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Publications in 2007

I. Articles in journals with editorial policy

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

II. Books, book chapters & guest edition

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Lisacek F, Appel RD. Special issue on Systems Biology (Guest Edition). Proteomics, Vol.7, No. 6. 2007.

  6. 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.

  7. Wilkins MR, Appel RD, Williams KL, Hochstrasser DF. Proteome Research: concepts, technology and application. Berlin Heidelberg, Springer Verlag; 2007.

IV. Conference proceedings

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

  2. 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.

V. Abstracts and posters

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Hoogland C, Mostaguir K, Appel RD, Lisacek F. World-2DPAGE: your proteomics data publicly available from the ExPASy server. SPS'07. Lausanne, Switzerland: Dec. 2007. pp. 201-202.

  8. 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.

  9. 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.

  10. 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.

  11. Robin X, Hoogland C, Appel RD, Lisacek F. MIAPEGelDB: a web-based submission tool and public repository for MIAPE Gel electrophoresis documents. SPS'07. Lausanne, Switzerland: Dec. 2007. pp. 227.

  12. 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.

  13. 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.

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