Appel RD, Binz PA, Bouchet G, Catherinet S, Gras R, Hernandez C, Hernandez D, Hernandez P, Hoogland C, Lisacek F, Mostaguir K, Müller M, Palagi P, Pelhatre S, Tuloup M, Walther D, Zangger N. Current developments at the Proteome Informatics Group, Swiss Institute of Bioformatics, Geneva. Quelle informatique et bioinformatique pour la protéomique ? Journée Rhône-Alpes Genopole. INRIA Rhône-Alpes, Montbonnot (Grenoble): June 2004.
Appel RD. Current and future challenges in proteome informatics. BC2, Basel Computational Biology Conference 2005. Basel: Mar. 2005.
Appel RD, Masselot A, Budin N, Evalet O, Cambria L, Binz PA. What’s in MS spectra? What’s in databases? Take the best to identify active proteins. HUPO 4th Annual Congress. Munich: Aug. 2005.
Appel RD, Binz PA, Bouchet G, Catherinet S, Dornevil D, Hernandez C, Hernandez P, Hoogland C, Ivanyi I, Lisacek F, Mostaguir K, Mangold V, Nikitin F, Paesano S, Palagi PM, Pelhatre S, Quandt A, Rossier G, Sapsezian C, Sonesson K, Tuloup M, Verbregue L, Walther D, Zangger N. Swiss-Prot and PIG: 20 years of fruitful collaboration. In-Silico Analysis of Proteins - Celebrating the 20th anniversary of Swiss-Prot. July 2006. Feb. 2006.
Appel RD, Hernandez P, Walther D, Lisacek F, Palagi PM, Hoogland C, Binz P-A, Masselot A, Nahas N, Sanchez JC, Hochstrasser DF. Analytical bioinformatics: from data to knowledge. MILA 2006 - First Latin-American Medical Informatics Congress. Dec. 6 A.D. 2006.
Appel RD. Making Protein Identification Reliable. HUPO Human Liver Proteome Project workshop. May 6 A.D. 2006.
Appel RD, Hernandez P, Walther D, Lisacek F, Palagi PM, Hoogland C, Binz PA, Masselot A, Sanchez JC, Hochstrasser DF. MS Analysis: imaging and protein identification tools. Joint Third AOHUPO and Fourth Structural Biology and Functional Genomics Conference. Dec. 2006. Singapore: Dec. 2006.
Appel RD, Quandt A, Walther D, Masselot A, Arhne E, Palagi PM, Binz P-A, Hernandez P, Hochstrasser DF, Lisacek F. Has the proteome informatics bottleneck been sufficiently widened? HUPO 6th Annual World Congress. Oct. 7 A.D. 2007.
Bairoch A, Appel RD, Offord RE, Hochstrasser DF. Bioinformatics for Proteome Analysis in Switzerland. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Baujard O, Baujard V, Aurel S, Boyer C, Appel RD. MARVIN - A multi-agent softbot to retrieve multilingual medical information on the Internet. MEDNET97 - European Congress on the Internet in Medicine. Brighton, U.K.: Nov. 1997.
Bienvenut W, Binz PA, Appel RD, Sanchez JC, Rose K, Veuthey JL, Hochstrasser DF. Parallel protein chemical processing during transblot. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Bienvenut W, Binz PA, Appel RD, Sanchez JC, Veuthey JL, Hochstrasser DF. Towards a molecular scanner for proteome research : parallel protein chemical processing during transblot. Journée des Sociétés Suisse et Française d’Electrophorèse. Bâle: Dec. 1998.
Bienvenut WV, Müller M, Paesano S, Gras R, Binz PA, Converset V, Déon C, Appel RD, Sanchez JC, Hochstrasser DF. Comprehensive proteome analysis: the molecular scanner. Congrès commun des sociétés de biochimie française et italienne. Sienne: Sept. 2000.
Bienvenut WV, Heller M, Müller M, Paesano S, Converset V, Gras R, Binz PA, Sanchez JC, Appel RD, Hochstrasser DF. Comprehensive one step analysis by the molecular scanner: quantitative evaluation. 4th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2000.
Binz PA, Bienvenut W, Fabbretti R, Gasteiger E, Bairoch A, Appel RD, Sanchez JC, Hochstrasser DF. The “molecular scanner”: an highly automated methos for protein identification and 2-D PAGE annotation. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Binz PA, 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 JC, Hochstrasser DF. Automation in Proteomics: the molecular scanner and the robotization of protein identification by peptide mass fingerprinting. 3ème Journée d'Interaction des Groupes de Recherche des Facultés de Médecine de Genève et Lausanne. Changins, Switzerland: Oct. 1999.
Binz PA, Bairoch A, Sanchez JC, Hochstrasser DF, Appel RD. Bioinformatics challenges in proteomics. MipTec-ICAR. 2000.
Binz PA, Bairoch A, Hochstrasser DF, Appel RD. Bioinformatics in proteomics. Proteomics Workshop. Korea: June 2000.
Binz PA, Gasteiger E, Gras R, Hoogland C, Müller M, Walther D, Bienvenut W, Zimmermann C, Sanchez JC, Bairoch A, Appel RD, Hochstrasser DF. Informatics of Proteomics and Possible Use in Laboratory Sciences. Computation in Clinical Laboratory 2000 Third Millenium CCL. Milano: Sept. 2000.
Binz PA, Müller M, Hoogland C, Walther D, Gay S, Gras R, Bienvenut WV, Pasquarello C, Paesano S, Corthals G, Sanchez JC, Bairoch A, Hochstrasser DF, Appel RD. The Synergy between Bioinformatics and Proteomics Research. Danish Society for Biochemistry and Molecular Biology. Oct. 2002.
Binz PA, Gay S, Hochstrasser DF, Appel RD. Knowledge Discovery to understand and predict peptide mass fingerprinting spectra. First Annual HUPO Congress. Versailles, France: Sept. 2002.
Binz PA, Bologna G, Gay S, Hernandez C, Hoogland C, Mostaguir K, Tuloup M, Appel RD. Bioinformatics tools in proteomics: issues and perspectives. Functional Genomics and Disease, ESF Workshop. Prague: May 2003.
Binz PA, Tuloup M, Hernandez C, Fabretti R, Hernandez P, Bologna G, Hoogland C, Mostaguir K, Walther D, Bouchet G, Palagi PM, Appel RD. Bioinformatics and Proteome Analysis in MS dominated workflows. Jahrestagung Chemie 2003 der Gesellschaft Deutscher Chemiker. München: Oct. 2003.
Binz PA, Paesano S, Zanini P, Scherl A, Hoogland C, Allard L, Zimmermann C, Carrette O, Sanchez JC, Borella S, Castelnovo R, Appel RD, Hochstrasser DF. Why and How? A LIMS in a proteomics research environment. Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 170-171.
Binz PA, Masselot A, Cambria L, Müller M, Tuloup M, Hernandez C, Appel RD. Phenyx: about compatibility of high-throughput and pertinence in protein identification. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 84.
Binz PA, Masselot A, Cambria L, Müller M, Tuloup M, Hernandez C, Walther D, Catherinet S, Appel RD. Bioinformatics and relevance in proteomics. Société française d'électrophorèse et d'analyse protéomique. Bordeaux: Oct. 2004.
Binz PA, Masselot A, Walther D, Appel RD. Interpretation of protein identification results: more questions than answers? The confidence and validation issue. BSPR/EBI Meeting – From Proteins to Systems. Cambridge: July 2005.
Binz PA, Masselot A, Appel RD. Proteome Bioinformatics: critically evaluating MS data. Swiss Proteomics Society 2004 Congress: Expanding proteomics. Zurich, Swizerland: Dec. 2005.
Binz PA, Masselot A, Budin N, Nahas N. Discover Multiple Facets of the Innovative Phenyx Platform and Achieve Increased Confidence in Protein Identification. HUPO 4th Annual Congress. Munich: Aug. 2005.
Binz PA. Phenyx: understand and manage. Proteomics Methods Forum. Apr. 2005. Aug. 2005.
Binz PA. Aspects de bioinformatique appliquée à l'étude du phosphoprotéome. Atelier phosphoprotéome. June 2005. Aug. 2005.
Binz PA, Masselot A, Mylonas R, Bouyssiè D, Niknejad A, Budin N, Appel RD. "Garbage in – Garbage out": The peaklist issue in proteomics. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 106.
Bologna G, Appel RD, Hochstrasser DF. Automatic Classification of 2-D PAGE Images. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 56-57.
Bologna G, Veuthey AL, Appel RD. N-terminal myristoylation predictions by neural network ensembles. 5th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2002.
Boyer C, Baujard O, Baujard V, Aurel S, Selby M, Appel RD. HON automated database of health and medical information. MEDNET96 - European Congress on the Internet in Medicine. Brighton, U.K.: Oct. 1996.
Boyer C, Selby M, Baujard V, Appel RD. Medical Information on the Internet: Who wants what? MEDNET97 - European Congress on the Internet in Medicine. Brighton, U.K.: Nov. 1997.
Boyer C, Selby M, Appel RD. The Health On the Net Code of Conduct for medical and health Web sites; its status in 1997. MEDNET97 - European Congress on the Internet in Medicine. Brighton, U.K.: Nov. 1997.
Boyer C, Baujard V, Scherrer JR, Appel RD. HON’s Third survey on the usage of the Internet for medical/health Internet purposes. MEDNET98 - World Congress on the Internet in Medicine. Brighton, U.K.: 1998.
Boyer C, Baujard O, Baujard V, Appel RD. New developments of MedHunt medical search engine. MEDNET98 - World Congress on the Internet in Medicine. Brighton, U.K.: 1998.
Boyer C, Baujard V, Nater T, Scherrer JR, Appel RD. HONselect: A new assisted-search facility for health information and resources integrating heterogeneous databases. MEDNET'99 - 4th World congress on the internet in medicine. Heidelberg, Germany: Sept. 1999.
Boyer C, Baujard V, Nater T, Scherrer JR, Appel R. HON's Fourth survey on the usage of the Internet for medical & health Internet purposes. MEDNET'99 - 4th World congress on the internet in medicine. Heidelberg, Germany: Sept. 1999.
Boyer C, Baujard V, Nater T, Scherrer JR, Appel RD. The Health On the Net Code of Conduct for medical and health-related Web sites: Three years on. MEDNET'99 - 4th World congress on the internet in medicine. Heidelberg, Germany: Sept. 1999.
Burke P, Appel RD, Funk M, Hochstrasser DF, Scherrer JR. Can AI Help The Physician ? SCAICO 1991. Biel: Oct. 1991.
Chauvet A, Binz P-A, Vaezzadeh A, Zimmermann-Ivol CG, Palagi PM, Appel RD, Thiele H, Hochstrasser DF. High-throughput data management of Shotgun IEF results by ProteinScape. ASMS Conference on Mass Spectrometry. Indianapolis, Indiana: June 2007.
Colinge J, Masselot A, Pitzer E, Mylonas R, Appel RD. Mass Spectrometry Data Mining supported by an open source initiative to develop new generic peak intensity models and evaluate peptide de novo sequencing algorithms. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 101.
Colinge J, Masselot A, Pitzer E, Appel RD. InSilicoSpectro - Proteomics Open-Source Library. 54th ASMS Conference on Mass Spectrometry. Jan. 2006. Seattle, Washington: Jan. 2006.
Corthals G, Schmidt G, Scherl A, Pasquarello C, Bienvenut W, Binz PA, Walther D, Voordijk S, Appel RD, Hochstrasser DF, Sanchez JC. Proteomics: tools and applications. Association of Clinical Biochemists (UK), Pharmacogenomics Meeting. Cambridge, UK: Sept. 2002.
Corthals G, Pasquarello C, Scherl A, Burgess J, Allard L, Deshusses J, Walter N, Paesano S, Carrette O, Bienvenut W, Hoogland C, Binz PA, Müller M, Appel RD, Hochstrasser DF, Sanchez JC. Tools and technologies in proteome analysis. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 9-10.
Corthals G, Pasquarello C, Scherl A, Burgess J, Vaezzadeh A, Deshusses J, Hochstrasser DF, Sanchez JC, Binz PA, Appel RD. Controlling data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry. MipTec. Basel: 2003.
Corthals GL, Pasquarello C, Scherl A, Burgess J, Vaezzadeh A, Binz PA, Deshusses J, Appel RD, Sanchez JC, Hochstrasser DF. Guiding data acquisition and data quality in proteomics via ordered peptide arrays and non-redundant mass-spectrometry (NRMS). 16th International Mass Spectrometry Conference. Edinburgh: Aug. 2003.
Fabbretti R, Binz PA, Bienvenut W, Gasteiger E, Bairoch A, Wilkins MR, Sanchez JC, Walther D, Hochstrasser DF, Appel RD. Towards fully automated identification of proteins on 2-D PAGE gels. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Funk M, Appel RD, Bost JM, Hochstrasser DF, Muller AF, Pellegrini C. A graphical Interface for the knowledge acquisition in the MELANIE expert system. Two-dimensional Electrophoresis. Vienna, Austria: Nov. 1988.
Golaz O, Gravel P, Walzer C, Sanchez JC, Pasquali C, Appel RD, Hochstrasser DF. Sugar detection at the picomole level using lectins and chemiluminescence. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 43.
Golaz O, Hughes G, Frutiger S, Paquet N, Sanchez JC, Pasquali C, Bairoch A, Appel RD, Hochstrasser DF. Plasma and red blood cell 2-D PAGE databases. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 158.
Golaz O, Sanchez JC, Heenan R, Ravier F, Rouge V, Tonella L, Wilkins MR, Appel RD, Hochstrasser DF. SWISS-2DISEASE: a 2-D database of samples in disease states. 2nd Siena 2D electrophoresis meeting. Siena, Italy: Sept. 1996.
Gras R, Gasteiger E, Müller M, Appel RD. New learning method to improve protein identification from peptide mass fingerprinting. The eighth International Conference on Computational Biology Intelligent Systems for Molecular Biology (ISMB). La Jolla, California: 2000.
Gras R, Gasteiger E, Chopard B, Müller M, Appel RD. New learning method to improving protein identification from peptide
mass fingerprinting. 4th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2000.
Gras R, Müller M, Hernandez D, Hernandez P, Zangger N, Palagi P, Binz PA, Lisacek F, Appel RD. New approaches of computational proteomics. JOBIM 2002. 2002: 143-147.
Gras R, Müller M, Hernandez D, Hernandez P, Zangger N, Palagi P, Binz PA, Appel RD. Cooperative metaheuristic for proteomics. Bioinformatics Workshop ISMIS. Lyon: 2002.
Gras R, Hernandez D, Hernandez P, Zangger N, Mescam Y, Frey J, Martin O, Nicolas J, Appel RD. Cooperative metaheuristics to solve complex bioinformatics problem. International Summer School on Metaheuristics. Tenerife: Feb. 2003.
Gras R, Frey J, Hernandez P, Appel RD. Un modèle hiérarchique "coarse-grained" de parallélisation d'algorithme de programmation génétique appliqué à des problèmes de bioinformatique. Workshop: Résolution Parallèle des Problèmes NP-complets. Nice: Oct. 2003.
Gras R, Hernandez D, Hernandez P, Mescam Y, Appel RD. Cooperation in Metaheuristics and Application in Bioinformatics. European Conference on Combinatorial Optimisation - ECCO XVII 2004. Beirut, Lebanon: June 2004.
Hernandez D, Gras R, Appel R. Automated learning of unknown length motifs in unaligned DNA sequences with genetic algorithms. ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology. Tivoli Gardens, Copenhagen, Denmark: July 2001.
Hernandez D, Gras R, Appel RD. Automated learning of unknown lenght motifs in unaligned biological sequences with genetic algorithm. Congress of the Swiss Proteomics Society. Geneva: Nov. 2001: 55-57.
Hernandez D, Gras R, Lisacek F, Appel RD. MoDEL: Inférence de motifs avec un algorithme évolutionniste. JOBIM. 2002.
Hernandez D, Gras R, Appel RD. Stratégies d’exploration de l’espace des alignements locaux multiples sans indels. Quatrièmes journées francophones de recherche opérationnelle (FRANCORO IV). Fribourg, Suisse: Aug. 2004.
Hernandez P, Gras R, Frey JP, Appel RD. Automated Protein Identification from Tandem Mass Spectrometric Data Using Bio-Inspired Algorithms. Congress of the Swiss Proteomics Society. Lausanne: Dec. 2002: 81-86.
Hernandez P, Gras R, Appel RD. Ant Colony Optimization Metaheuristic Applied to Automated Protein Identification from Tandem Mass Spectrometric Data. Second International Workshop on "AGENTS IN BIOINFORMATICS". Bologna, Italy: July 2002.
Hernandez P, Gras R, Appel RD. Automated Protein Identification from Tandem Mass Spectrometric Data Using Bio-Inspired Algorithms. 5th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2002.
Hernandez P, Gras R, Appel RD. Popitam loves being fed on modified MS/MS spectra. Peptide Fragmentation and identification Workshop, NIST. Gaithersburg, Maryland: May 2004.
Hernandez P, Gras R, Appel RD. Popitam squints to better identify ms/ms spectra of modified peptides. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 227.
Hernandez P, Gras R, Hernandez C, Appel RD. Peptide identification and characterization using tandem mass spectrometry data: an open-modification search approach with Popitam. Swiss Proteomics Society 2005 Congress: Expanding proteomics. Dec. 2005: 187-190.
Hernandez P, Quandt A, Hernandez C, Müller M, Appel RD. swissPIT - A platform for knowledge extraction from mass spectrometry data. 7th Siena meeting - From Genome to Proteome. Siena, Italy: 2006: 43.
Hernandez P, Quandt A, Hernandez C, Appel RD. swissPIT, une plateforme pour l'identification de protéines à partir de spectres de masses. Grille Bioinformatique: expériences et perspectives, Vendredi 12 mai, IBCP, Lyon. Lyon: 2006.
Hochstrasser D, Funk M, Appel R, Pellegrini C, Muller AF. Electrophorèses bidimensionnelles : analyse et comparaison automatique par ordinateur. Société Suisse de chimie clinique. Zürich: 1985.
Hochstrasser D, Siegenthaler G, De Moerloose P, Funk M, Appel R, Pellegrini C, Saurat JH, Muller AF. Elévation de la protéine sérique liant le rétinol et de l'antithrombine III. Société Suisse de Médecine Interne. 1987.
Hochstrasser D, Maignan MF, Dumont JM, Funk M, Appel R, Aellig A, Grandjean EM, Pellegrini C, Muller AF. 2-dimensional gel electrophoresis : a new tool for the evaluation of a therapeutic agent. 18th Congress of the International Union of Therapeutics. Geneva: Apr. 1987.
Hochstrasser D, Bjellqvist B, Bairoch A, Sanchez JC, Appel R, Hughes GJ. From the genome to 2D-PAGE or predicting the position of a polypeptide on protein maps. ICES-ELPHO 93. Oslo: June 1993.
Hochstrasser D, Wilkins M, Sanchez JC, Gasteiger E, Appel R. Proteome Research: State of the art. Electrophorese Forum '97. Strasbourg: Nov. 1997.
Hochstrasser D, Sanchez JC, Fabretti R, Müller M, Gasteiger E, Bienvenut W, Rosselat G, Binz PA, Bairoch A, Appel R. Proteome research and its impact on laboratory medicine. WorldLab 99. Florence: June 1999.
Hochstrasser D, Appel R, Bienvenut W, Binz PA, Chiappe D, Demalte I, Jung E, Sanchez JC. Proteomic complexity and computational aspects in oncology. 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). Heidelberg, Germany: Mar. 1999.
Hochstrasser DF, Hochstrasser AC, Villars V, Funk M, Appel RD, Pellegrini C, Muller AF. Storable precast IEF gels with urea. Two-dimensional Electrophoresis. Vienna, Austria: Nov. 1988.
Hochstrasser DF, Appel RD, Wiederkehr F, Funk M, Vonderschmidt D, Scherrer JR, Muller AF. Electrophorèses Bidimensionnelles en Chimie Clinique. Schweizerische Medizinische Wochenschrift, 121: suppl. 38, 59ème Assemblée Générale de la Société Suisse de Médecine. Lugano: May 1991.
Hochstrasser DF, Appel RD, Sanchez JC. Clinical Applications of 2D-PAGE. ATB'93. Milan: Nov. 1993.
Hochstrasser DF, Appel RD, Golaz O, Pasquali C, Sanchez JC. De la cartographie protéique au génome. Réunion annuelle de la Société Française d'Electrophorèse. Chambéry: Dec. 1993.
Hochstrasser DF, Wilkins M, Appel R, Bairoch A, Sanchez JC, Williams K. From Genomes to “Proteomes”: EXPASY & SWISS-2DPAGE. The Protein Society First European Symposium. Davos, Switzerland: May 1995.
Hochstrasser DF, Appel RD, Bienvenut W, Binz PA, Müller M, Rouge V, Tonella L, Sanchez JC. Present status of proteomics. Biochemical society transactions. Glasgow: Apr. 1999.
Hochstrasser DF, Sanchez JC, Binz PA, Bienvenut W, Gasteiger E, Müller M, Gras R, Fabretti R, Appel RD. The role of the virtual or computer “dry” laboratory in proteomics. 31st Annual Meeting of USGEB 99. 1999.
Hochstrasser DF, Binz PA, Bairoch A, Appel RD, Sanchez JC. From genome to proteome: a new look at Nature complexity. Miami conference. Sept. 1999.
Hochstrasser DF, Binz PA, Bairoch A, Appel RD, Sanchez JC. From Genome to Proteome: a New Look at Nature Complexity. Elektrophorese Forum’99. Munich: Oct. 1999.
Hochstrasser DF, Binz PA, Bienvenut W, Müller M, Walther D, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins M, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Appel RD, Sanchez JC. Proteomics Technology Development in Geneva. Elektrophorese Forum’99. Munich: Oct. 1999.
Hochstrasser DF, Binz PA, Müller M, Walther D, Bienvenut W, Gras R, Hoogland C, Bouchet G, Gasteiger E, Fabbretti R, Gay S, Palagi P, Wilkins M, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Sanchez JC, Appel RD. MALDI-TOF “Imaging”: a Molecular Scanner for Proteomic Research. ABRF. 2000.
Hochstrasser DF, Sanchez JC, James R, Appel RD. The use of proteomics in plasma investigation. Clinical Chemistry Society Conference. Rabat: May 2000.
Hochstrasser DF, Sanchez JC, Binz PA, Bienvenut W, Appel RD. Analytical techniques for proteome research. PBA 2000. May 2000.
Hochstrasser DF, Bienvenut W, Müller M, Gras R, Binz PA, Appel RD, Sanchez JC. From Genome to Proteome: the development of a molecular scanner. Colloque AcM/MdA - Acquisition conduite par le Modèle - Model driven Acquisition. Grenoble: Nov. 2000.
Hochstrasser DF, Sanchez JC, Appel RD. Proteomics (and its trends facing nature complexity). Congress of the Swiss Proteomics Society. Geneva: Nov. 2001: 5.
Hochstrasser DF, Sanchez JC, Corthals G, Binz PA, Müller M, Walther D, Appel RD. Bioinformatics in proteomics. International Conference "Genomics, Proteomics and Bioinformatics for Medicine". Moscow: June 2002.
Hochstrasser DF, Sanchez JC, Scherl A, Corthals G, Appel RD. Proteomics: three approaches. Endoderm. Arolla, Switzerland: Aug. 2002.
Hochstrasser DF, Corthals G, Appel RD, Sanchez JC. Large scale proteomics in medecine. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 25.
Hochstrasser DF, Corthals G, Appel RD, Sanchez JC. Proteomics in medecine. Barnett Lecture, Barnett Institute. Boston: Apr. 2003.
Hochstrasser DF, Sanchez JC, Corthals G, Binz PA, Müller M, Appel RD, Bougueleret L, Rose K. Proteomics in laboratory medicine. EUROMEDLAB Barcelona 2003, 15th IFCC - FESCC European Congress of Clinical Chemistry and Laboratory Medicine. Barcelona: 2003.
Hochstrasser DF, Sanchez JC, Corthals G, Scherl A, Rose K, Bougueleret L, Colinge J, Bairoch A, Appel RD. Proteomics & Mass Spectrometry in Medicine. 16th International Mass Spectrometry Conference. Edinburgh: Aug. 2003.
Hochstrasser DF, Sanchez JC, Rose K, Bougueleret L, Appel RD, Bairoch A, Corthals G. Clinical Proteomics. Proteomic Forum '03. Münich: Sept. 2003.
Hochstrasser DF, Corthals G, Rose K, Bougueleret L, Appel RD, Bairoch A, Sanchez JC. The five dimensions of diseases. Second Annual HUPO Congress. Montreal: Oct. 2003.
Hochstrasser DF, Corthals G, Sanchez JC, Appel RD, Bairoch A, Bougueleret L, Rose K. Clinical proteomics: a challenge for diagnostic laboratories and the pharma industry? AACC 2004 Annual meeting. Los Angeles, CA: July 2004.
Hochstrasser DF, Zimmermann-Ivol CG, Corthals GL, Appel RD, Sanchez JC. Clinical Proteomics. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 10.
Hochstrasser DF, Walther D, Quadroni M, Catherinet S, Tuloup M, Binz PA, Burgess J, Vaezzadeh A, Zimmermann-Ivol CG, Corthals GL, Appel RD, Sanchez JC, Appel RD. Clinical Proteomics and MS imaging. ASBMB 2005, American Society for Biochemistry and Molecular biology. San Diego, CA: Apr. 2005.
Hochstrasser DF, Appel RD, Paesano S, Binz PA, Sanchez JC, Zimmermann C. Proteomics & Clinical Chemistry. Fourth HUPO annual meeting. Munich: Aug. 2005.
Hochstrasser DF, Scherl A, Binz PA, Zimmerman C, Sanchez JC, Appel RD. Complex Specimen struggling to survive. BSPR/EBI Meeting – From Proteins to Systems. Cambridge: July 2005.
Hochstrasser DF, Walther D, Quadroni M, Catherinet S, Tuloup M, Binz P-A, Burgess J, Vaezzadeh A, Zimmerman C, Corthals GL, Sanchez JC, Appel RD. MS imaging in Clinical Proteomics. Beyond Genome. San Francisco, CA: June 2005.
Hochstrasser DF, Lescuyer P, Moll S, Vaezzadeh A, Sanchez JC, Zimmerman C, Appel RD. Clinical Proteomics & Biomarker Discovery. Congress on Proteomic & Pathology. Valencia, Spain: Feb. 2007.
Hochstrasser DF, Lescuyer P, Moll S, Vaezzadeh A, Sanchez JC, Zimmerman C, Appel RD. Clinical Proteomics & Biomarker Discovery. International Symposium on High Performance Proteomics. Dortmund: May 2007.
Hoogland C, Mostaguir K, Appel RD, Lisacek F. World-2DPAGE: your proteomics data publicly available from the ExPASy server. SPS'07: Pushing the limits. Lausanne, Switzerland: Dec. 2007. pp. 201-202.
Hoogland C, Mostaguir K, Appel RD, Lisacek F. World-2DPAGE Repository: your contribution to a large proteomics data network. 8th Siena meeting "From genome to proteome: Integration and proteome completion". Siena, Italy: Sept. 2008.
Hoogland C, Mostaguir K, Appel RD, Lisacek F. World-2DPAGE Repository: your contribution to a large proteomics data network. HUPO 8th Annual World Congress. Amsterdam, Netherlands: Aug. 2008.
Hoogland C, Sanchez JC, Tonella L, Hochstrasser DF, Appel RD. SWISS-2DPAGE, My-2DPAGE, Your-2DPAGE...: how to publish 2-DE data on the Web. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Hoogland C, Mostaguir K, Hochstrasser DF, Sanchez JC, Appel RD. SWISS-2DPAGE, 10 years later... Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 172-173.
Hoogland C, Lion N, Palagi PM, Rossier J, Sanchez JC, Stocklin R, Tissot JD, Voshol H. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. Swiss Proteomics Society 2004 Congress: Proteomics for Health. Aug. 2004. Bern, Switzerland: Dec. 2004: 230.
Hoogland C, Lion N, Palagi PM, Sanchez JC, Tissot JD. SPS' Digest: the Swiss Proteomics Society selection of proteomics articles. 6th Siena Meeting From genome to proteome: Biomarker discovery & Proteome imaging. Siena, Italy: 2004: 230.
Jaconi M, Theler JM, Schlegel W, Appel RD, Wright SD, Lew PD. Repetitive cytosolic free CA2+ elevations in human neutrophils are initiated by adherence receptors of the integrin family. European Society for Clinical Investigation. Pisa: Apr. 1991.
Jaconi MEE, Theler JM, Schlegel W, Appel RD, Wright SD, Lew PD. Fluctuations of cytosolic free Ca2+ in human neutrophils: initiation by adherence receptors of the integrin family. American Society for Cell Biology. 1990.
Mascarini C, Ratib O, Trayser G, Ligier Y, Appel RD. In-house access to PACS images and related data through World Wide Web. SGMR, 83. Jahresversammlung. Lausanne: May 1996.
Masselot A, Binz PA, Cambria L, Appel RD. Phenyx: combining high-throughput and pertinence in protein identification. Third Annual HUPO Congress (proceedings in Molecular & Cell Proteomics). Beijing: Oct. 2004: 257.
Masselot A, Binz PA, Cambria L, Appel RD. Phenyx: Manage Protein Identification With Flexibility and Pertinence. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 168.
Mostaguir K, Hoogland C, Appel RD. Migration des bases de données de gels 2-DE vers un format relationnel. JOBIM. 2002.
Mostaguir K, Hoogland C, Binz PA, Appel RD. The Make 2D-DB II Package - Conversion of federated 2-DE gel databases into a relational format and interconnection of distributed databases. 5th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2002.
Mostaguir K, Hoogland C, Binz PA, Appel RD. The Make 2D-DB II Package - Conversion of federated 2-DE gel databases into a relational format and interconnection of distributed databases. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 73-74.
Mostaguir K, Hoogland C, Appel RD. The Make2D-DB II Tool: building a large federated 2-DE database network. ISMB/ECCB04. Glasgow: July 2004.
Mostaguir K, Hoogland C, Appel RD. The Make2D-DB II Tool: building a large federated 2-DE gel databases network. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 294.
Mostaguir K, Hoogland C, Appel RD. Evolution et interconnexion des bases de données protéomiques avec l'outil Make2D-DB II : un exemple appliqué aux bases de données de gels 2-DE. JOBIM. July 2005.
Mostaguir K, Hoogland C, Appel RD. Creation and interconnection of distributed proteomic databases: the Make2D-DB II tool, an example applied to 2-DE datasets. Fourth HUPO annual meeting. Munich: Aug. 2005.
Müller M, Gras R, Bienvenut WV, Hochstrasser DF, Appel RD. Visualisation and Analysis of Molecular Scanner Peptide Mass Spectra. Congress of the Swiss Proteomics Society. Geneva: Nov. 2001: 39-43.
Müller M, Gras R, Appel R. Vizualization and Interpretation of the Molecular Scanner Data. ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology. Tivoli Gardens, Copenhagen, Denmark: July 2001.
Müller M, Gras R, Bienvenut WV, Binz PA, Pasquarello C, Hochstrasser DF, Appel RD. Using Peptide Signal Intensity Distributions for a Better Interpretation of Molecular Scanner Data. 5th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2002.
Mylonas R, Masselot A, Binz PA, Appel RD. An opensource toolkit for quality assessment and filtering of peptide mass spectra. HUPO 5th Annual World Congress. Oct. 2006. Long Beach, California: Oct. 2006.
Nadler T, Huang Y, Wagenfeld B, Parker B, Lotti R, Vella GJ, Binz PA, Müller M, Gras R, Hochstrasser DF, Bienvenut W, Sanchez JC, Corthals G, Appel RD. Proteome Analysis by Multi-Dimensional Liquid Chromatography Gel-Electrophoresis and the Molecular Scanner. 5th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2002.
Palagi PM, Walther D, Bologna G, Vargas JR, Sanchez JC, Cremona O, Hochstrasser DF, Appel RD. 2-DE classification using heuristic clustering and neural nets. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Palagi PM, Hoogland C, Gras R, Mueller M, Binz PA, Fabbretti R, Bouchet G, Walther D, Gay S, Gasteiger E, Bairoch A, Sanchez JC, Hochstrasser DF, Appel RD. Human proteomics and bioinformatics tools. The first draft of the human genome : an academic and industrial perspective. Berlin, Germany: Oct. 2000.
Palagi PM, Binz PA, Bairoch A, Hochstrasser DF, Appel RD. Bioinformatics challenges in proteomics. Symposium " Bioinformatics and proteomics ". Seoul, Korea: June 2000.
Palagi PM, Binz PA, Bairoch A, Hochstrasser DF, Appel RD. Bioinformatics in Proteomics. CCP11 GPCVI Conference "Bioinformatics and the Molecular Biologist". Chester, England: Apr. 2000.
Palagi PM, Appel RD, Bairoch A, Bittar.G., Bucher P, Chopard B, Goudet J, Guex N, Jongeneel V, Peitsch MC, Pellegrini C. A Masters Degree in Bioinformatics in Switzerland. Workshop on Education in Bioinformatics 2001, ISMB2001 - The 9th International Conference on Intelligent Systems for Molecular Biology. Tivoli Gardens, Copenhagen, Denmark: July 2001.
Palagi PM, Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Binz PA, Hochstrasser DF, Appel RD. Proteome imaging: a prerequisite for any MS-related proteomic study? Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 61-63.
Palagi PM, Bucher P, Notredame C, Schwede T, Galisson G, Appel RD. Evolution of bioinformatics education in Switzerland and the role of the Swiss Institute of Bioinformatics. WEB'04 - Workshop on Education in Bioinformatics 2004, ISMB2004. Glasgow, Scotland: July 2004.
Palagi PM, Walther D, Quadroni M, Catherinet S, Binz PA, Hochstrasser DF, Appel RD. MSight: an LC-MS image analysis software. ISMB 2005, 13th Annual International Conference on Intelligent Systems for Molecular Biology. Michigan: June 2005.
Palagi PM, Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Hernandez P, Hernandez C, Quandt A, Lisacek F, Hoogland C, Binz P-A, Rossier G, Mostaguir K, Nikitin F, Zangger N, Appel RD. Bioinformatics to explore and integrate proteomics data. PROTEOME ANALYSIS IN SYSTEMS BIOLOGY. Dec. 2006. Antwerp, Belgium: Sept. 2006.
Palagi PM, Hernandez P, Quandt A, Hernandez C, Appel RD. swissPIT - swiss Protein Identification Toolbox : A pipeline for knowledge extraction from MS data. Münster Proteomics Meeting. May 2006.
Palagi PM, Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Hernandez P, Hernandez C, Quandt A, Arhne E, Mauron Y, Mylonas R, Hoogland C, Binz P-A, Rossier G, Mostaguir K, Nikitin F, Zangger N, Masselot A, Lisacek F, Appel RD. Exploring and integrating proteomics data. BSPR/EBI 4th Annual Proteomics meeting. July 2007. Hinxton, UK: July 2007.
Pasquali C, Schaller D, Appel RD, Sanchez JC, Golaz O, Humpherey-Smith I, Wilkins M, Williams K, Hughes GJ, Frutiger S, Paquet N, Hochstrasser DF. Two-dimensional gel electrophoresis of escherichia coli homogenates: identification of proteins spots by amino acid composition. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 84.
Peitsch MC, Tonella L, Sanchez JC, Wilkins MR, Appel RD, Hochstrasser DF. Automated comparative protein modelling and its integration with the SWISS-2DPAGE database. 2nd Siena 2D electrophoresis meeting. Siena, Italy: Sept. 1996.
Potts A, Walther D, Catherinet S, Bienvenut W, Appel RD, Quadroni M. The application of a software tool for the two-dimensional representation of LC-MS data to the analysis of post-translational modifications and the comparison of complex peptide mixtures. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 323.
Quadroni M, Walther D, Appel R, Bienvenut W, Potts A. Comparative mass spectrometric analysis of complex peptide mixtures using a novel software tool for two-dimensional data visualization. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 150.
Quadroni M, Baruthio F, Walther D, Appel R, Ruegg C, Mariotti A. Label-free differential analysis of proteins in lipid rafts using LC-MS and the MSIGHT software tool. 53rd ASMS Conference on Mass Spectrometry. San Antonio, Texas: June 2005.
Quandt A, Hernandez P, Hernandez C, Müller M, Appel RD. swissPIT, a multi-tool protein identification platform. In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot. July 6 A.D. Fortaleza, Brazil: 2006: 227.
Quandt A, Masselot A, Hernandez P, Hernandez C, Appel RD. The Swiss Protein Identification Toolbox - A platform for workflow exectution and optimisation studies in proteomics. BSPR, EBI 4th Annual Proteomics meeting. Hinxton: July 2007.
Quandt A, Masselot A, Hernandez C, Budin N, Arhne E, Hernandez P, Palagi P, Binz P-A, Appel RD. The swissPIT: a web platform for workflow exectution and optimization studies in MS-based proteomics. HUPO annual meeting. Seoul, Korea: Oct. 2007.
Ratib O, Appel RD, Scherrer JR. Papyrus : A Multimodality Image File Format for PACS and Teleradiology. Radiology. Nov. 1990: 320.
Ratib O, Mascarini C, Ligier Y, Appel RD, Trayser G. The World Wide Web for Intra- and Extra-Hospital Communication of Images and Patient Records. 3rd INCIS Workshop. Mainz: Apr. 1996.
Robin X, Hoogland C, Appel RD, Lisacek F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. SPS'07: Pushing the limits. Lausanne, Switzerland: Dec. 2007. pp. 227.
Robin X, Hoogland C, Appel RD, Lisacek F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. HUPO 8th Annual World Congress. Amsterdam, Netherlands: Aug. 2008.
Robin X, Hoogland C, Appel RD, Lisacek F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. 8th Siena meeting "From genome to proteome: Integration and proteome completion". Siena, Italy: Sept. 2008.
Rossier G, Lisacek F, Appel RD. E-PROXEMIS: A BIOINFORMATICS LEARNING PORTAL
FOR PROTEOMICS. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 334.
Sanchez JC, Appel R, Schaller D, Belet M, Muslena N, Deshusses J, Hochstrasser D. Global yeast genome expression analysed by 2-D PAGE after TCTP homolog gene (YKL312) disruption. 26th Annual Meeting of USGEB 94. Berne: 1994: 10-19.
Sanchez JC, Hughes G, Frutiger S, Paquet N, Pasquali C, Golaz O, Bairoch A, Appel RD, Hochstrasser DF. Human liver 2-D PAGE database. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 156.
Sanchez JC, Golaz O, Schaller D, Morch F, Frutiger S, Hughes G, Appel RD, Deshusses J, Hochstrasser DF. The yeast SWISS-2DPAGE database. XVII International Conference on Yeast Genetics and Molecular Biology. Lisboa, Portugal: June 1995.
Sanchez JC, Golaz O, Schaller D, Frutiger S, Hughes G, Appel RD, Bairoch A, Linder P, Hochstrasser DF. The yeast SWISS-2DPAGE database. Swiss Yeast Meeting. Geneva: Sept. 1995.
Sanchez JC, Frutiger S, Hughes G, Hoogland C, Appel RD, Binz PA, Hochstrasser DF, Cowthorne M. The mouse SWISS-2DPAGE database: a bridge between genomic and phenomic analysis of non-insulin-dependent diabetes-mellitus. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Scherl A, Francois P, Bento M, Deshusses JM, Charbonnier Y, Converset V, Huyghe A, Walter N, Hoogland C, Appel RD, Sanchez JC, Zimmermann-Ivol CG, Corthals GL, Hochstrasser DF, Schrenzel J. Exploring the proteome and transcriptome of Staphylococcus aureus. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 352.
Scherl A, Zimmermann-Ivol CG, Bento M, Francois P, Sanchez JC, Appel RD, Schrenzel J, Hochstrasser DF. Characterization of Staphylococcus aureus Proteins involved in glycopeptide tolerance with mass spectrometric based quantitative methods. Congress of the Swiss Proteomics Society. Dec. 2005: 26.
Scherl A, Kulasekara H, Binz PA, Hernandez P, Schaffer S, Taylor G, Ryu S, Masselot A, Appel RD, Radulovic D, Miller SI, Goodlett DR. High measured mass accuracy on CID fragments: What do we gain, what do we lose? 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 40.
Selby M, Boyer C, Jenefski DA, Appel RD. Health On the Net Foundation Code of Conduct for Medical and Health Websites. MEDNET96 - European Congress on the Internet in Medicine. Brighton, U.K.: Oct. 1996.
Tonella L, Ou K, Wilkins M, Sanchez JC, Frutiger S, Appel R, Bairoch A, Walsh BJ, Yan JX, Tyler M, Hoogland C, Rouge V, Morsch FS, Gooley AA, Hughes GJ, Williams KL, Hochstrasser DF. '97 Escherichia coli SWISS-2DPAGE database update. Electrophorese Forum '97. Strasbourg: Nov. 1997.
Tonella L, Walsh BJ, Sanchez JC, Ou K, Wilkins M, Tyler M, Frutiger S, Binz PA, Gooley AA, Pescaru I, Appel R, Yan JX, Bairoch A, Hoogland C, Hughes GJ, Williams KL, Hochstrasser DF. ‘98 Escherichia coli SWISS-2DPAGE database update. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Tonella L, Sanchez JC, Binz PA, Appel RD, Bairoch A, Hoogland C, Hochstrasser DF. New strategies in the Escherichia coli analysis: a combination of one unit pH range PGIsand peptide mass fingerprinting. Journée des Sociétés Suisse et Française d’Electrophorèse. Bâle: Dec. 1998.
Tonella L, Sanchez JC, Hoogland C, Appel RD, Bairoch A, Hochstrasser DF. New strategies in the escherichia coli proteome analysis: a combination of narrow pH range IPGs and peptide mass fingerprinting. 4th Siena 2D electrophoresis meeting. Siena, Italy: Sept. 2000.
Tuloup M, Hoogland C, Binz PA, Appel RD. A new Peptide Mass Fingerprinting tool on ExPASy : ALDentE. Congress of the Swiss Proteomics Society. Lausanne: Dec. 2002: 93-96.
Tuloup M, Hoogland C, Binz PA, Appel RD. Utilisation de la transformée de Hough dans le cadre de l’identification des protéines par spectrométrie de masse. JOBIM. 2002.
Tuloup M, Hernandez C, Coro I, Hoogland C, Binz PA, Appel RD. Aldente and BioGraph : An improved peptide mass fingerprinting protein identification environment. Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 174-176.
Vaezzadeh A, Zimmermann-Ivol CG, Lassout O, Francois P, Hoogland C, Appel RD, Schrenzel J, Hochstrasser DF. High-throughput profiling of bacterium proteome by Shotgun IEF. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 67.
Vaezzadeh A, Deshusses J, Lescuyer P, Zimmermann-Ivol CG, Chauvet A, Hernandez C, Walther D, Appel RD, Hochstrasser DF. Towards High-Throughput Shotgun IEF. ASMS Conference on Mass Spectrometry. Indianapolis, Indiana: June 2007.
Vaezzadeh A, Simicevic J, Vadas O, Deshusses JM, Lescuyer P, Hernandez C, Hochstrasser DF. Pushing the limits of the shotgun IPG-IEF workflow. SPS'07. Lausanne, Switzerland: Dec. 2007.
Voordijk S, Rossier G, Walther D, Bouchet G, Appel RD. New features in the Melanie 2D gel analysis software. Congress of the Swiss Proteomics Society. Lausanne: Feb. 2003: 91-92.
Walther D, Quadroni M, Catherinet S, Burgess J, Zimmermann-Ivol CG, Sanchez JC, Hochstrasser DF, Appel RD. Why not exploit ms data to its fullest? Using data-redundancy in mass spectra. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 41.
Walther D, Quadroni M, Catherinet S, Hochstrasser DF, Palagi PM, Appel RD. MSight: an LC-MS image analysis software. Fourth HUPO annual meeting. Munich: Aug. 2005.
Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Powered by Melanie: a general framework for proteome imaging. Swiss Proteomics Society 2005 Congress: Expanding proteomics. Dec. 2005. Zurich, Switzerland: 2005.
Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Bioinformatics for proteome imaging: Melanie's example. In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot. July 6 A.D. Fortaleza, Brazil: 2006: 227.
Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Analysis of liquid chromatography/mass spectrometry data with the MSight software. 7th Siena meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: 2006: 227.
Walther D, Bouchet G, Catherinet S, Pelhatre S, Tuloup M, Palagi PM, Appel RD. Imaging in proteomics: 2-DE vs. LC/MS data analysis. 7th Siena Meeting - From Genome to Proteome - Back to the future. Sept. 2006. Siena, Italy: Sept. 2006: 77.
Wilkins M, Gooley A, Williams K, Humpherey-Smith I, Cordwell S, Appel RD, Sanchez JC, Golaz O, Pasquali C, Hochstrasser DF. Towards the Protein Genome: Rapid Identification of 2D Spots by Amino Acid Analysis. Siena Meeting on 2D Electrophoresis. Siena: Sept. 1994: 35-36.
Wilkins MR, Gasteiger E, Sanchez JC, Appel RD, Hochstrasser DF. Protein identification with sequence tags. Curr Biol 1996; 6: 1543-1544.
Wilkins MR, Lindskog I, Ou K, Wheeler C, Sanchez JC, Yan J, Cartier P, Farnsworth V, Frutiger S, Hughes G, Ravier F, Tonella L, Gooley AA, Appel RD, Dunn MJ, Williams KL, Hochstrasser DF. Rapid protein identification for proteome projects. 2nd Siena 2D electrophoresis meeting. Siena, Italy: Sept. 1996.
Wilkins MR, Sanchez JC, Ravier F, Tonella L, Appel RD, Hochstrasser DF. Vector maps in two-dimensional polyacrylamide gel electrophoresis - a means of predicting protein post-translational modification. 2nd Siena 2D electrophoresis meeting. Siena, Italy: Sept. 1996.
Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Hochstrasser DF, Appel RD. Software tools for mass spectrometric data analysis of proteins separated by 2-D gel electrophoresis. ICES’97. Seattle, Washington: Mar. 1997.
Wilkins MR, Gasteiger E, Sexton DK, Herbert BR, Molloy MP, Ou K, Binz PA, Bairoch A, Appel RD, Gooley AA, Hochstrasser DF, Williams KL. Protein modifications, processing and identification in proteomics projects. 3rd Siena 2D electrophoresis meeting. Siena, Italy: Aug. 1998.
Zangger N, Gras R, Appel RD. Biological Sequence Clustering by Cooperative Agents. Congress of the Swiss Proteomics Society. Lausanne: Dec. 2002: 75-80.
Zangger N, Gras R, Appel RD. A Symmetric Cooperative Metaheuristic for Biological Sequence Clustering Using Local Entropy as Similarity Criterion. Second International Workshop on "AGENTS IN BIOINFORMATICS". Bologna, Italy: July 2002.
Zimmermann-Ivol CG, Vaezzadeh A, Converset V, Hoogland C, Walther D, Catherinet S, Tuloup M, Hernandez C, Müller M, Moll S, Corthals GL, Pasquarello C, Appel RD, Hochstrasser DF. Distribution and visualisation of urine protein profile with the Molecular Scanner. 6th Siena meeting - From Genome to Proteome. Siena, Italy: Aug. 2004: 411.
Zimmermann-Ivol CG, Vaezzadeh A, Demalte I, Converset V, Di Dio J, Scherl A, Corthals GL, Appel RD, Hochstrasser DF. The Molecular Scanner. Congress of the Swiss Proteomics Society. Bern: Dec. 2004: 136.

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