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Publications in 2007

Thesis

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

Journal Articles

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

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

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

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

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

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

Journal Articles - non peer-reviewed

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

Conference Proceedings

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

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

Books

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

Book Chapters

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

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

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

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

Guest Edition

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

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

Abstracts & Posters

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

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

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

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

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

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

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

8. Palagi, P.M., Walther, D., Bouchet, G., Catherinet, S., Pelhatre, S., Tuloup, M., Hernandez, P., Hernandez, C., Quandt, A., Ahrné, E., Mauron, Y., Mylonas, R., Hoogland, C., Binz, P.A., Rossier, G., Mostaguir, K., Nikitin, F., Zangger, N., Masselot, A., Lisacek, F., and Appel, R.D. Exploring and integrating proteomics data. in BSPR/EBI 4th Annual Proteomics meeting. 2007. Hinxton, UK.

9. Quandt, A., Masselot, A., Hernandez, C., Budin, N., Ahrné, E., Hernandez, P., Palagi, P., Binz, P.A., and Appel, R.D. The swissPIT: a web platform for workflow exectution and optimization studies in MS-based proteomics. in HUPO annual meeting. 2007. Seoul, Korea.

10. Quandt, A., Masselot, A., Hernandez, P., Hernandez, C., and Appel, R.D. The Swiss Protein Identification Toolbox - A platform for workflow exectution and optimisation studies in proteomics. in BSPR, EBI 4th Annual Proteomics meeting. 2007. Hinxton.

11. Robin, X., Hoogland, C., Appel, R.D., and Lisacek, F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. in Swiss Proteomics Society 2007 Congress: Pushing the limits. 2007. Lausanne, Switzerland.

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

13. Vaezzadeh, A., Simicevic, J., Vadas, O., Deshusses, J.M., Lescuyer, P., Hernandez, C., and Hochstrasser, D.F. Pushing the limits of the shotgun IPG-IEF workflow. in SPS'07. 2007. Lausanne, Switzerland.

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