Scientific publications
Research - Publications - 2005
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2005


Journal Articles – peer-reviewed

  • Alemani, D., Chopard, B., Galceran, J., Buffle, J., 2005, LBGK method coupled to time splitting technique for solving reaction-diffusion processes in complex systems, Phys Chem Chem Phys, 7, (18), 3331-3341, (PubMed)

  • Anderle, P., Sengstag, T., Mutch, D. M., Rumbo, M., Praz, V., Mansourian, R., Delorenzi, M., Williamson, G., Roberts, M. A., 2005, Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes, BMC Genomics, 6, (1), 69, (PubMed)

  • Armand, F., Bucher, P., Jongeneel, C. V., Farmer, E. E., 2005, Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge, Bioinformatics, 21, (12), 2906-2908, (PubMed)

  • Aubourg, S., Brunaud, V., Bruyere, C., Cock, M., Cooke, R., Cottet, A., Couloux, A., Dehais, P., Deleage, G., Duclert, A., Echeverria, M., Eschbach, A., Falconet, D., Filippi, G., Gaspin, C., Geourjon, C., Grienenberger, J. M., Houlne, G., Jamet, E., Lechauve, F., Leleu, O., Leroy, P., Mache, R., Meyer, C., Nedjari, H., Negrutiu, I., Orsini, V., Peyretaillade, E., Pommier, C., Raes, J., Risler, J. L., Riviere, S., Rombauts, S., Rouze, P., Schneider, M., Schwob, P., Small, I., Soumayet-Kampetenga, G., Stankovski, D., Toffano, C., Tognolli, M., Caboche, M., Lecharny, A., 2005, GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts, Nucleic Acids Res, 33, (Database issue), D641-646, (PubMed)

  • Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N., Yeh, L. S., 2005, The Universal Protein Resource (UniProt), Nucleic Acids Res, 33, (Database issue), D154-159, (PubMed)

  • Beckmann, J. S., Maurer, F., Delorenzi, M., Falquet, L., 2005, On ubiquitin ligases and cancer, Hum Mutat, 25, (6), 507-512, (PubMed)

  • Bertucci, F., Finetti, P., Rougemont, J., Charafe-Jauffret, E., Cervera, N., Tarpin, C., Nguyen, C., Xerri, L., Houlgatte, R., Jacquemier, J., Viens, P., Birnbaum, D., 2005, Gene expression profiling identifies molecular subtypes of inflammatory breast cancer., Cancer Res., 65, (6), 2170-2178, (PubMed)

  • Boeckmann, B., Blatter, M. C., Famiglietti, L., Hinz, U., Lane, L., Roechert, B., Bairoch, A., 2005, Protein variety and functional diversity: Swiss-Prot annotation in its biological context, C R Biol, 328, (10-11), 882-899, (PubMed)

  • Boyer, F., Morgat, A., Labarre, L., Pothier, J., Viari, A., 2005, Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data, Bioinformatics, 21, (23), 4209-4215, (PubMed)

  • Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schonbach, C., Sekiguchi, K., Semple, C. A., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J., Hayashizaki, Y., 2005, The transcriptional landscape of the mammalian genome, Science, 309, (5740), 1559-1563, (PubMed)

  • Cebecauer, M., Guillaume, P., Mark, S., Michielin, O., Boucheron, N., Bezard, M., Meyer, B. H., Segura, J. M., Vogel, H., Luescher, I. F., 2005, CD8+ cytotoxic T lymphocyte activation by soluble major histocompatibility complex-peptide dimers, J Biol Chem, 280, (25), 23820-23828, (PubMed)

  • Chen, P. Y., Manninga, H., Slanchev, K., Chien, M., Russo, J. J., Ju, J., Sheridan, R., John, B., Marks, D. S., Gaidatzis, D., Sander, C., Zavolan, M., Tuschl, T., 2005, The developmental miRNA profiles of zebrafish as determined by small RNA cloning, Genes Dev, 19, (11), 1288-1293, (PubMed)

  • Chen, Y. T., Scanlan, M. J., Venditti, C. A., Chua, R., Theiler, G., Stevenson, B. J., Iseli, C., Gure, A. O., Vasicek, T., Strausberg, R. L., Jongeneel, C. V., Old, L. J., Simpson, A. J., 2005, Identification of cancer/testis-antigen genes by massively parallel signature sequencing, Proc Natl Acad Sci U S A, 102, (22), 7940-7945, (PubMed)

  • Chen, Y. T., Venditti, C. A., Theiler, G., Stevenson, B. J., Iseli, C., Gure, A. O., Jongeneel, C. V., Old, L. J., Simpson, A. J., 2005, Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein, Cancer Immun, 5, 9, (PubMed)

  • Christensen, N. M., Axelsen, K. B., Nicolaisen, M., Schulz, A., 2005, Phytoplasmas and their interactions with hosts, Trends Plant Sci, 10, (11), 526-535, (PubMed)

  • Christensen, N. M., Axelsen, K. B., Nicolaisen, M., Schulz, A., 2005, Phytoplasmas and their interactions with hosts, Trends Plant Sci, 10, (11), 526-535, (PubMed)
  • De Los Rios, P., Cecconi, F., Pretre, A., Dietler, G., Michielin, O., Piazza, F., Juanico, B., 2005, Functional dynamics of PDZ binding domains: a normal-mode analysis, Biophys J, 89, (1), 14-21, (PubMed)
  • Deutsch, S., Lyle, R., Dermitzakis, E. T., Attar, H., Subrahmanyan, L., Gehrig, C., Parand, L., Gagnebin, M., Rougemont, J., Jongeneel, C. V., Antonarakis, S. E., 2005, Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes, Hum Mol Genet, 14, (23), 3741-3749, (PubMed)

  • Dobrokhotov, P. B., Goutte, C., Veuthey, A. L., Gaussier, E., 2005, Assisting medical annotation in Swiss-Prot using statistical classifiers, Int J Med Inform, 74, (2-4), 317-324, (PubMed)

  • Efe, J. A., Plattner, F., Hulo, N., Kressler, D., Emr, S. D., Deloche, O., 2005, Yeast Mon2p is a highly conserved protein that functions in the cytoplasm-to-vacuole transport pathway and is required for Golgi homeostasis, J Cell Sci, 118, (Pt 20), 4751-4764, (PubMed)

  • Egener, T., Roulet, E., Zehnder, M., Bucher, P., Mermod, N., 2005, Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts, Nucleic Acids Res, 33, (8), e79, (PubMed)

  • Farmer, P., Bonnefoi, H., Becette, V., Tubiana-Hulin, M., Fumoleau, P., Larsimont, D., Macgrogan, G., Bergh, J., Cameron, D., Goldstein, D., Duss, S., Nicoulaz, A. L., Brisken, C., Fiche, M., Delorenzi, M., Iggo, R., 2005, Identification of molecular apocrine breast tumours by microarray analysis, Oncogene, 24, (29), 4660-4671, (PubMed)

  • Feytmans, E., Noble, D., Peitsch, M. C., 2005, Genome Size and Numbers of Biological Functions T. Comp. Sys. Biology, 1, 44-49

  • Filges, I., Zaman, K., Michielin, O., Vulliemoz, D., Perey, L., Stupp, R., 2005, Present chemoprevention and future vision, Rev Med Suisse, 1, (20), 1343-1346, 1349, (PubMed)

  • Fishilevich, E., Domingos, A. I., Asahina, K., Naef, F., Vosshall, L. B., Louis, M., 2005, Chemotaxis behavior mediated by single larval olfactory neurons in Drosophila, Curr Biol, 15, (23), 2086-2096, (PubMed)

  • Gardner, T. J., Naef, F., Nottebohm, F., 2005, Freedom and rules: the acquisition and reprogramming of a bird's learned song, Science, 308, (5724), 1046-1049, (PubMed)

  • Genolet, R., Kersten, S., Braissant, O., Mandard, S., Tan, N. S., Bucher, P., Desvergne, B., Michalik, L., Wahli, W., 2005, Promoter rearrangements cause species-specific hepatic regulation of the glyoxylate reductase/hydroxypyruvate reductase gene by the peroxisome proliferator-activated receptor alpha, J Biol Chem, 280, (25), 24143-24152, (PubMed)

  • Girod, P. A., Zahn-Zabal, M., Mermod, N., 2005, Use of the chicken lysozyme 5' matrix attachment region to generate high producer CHO cell lines., Biotechnol Bioeng, 91, (1), 1-11, (PubMed)

  • Gomes, A. R., Vinga, S., Zavolan, M., de Lencastre, H., 2005, Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus, Antimicrob Agents Chemother, 49, (1), 366-379, (PubMed)

  • Guimil, S., Chang, H. S., Zhu, T., Sesma, A., Osbourn, A., Roux, C., Ioannidis, V., Oakeley, E. J., Docquier, M., Descombes, P., Briggs, S. P., Paszkowski, U., 2005, Comparative transcriptomics of rice reveals an ancient pattern of response to microbial colonization., Proc Natl Acad Sci USA, 102, (22), 8066-8070, (PubMed)

  • Hermida, L., Brachat, S., Voegeli, S., Philippsen, P., Primig, M., 2005, The Ashbya Genome Database (AGD)--a tool for the yeast community and genome biologists, Nucleic Acids Res, 33, (Database issue), D348-352, (PubMed)

  • Hochwagen, A., Wrobel, G., Cartron, M., Demougin, P., Niederhauser-Wiederkehr, C., Boselli, M. G., Primig, M., Amon, A., 2005, Novel response to microtubule perturbation in meiosis, Mol Cell Biol, 25, (11), 4767-4781, (PubMed)

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

  • Jacquemier, J., Ginestier, C., Rougemont, J., Bardou, V. J., Charafe-Jauffret, E., Geneix, J., Adelaide, J., Koki, A., Houvenaeghel, G., Hassoun, J., Maraninchi, D., Viens, P., Birnbaum, D., Bertucci, F., 2005, Protein expression profiling identifies subclasses of breast cancer and predicts prognosis, Cancer Res., 65, (3), 767-779, (PubMed)

  • Jongeneel, C. V., Delorenzi, M., Iseli, C., Zhou, D., Haudenschild, C. D., Khrebtukova, I., Kuznetsov, D., Stevenson, B. J., Strausberg, R. L., Simpson, A. J., Vasicek, T. J., 2005, An atlas of human gene expression from massively parallel signature sequencing (MPSS), Genome Res, 15, (7), 1007-1014, (PubMed)

  • Jungo, F., Bairoch, A., 2005, Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase, Toxicon, 45, (3), 293-301, (PubMed)

  • Kersey, P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I., Gattiker, A., Kulikova, T., Faruque, N., Duggan, K., McLaren, P., Reimholz, B., Duret, L., Penel, S., Reuter, I., Apweiler, R., 2005, Integr8 and Genome Reviews: integrated views of complete genomes and proteomes, Nucleic Acids Res, 33, (Database issue), D297-302, (PubMed)

  • Koffel, R., Tiwari, R., Falquet, L., Schneiter, R., 2005, The Saccharomyces cerevisiae YLL012/YEH1, YLR020/YEH2, and TGL1 genes encode a novel family of membrane-anchored lipases that are required for steryl ester hydrolysis, Mol Cell Biol, 25, (5), 1655-1668, (PubMed)

  • Kumar, A., Yip, Y. L., Smith, B., Grenon, P., 2005, Bridging the gap between medical and bioinformatics: An ontological case study in colon carcinoma, Comput Biol Med, (PubMed)

  • Kumar, A., Yip, Y. L., Smith, B., Marwede, D., Novotny, D., 2005, An ontology for carcinoma classification for clinical bioinformatics, Stud Health Technol Inform, 116, 635-640, (PubMed)

  • Lane-Guermonprez, L., Morot-Gaudry-Talarmain, Y., Meunier, F. M., O'Regan, S., Onofri, F., Le Caer, J. P., Benfenati, F., 2005, Synapsin associates with cyclophilin B in an ATP- and cyclosporin A-dependent manner, J. Neurochem., 93, (6), 1401-1411, (PubMed)

  • Leidel, S., Delattre, M., Cerutti, L., Baumer, K., Gonczy, P., 2005, SAS-6 defines a protein family required for centrosome duplication in C. elegans and in human cells, Nat Cell Biol, 7, (2), 115-125, (PubMed)

  • Lim, D. A., Suarez-Farinas, M., Naef, F., Hacker, C. R., Menn, B., Takebayashi, H., Magnasco, M., Patil, N., Alvarez-Buylla, A., 2005, In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis, Epub, Dec 5

  • Michielin, O., Blanchet, J. S., Fagerberg, T., Valmori, D., Rubio-Godoy, V., Speiser, D., Ayyoub, M., Alves, P., Luescher, I., Gairin, J. E., Cerottini, J. C., Romero, P., 2005, Tinkering with nature: the tale of optimizing peptide based cancer vaccines, Cancer Treat Res, 123, 267-291, (PubMed)

  • Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A. N., Orchard, S., Pagni, M., Ponting, C. P., Quevillon, E., Selengut, J., Sigrist, C. J., Silventoinen, V., Studholme, D. J., Vaughan, R., Wu, C. H., 2005, InterPro, progress and status in 2005, Nucleic Acids Res., 33, (Database issue), D201-205 (PubMed)

  • Naef, F., 2005, Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria, Mol Syst Biol, 1, (PubMed)

  • Naef, F., Huelsken, J., 2005, Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks, Nucleic Acids Res., 33, (13), e111, (PubMed)

  • Orchard, S., Hermjakob, H., Binz, P. A., Hoogland, C., Taylor, C. F., Zhu, W., Julian, R. K., Jr., Apweiler, R., 2005, Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004, Proteomics, 5, (2), 337-339, (PubMed)

  • Ouared, R., Chen, H., Succi, S., Latt, J., Chopard, B., 2005, Lattice Boltzmann simulations of blood flow : non-Newtonian rheology and clottin processes, J Stat Phys, 121 (1-2), 209-221

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

  • Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F. A., van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M., Russo, J. J., Ju, J., Randall, G., Lindenbach, B. D., Rice, C. M., Simon, V., Ho, D. D., Zavolan, M., Tuschl, T., 2005, Identification of microRNAs of the herpesvirus family, Nat Methods, 2, (4), 269-276, (PubMed)

  • Pillet, V., Zehnder, M., Seewald, A. K., Veuthey, A. L., Petrak, J., 2005, GPSDB: a new database for synonyms expansion of gene and protein names, Bioinformatics, 21, (8), 1743-1744, (PubMed)

  • Ruch, P., Baud, R., Chichester, C., Geissbuhler, A., Lisacek, F., Marty, J., Rebholz-Schuhmann, D., Tbahriti, I., Veuthey, A. L., 2005, Extracting key sentences with latent argumentative structuring, Stud Health Technol Inform, 116, 835-840, (PubMed)

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

  • Scherl, A., Zimmermann-Ivol, C. G., Di Dio, J., Vaezzadeh, A. R., Binz, P. A., Amez-Droz, M., Cochard, R., Sanchez, J. C., Gluckmann, M., Hochstrasser, D. F., 2005, Gold coating of non-conductive membranes before matrix-assisted laser desorption/ionization tandem mass spectrometric analysis prevents charging effect, Rapid Commun. Mass Spectrom., 19, (5), 605-610, (PubMed)

  • Schneider, M., Bairoch, A., Wu, C. H., Apweiler, R., 2005, Plant protein annotation in the UniProt Knowledgebase, Plant Physiol, 138, (1), 59-66, (PubMed)

  • Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M. J., Tuschl, T., van Nimwegen, E., Zavolan, M., 2005, Identification of clustered microRNAs using an ab initio prediction method, BMC Bioinformatics, 6, 267, (PubMed)

  • Siddharthan, R., Siggia, E. D., van Nimwegen, E., 2005, PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny, PLoS Comput Biol, 1, (7), e67, (PubMed)

  • Sigrist, C. J., De Castro, E., Langendijk-Genevaux, P. S., Le Saux, V., Bairoch, A.,
    Hulo, N., 2005, ProRule: a new database containing functional and structural information on PROSITE profiles, Bioinformatics, 21, (21), 4060-4066, (PubMed)

  • Speirs, C., van Nimwegen, E., Bolton, D., Zavolan, M., Duvall, M., Angleman, S., Siegel, R., Perelson, A. S., Lenardo, M. J., 2005, Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture, J Virol, 79, (7), 4025-4032, (PubMed)

  • Sperisen, P., Pagni, M., 2005, JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture., BMC Bioinformatics, 6, 216, (PubMed)

  • Sperisen, P., Schmid, C. D., Bucher, P., Zilian, O., 2005, Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense, PLoS Comput Biol, 1, (6), e63, (PubMed)
  • Stephan, C., Hamacher, M., Bluggel, M., Korting, G., Chamrad, D., Scheer, C., Marcus, K., Reidegeld, K. A., Lohaus, C., Schafer, H., Martens, L., Jones, P., Muller, M., Auyeung, K., Taylor, C., Binz, P. A., Thiele, H., Parkinson, D., Meyer, H. E., Apweiler, R., 2005, 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame, Proteomics, 5, (14), 3560-3562, (PubMed)

  • Suarez, M., Haenni, M., Canarelli, S., Fisch, F., Chodanowski, P., Servis, C., Michielin, O., Freitag, R., Moreillon, P., Mermod, N., 2005, Structure-function characterization and optimization of a plant-derived antibacterial peptide, Antimicrob Agents Chemother, 49, (9), 3847-3857, (PubMed)

  • Tavernier, G., Jimenez, M., Giacobino, J. P., Hulo, N., Lafontan, M., Muzzin, P., Langin, D., 2005, Norepinephrine induces lipolysis in beta1/beta2/beta3-adrenoceptor knockout mice, Mol Pharmacol, 68, (3), 793-799, (PubMed)

  • Tbahriti, I., Chichester, C., Lisacek, F., Ruch, P., 2005, Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library, Int J Med Inform, (Sep 12), (PubMed)
  • Wijnen, H., Naef, F., Young, M. W., 2005, Molecular and statistical tools for circadian transcript profiling, Methods Enzymol, 393, 341-365, (PubMed)

  • Wrobel, G., Chalmel, F., Primig, M., 2005, goCluster integrates statistical analysis and functional interpretation of microarray expression data, Bioinformatics, 21, (17), 3575-3577, (PubMed)

  • Wrobel, G., Primig, M., 2005, Mammalian male germ cells are fertile ground for expression profiling of sexual reproduction, Reproduction, 129, (1), 1-7, (PubMed)


  • Review


  • Boeckmann, B., Blatter, M. C., Famiglietti, L., Hinz, U., Lane, L., Roechert, B., Bairoch, A., 2005, Protein variety and functional diversity: Swiss-Prot annotation in its biological context, C R Biol, 328, (10-11), 882-899, (PubMed)

  • Hernandez, P., Müller, M., Appel, R. D., 2005, Automated protein identification by tandem mass spectrometry: Issues and strategies, Mass Spectrom Rev, 25 (2), 235-254


  • Guest Edition


  • Palagi, P. M., Sanchez, J. C., Stöecklin, R., 2005, Special Issue on the Proceedings of the 4th Annual Congress of the Swiss Proteomics Society, Proteomics, 5, (12

  • Book Chapters


  • Aebersold, R., Affolter, M., Agurri, A., Elia, G., Gruissem, W., Neri, D., Palagi, P. M., Sanchez, J. C., Schlapbach, R., Rossier, J. S., Stöecklin, R., Proceedings of the Swiss Proteomics Society 2005, Congress, Expanding proteomics (Editors). Zürich, Switzerland, 2005

  • Bairoch, A., Boeckmann, B., Ferro Rojas, S., Gasteiger, E., Swiss-Prot: juggling between evolution and stability (In)Essays in Bioinformatics, in  Moss, D. S., Jelaska, S. and Pongor, S. (Ed.), NATO Science Series: Live and Behavioural Sciences, IOS Press, 2005
  • Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., Bairoch, A., Protein Identification and Analysis Tools on the ExPASy Server, in  Walker, J. M. (Ed.), Methods in Molecular Biology, Humana Press, 2005

  • Goldstein, D. R., Delorenzi, M., Statistical Design and Data Analysis for Microarray Experiments, in  Berger, A. and Roberts, M. A. (Ed.), Unraveling Lipid Metabolism with Microarrays, Marcel Dekker, New York, 2005
    Hoogland, C., Mostaguir, K., Appel, R. D., 2-DE Databases on the World-Wide Web, in  J.M., W. (Ed.), The Proteomics Protocols Handbook, Humana Press, 2005

  • Latt, J., Chopard, B., An implicitly parallel object-oriented matrix library and its application to medical physics in  Yang, Y. P. a. L. T. (Ed.), Advances in Computation: Theory and Practice, Nova Science, Inc, 2005
  • Palagi, P. M., Walther, D., Bouchet, G., Voordijk, S., Appel, R. D., Computer Analysis of 2D Images, in  Walker, J. M. (Ed.), The Proteomics Protocols Handbook, Humana Press 2005

  • Sigrist, C. J. A., De Castro, E., Langendijk-Genevaux, P. S., Le Saux, V., Bairoch, A., Hulo, N., Functionally and structurally relevant residues in PROSITE motif descriptors, in  (Ed.), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (Part 3, Proteomics 3.6, Proteome Families Copyright), John Wiley & Sons, 2005


  • Conference Proceedings


  • Lima, T., Apweiler, R., Bairoch, A., Wu, C., Consortium, U., The UniProt Knowledgebase, EU/US Workshop on Genomic Approaches for Studying the Marine Environment and Resources, Bremen, Germany, May 2005

  • Lisacek, F., Knowledge shift patterns in biomedical abstracts, Third Birlinghoven Symposium on Text Mining in the Life Sciences, Sankt Augustin, Germany, October 2005

  • 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), European Bioinformatics Institute, Hinxton, UK, April 2005

  • Monteiro-Vitorello, C. B., Nicolás, M. F., Moreira, C. G., Lima, T., Michoud, K., Rivoire, C., Coudert, E., Auchincloss, A., Keller, G., Gattiker, A., Bairoch, A., SwissProt Brazil and the annotation of proteins from pathogenic bacteria, 51 Congresso Brasileiro de Genética, Águas de Lindóia, Brazil, September 2005

  • Monteiro-Vitorello, C. B., Nicolás, M. F., Moreira, C. G., Lima, T., Michoud, K., Rivoire, C., Coudert, E., Auchincloss, A., Keller, G., Gattiker, A., Bairoch, A., SwissProt Brazil and the annotation of proteins from pathogenic bacteria, 11th International Workshop on Virus Evolution and Molecular Epidemiology, Petrópolis, Brazil, September 2005

  • Nicolás, M. F., Monteiro-Vitorello, C. B., Moreira, C. G., Lima, T., Michoud, K., Rivoire, C., Coudert, E., Auchincloss, A., Keller, G., Gattiker, A., Bairoch, A., SwissProt Brazil and the annotation of proteins from pathogenic bacteria, XXIII Congresso Brasileiro de Microbiologia, Santos, Brazil, November 2005


  • Abstracts & Posters


  • Appel, R. D., Current and future challenges in proteome informatics., BC2-Basel Computational Biology Conference 2005., Basel, Switzerland, March 2005

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

  • Arnold, K., Bordoli, L., Kopp, J., Schwede, T., The SWISS-MODEL Workspace: A web-based protein structure modelling environment, ECCB Madrid, Spain, September - October 2005

  • Arnold, K., Bordoli, L., Kopp, J., Schwede, T., The SWISS-MODEL Workspace: A web-based protein structure modelling environment, Biozentrum Symposium, Basel, Switzerland, October 2005

  • Auchincloss, A. H., Michoud, K., Consortium., U., HAMAP, a semi-automatic annotation system in UniProtKB/ Swiss-Prot, 1st International Biocurator Meeting, Pacific Grove, CA-USA, December 2005

  • Bienvenut, W. V., Estreicher, A., Potts, A., Quadroni, M., Identification by tandem mass spectrometry of N-terminal acetylated proteins in eukaryotic samples., 1er Symposium de Chimie et Biologie Analytiques, Corum de Montpellier, France, September 2005

  • Binz, P.-A., Aspects de bioinformatique appliquée à l'étude du phosphoprotéome, Atelier phosphoprotéome, Cap d’Agde, France, June - August  2005

  • Binz, P.-A., 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, Germany, August 2005

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

  • Binz, P.-A., Phenyx: understand and manage Proteomics Methods Forum, York, UK, April & August 2005

  • Binz, P.-A., Masselot, A., Appel, R. D., Proteome Bioinformatics: critically evaluating MS data Swiss Proteomics Society 2004 Congress: Expanding proteomics, Zürich, Switzerland, December 2005

  • Blatter, M.-C., Schneider, M., Estreicher, A., Bairoch, A., The Swiss-Prot protein knowledgebase and UniProt: Providing the scientific community with high quality protein data and proteomic tools, USGEB Congress, Zürich, Switzerland, February 2005

  • Boeckmann, B., Phan, I., New developments in Swiss-Prot  ECCB-European Conferences on Computational Biology, Madrid, Spain, September-October 2005

  • Bonnefoi, H., Farmer, P., Delorenzi, M., Becette, V., Piccart, M., Campone, M., Tubiana-Hulin, M., Mauriac, L., Jassem, J., Petit, T., Rouanet, P., Blot, E., Bergh, J., Cameron, D., Bogaerts, J., Iggo, R., Is there a regimen-specific gene signature predicting for pathological complete response after neoadjuvant chemotherapy in hormone-negative breast cancer patients? A microarray substudy of 101 patients included in EORTC 10994/BIG 00-01 Trial, San Antonio Breast Cancer Symposium (SABCS), San Antonio, Texas, USA, December 2005

  • Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., Bairoch, A., The Swiss-Prot Plant Proteome Annotation Program (PPAP) The 14th Swiss Plant Molecular and Cell Biology Conference - SKMB, Les Diablerets, Switzerland, March 2005

  • Cardoso, F., Piccart, M. J., Viale, G., Van 't Veer, L., Saghatchian-d'Assignies, M., Glas, A., Ellis, P., Harris, A., Bergh, J., Lidereau, R., Rutgers, E., Delorenzi, M., Bogaerts, J., Therasse, P., Lazar, V., Amakrane, M., Sotiriou, C., Loi, S., Buyse, M., Multi-centre independent validation of a gene prognostic signature for patients with node-negative breast cancer (BC), final results, San Antonio Breast Cancer Symposium (SABCS), San Antonio, USA, December  2005

  • Chern, T., Van Nimwegen, E., Zavolan, M., Analyses of NAGNAG acceptor sites in mouse full-length cDNAs   Biozentrum Symposium, St. Chrischona, 2005

  • Chopard, B., Ouared, R., Ruefenacht, D., Comparison of various Stent performancemetrics: alatticeBoltzmannapproach, AFI-2005, Sendai, Japan, December 2005

  • Estreicher, A., The Universal Protein Resource (UniProt)  EMBnet collaborative workshop, Smolenice, Slovakia, September 2005

  • Estreicher, A., Bairoch, A., The UniProtKB/Swiss-Prot: Providing the science community with high quality proteomic data 1er Symposium de Chimie et Biologie Analytiques, Corum de Montpellier, France, Septembre 2005

  • Estreicher, A., Uniprot Consortium, Sequence annotation in UniProtKB/Swiss-Prot   1st International Biocurator Meeting, Pacific Grove, CA - USA December 2005

  • Farmer, P., Bonnefoi, H., Becette, V., Tubiana-Hulin, M., Fumoleau, P., Larsimont, D., MacGrogan, G., Bergh, J., Cameron, D., Goldstein, D. R., Duss, S., Nicoulaz, A. L., Brisken, C., Fiche, M., M., D., Iggo, R., Identification of molecular apocrine breast tumours by microarray analysis, 5th international ISREC Conference "Cell and Molecular Biology of Cancer", Lausanne, Switzerland, January 2005

  • Farmer, P., Bonnefoi, H., Becette, V., Tubiana-Hulin, M., Fumoleau, P., Larsimont, D., MacGrogan, G., Bergh, J., Cameron, D., Goldstein, D. R., Duss, S., Nicoulaz, A. L., Brisken, C., Fiche, M., M., D., Iggo, R., Identification of molecular apocrine breast tumours by microarray analysis, 5th international ISREC Conference "Cell and Molecular Biology of Cancer", Saas-Fee, Switzerland, November 2005

  • Farmer, P., Duss, S., Bonnefoi, H., Becette, V., Nicoulaz, A. L., Delorenzi, M., Iggo, R., Identification of Molecular Apocrine Breast Tumours by Microarray Analysis, 7th Charles Rodolphe Brupbacher Symposium, Advances in Oncology: From Model System to the Clinic, Zürich, Switzerland, March 2005

  • Farriol-Mathis, N., Garavelli, J. S., Bairoch, A., Post-translational modifications and the UniProt/Swiss-Prot Knowledgebase USGEB Congress, Zürich, Switzerland, February 2005

  • Farriol-Mathis, N., Lane-Guermonprez, L., Bairoch, A., Annotation of post-translational modifications in UniProtKB/Swiss-Prot and their effect in cell context 30th FEBS Congress - 9th IUBMB Conference Budapest, Hungary, July 2005

  • Feuermann, M., Pedruzzi, I., Junker, V., Laiho, K., Apweiler, R., Bairoch, A., The Fungal Proteome Annotation Program (FPAP) in the frame of the UniProt knowledgebase, ESF-EMBO Symposia Comparative genomics of Eukaryotic Microorganisms Eukaryotic Genome Evolution, approaches with yeasts and fungi, Sant Feliu de Guixols, Spain, November 2005

  • Hermida, L., Schaad, O., Descombes, P., Primig, M., MIMAS: A Microarray Information Management and Analysis System for Affymetrix GeneChip Experiments, 8th International Meeting of the Microarray Gene Expression Data Society, Bergen, Norway, 2005

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

  • Hinz, U., Bairoch, A., Uniprot & Swiss-Prot: providing a link between protein sequences and state of the art knowledge  30th FEBS Congress - 9th IUBMB Conference, Budapest, Hungary, July 2005

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

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

  • Hochstrasser, D. F., Walther, D., Quadroni, M., Catherinet, S., Tuloup, M., Binz, P.-A., Burgess, J., Vaezzadeh, A., Zimmerman, C., Corthals, G. L., Sanchez , J.-C., Appel, R. D., MS imaging in Clinical Proteomic, Beyond Genome, San Francisco, USA, June 2005

  • Hochstrasser, D. F., Appel, R. D., Paesano, S., Binz, P.-A., Sanchez , J.-C., Zimmermann, C., Proteomics & Clinical Chemistry, HUPO 4th Annual meeting, Munich, Germany August 2005

  • Jimenez, S., Ferro Rojas, S., Bairoch, A., UniProtKB/Swiss-Prot and the Human Proteomics Initiative, HUPO 4th Annual Congress, Munich, Germany, August 2005

  • Lambiv, W. L., Misra, A., Delorenzi, M., Stupp, R., Feuerstein, B. G., Hegi, M. E., Relationships Among Genomic Copy Number Aberrations, MGMT-Methylation, and Outcome in Glioblastoma, Oncogenomics 2005, " Dissecting Cancer Through Genome Research", San Diego, California, February 2005

  • Lane, L., Farriol-Mathis, N., Duvaud, S., Gasteiger, E., Bairoch, A., Post-translational modifications in Swiss-Prot : recent developments, Congress of the Swiss Proteomics Society, Zürich, Switzerland,, December 2005.

  • Lieberherr, D., Boutet, E., Tognolli, M., Schneider, M., Bairoch, A., The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot, 30th FEBS Congress - 9th IUBMB Conference, Budapest, Hungary, July 2005

  • Lieberherr, D., Boutet, E., Tognolli, M., Schneider, M., Bairoch, A., From DNA sequence to protein sequence and functional information: annotation of rice proteins in UniProtKB/Swiss-Prot, 5th International Rice Genetics Simposium, Manila, Philippines, November 2005

  • Lima, T., Michoud, K., Rivoire, C., Coudert, E., Auchincloss, A., Keller, G., Gattiker, A., Bairoch, A., Annotation of microbial proteins in Swiss-Prot, 64th Annual Assembly Swiss Society of Microbiology, Geneva, Switzerland, March  - April 2005

  • Lima, T., Michoud, K., Rivoire, C., Auchincloss, A., Coudert, E., Keller, G., Le Saux, V., Monteiro-Vitorello, C. B., Gattiker, A., Bairoch, A., Annotation of microbial proteins in Swiss-Prot, International Conference on Microbial Genomes, Halifax, Canada, April 2005

  • Lisacek, F., Knowledge shift patterns in biomedical abstracts, Third Birlinghoven Symposium on Text Mining in the Life Sciences, Sankt Augustin, Germany, October 2005

  • Monteiro-Vitorello, C. B., Michoud, K., Rivoire, K., Auchincloss, A., Coudert, E., Lima, T., Keller, G., Le Saux, V., Gattiker, A., Bairoch, A., Swiss-Prot and the annotation of microbial proteomes, 2nd European Conference on Prokaryotic Genomes, Gottingen, Germany, September 2005

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

  • Mostaguir, K., Hoogland, C., Appel, R. D., 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, Lyon, France, Juillet 2005

  • Murat, A., Migliavacca, E., Shay, T., Stupp, R., Domany, E., Delorenzi, M., Hegi ME Molecular profiles of gliomas, mechanistic insights and associations with outcome, Oncogenomics 2005, " Dissecting Cancer Through Genome Research", San Diego, California, February 2005

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

  • Palagi, P. M., Walther, D., Quadroni, M., Catherinet, S., Binz, P.-A., Hochstrasser, D. F., Appel, R. D., MSight: an LC-MS image analysis software, ISMB 2005-13th Annual International Conference on Intelligent Systems for Molecular Biology, Michigan, USA, June 2005

  • Parisi, F., Integration of genomic data to infer direct targets of transcription regulators, DDays 2005 UNIL, Lausanne, Switzerland, 2005

  • Pedruzzi, I., Junker, V., Feuermann, M., Laiho, K., Apweiler, R., Bairoch, A., The Swiss-Prot Fungal Proteome Annotation Program (FPAP), XXII International Conference on Yeast Genetics & Molecular Biology, Bratislava, Slovak Republic, August 2005

  • Perret, D., Bairoch, A., Veuthey, A.-L., CaPSuLo, an evaluation-based integrative web tool for predicting subcellular location of proteins, ECCB 2005 - Fourth European Conference on Computational Biology, Madrid, Spain, September 2005

  • Pillet, V., Zehnder, M., Veuthey, A.-L., consortium., T. B., BioMinT: a database curator's assistant for biomedical text processing, First International Symposium on Semantic Mining in Biomedicine, Hinxton, UK, April 2005

  • Poux, S., Bairoch, A., team., S.-P., UniprotKB/Swiss Prot: from the protein sequence to the knowledge, The Swiss Proteomics Society 2005 Congress: Expanding proteomics, Zürich, Switzerland, December 2005

  • Quadroni, M., Baruthio, F., Walther, D., Appel, R. D., 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, USA, June 2005

  • Rebholz-Schuhman, D., Veuthey, A.-L., Blaske, C., Hahn, U., Future of text-mining and its relation with database annotations, Workshop on Biomedical Ontologies and Text Processing ECCB'05, Madrid, Spain, September 28th (panel discussion)

  • Yip, Y. L., Kumar, A., Tutorial: Online Cancer Information Resources: From Clinics to Biology The Medical Informatics Europe (MIE) congress 2005, Geneva, Switzerland, September 2005

  • Retelska, D., Beaudoing, E., Notredame, C., Jongeneel, V., Bucher, P., Comparative analysis of genomic conservation patterns in vertebrates and insects, ECCB/JBI, Madrid, Spain, September 2005

  • Rolland, A., Niederhauser-Wiederkehr, C., Chalmel, F., Demougin, P., Cartron, M., Chung, S., Wolgemuth, D., Jegou, B., Primig, M., The conserved protein-coding transcriptome of mammalian male germ cells, 9th ICEM Meeting on Environmental Mutagenesis San Francisco, USA, September 2005

  • Rolland, A., Niederhauser-Wiederkehr, C., Chalmel, F., Demougin, P., Chern, T., Cartron, M., Chung, S., Hermida, L., Zavolan, M., Wolgemuth, D., Jégou, B., Primig, M., The conserved protein-coding transcriptome of mammalian male germ cells, Affymetrix User Group Meeting 2005, Berlin, Germany, May 2005

  • Scarsi, M., Rücker, C., Dannecker, R., Hug, H., Gut, J., A., M. U., Molecular Modeling of PPARgamma agonists, Third internationalsymposium on PPARs efficacy and safety, Monte Carlo, Monaco, March 2005

  • Scarsi, M., Rücker, C., Dannecker, R., Hug, H., Bagatto, D., J., G., Meyer, U., A new Mode of Action for Sulfonylureas as Antidiabetic Drugs: Modelling of PPARg Agonists, CTI Medtech Event, University Hospital Bern, Switzerland, September 2005

  • Scherl, A., Zimmermann-Ivol, C. G., Bento, M., Francois, P., Sanchez , J.-C., Appel, R. D., Schrenzel, J., Hochstrasser, D. F., Characterization of Staphylococcus aureus Proteins involved in glycopeptide tolerance with mass spectrometric based quantitative methods,  Congress of the Swiss Proteomics Society, Zürich, Switzerland, December 2005

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

  • Schlecht, U., Niederhauser-Wiederkehr, C., Demougin, P., Robine, N., Borde, V., Nicolas, A., Primig, M., Systems-based analysis of Abf1 reveals coordination of mitotic growth and meiotic development via a highly dynamic protein-DNA interaction profile, 7th European Meiosis Meeting, Madrid, Spain, September 2005

  • Schlecht, U., Niederhauser-Wiederkehr, C., Demougin, P., Robine, N., Borde, V., Nicolas, A., Primig, M., Systems-based analysis of Abf1 reveals coordination of mitotic growth and meiotic development via a highly dynamic protein-DNA interaction profile, 22nd International Conference on Yeast Genetics and Molecular Biology Bratislava, Slovenia, August 2005

  • Schneider, M., Estreicher, A., Bairoch, A., Swiss-Prot, the manually annotated section of the UniProt knowledgebase, Plant and Animal Genome XIII Conference, San Diego, CA, USA, January 2005

  • Schneider, M., Boutet, E., Lieberherr, D., Tognolli, M., Bairoch, A., Annotation of plant proteins in UniProtKB/Swiss-Prot Plant-GEMs 4, Amsterdam, Netherlands, September  2005

  • Schneider, M., Consortium, T. U., Connecting biological knowledge via UniProtKB/Swiss-Prot,1st International Biocurator Meeting, Pacific Grove, CA, USA, December 2005

  • Sewer, A., Zavolan, M., Computational prediction of clustered miRNAs, Symposium on “RNA secondary structure beyond neutral networks, Leipzig, Austria, 2005

  • Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M. J., Tuschl, T., van Nimwegen, E., Zavolan, M., Ab initio prediction of miRNA genes, ISMB 2005, Detroit, Michigan, USA, June 2005

  • Siddharthan, R., Siggia, E. D., van Nimwegen, E., PhyloGibbs: A motif sampling algorithm that incorporates phylogeny, ISMB 2005, PLoS Computational Biology ,late-breaking poster session, Detroit, Michigan, USA, June 2005

  • Sotiriou, C., Wirapati, P., Loi, S., Desmedt, C., Harris, A. L., Bergh, J., Smeds, J., Praz, V., Cardoso, F., Farmer, P., Haibe-Kains, B., Lallemand, F., Buyse, M., Piccart, M., Delorenzi, M., Refining Tumor Grade and ist Prognostic Relevance by Expression Profiling, The third international Symposium on the Molecular Biology of Breast Cancer, Molde, Norway, June 2005

  • Sotiriou, C., Wirapati, P., Loi, S., Viale, G., Harris, A., Bergh, J., Smeds, J., Farmer, P., Praz, V., Haibe-Kains, B., Lallemand, F., Desmedt, C., Durbecq, V., Larsimont, D., Cardoso, F., Buyse, M., Delorenzi, M., Piccart, M., Breast tumours with intermediate histological grade can be reclassified into prognostically distinct groups by gene expression profiling, San Antonio Breast Cancer Symposium (SABCS), San Antonio, Texas, USA, December 2005

  • Thorsteinsdottir, H., Schwede, T., Zoete, V., Meuwly, M., Quantitative Evaluation of Homology Models for Structure-Based Drug Design: HIV-I Protease as a Test Bed, ECCB, Madrid, Spain, September - October 2005

  • Thorsteinsdottir, H., Schwede, T., Zoete, V., Meuwly, M., Computational Aspects of ATP Analogue Binding in Kinases, Meeting of the Swiss Chemical Society SCS, Lausanne, Switzerland, October 2005

  • Thorsteinsdottir, H., Schwede, T., Zoete, V., Meuwly, M., Quantitative Evaluation of Homology Models for Structure-Based Drug Design: HIV-I Protease as a Test Bed, Biozentrum Symposium, Basel, Switzerland, October 2005

  • Van Nimwegen, E., Sheridan, R., Paul, N., Zavolan, M., SPA : A Probabilistic Algorithm for Spliced Alignment, Biozentrum Symposium, St. Chrischona, Switzerland, 2005

  • Van Nimwegen, E., Sheridan, R., Paul, N., Zavolan, M., SPA : A Probabilistic Spliced Alignment Algorithm, ISMB 2005, Special Interest Group meeting on Alternative Splicing, Detroit, Michigan, USA, June 2005

  • Veuthey, A.-L., Pillet, V., Zehnder, M., consortium, T. B., BioMinT: a database curator's assistant for biomedical text processing, ECCB'05-European Conference of Computational Biology Madrid, Spain, September - October 2005

  • Walther, D., Quadroni, M., Catherinet, S., Hochstrasser, D. F., Palagi, P. M., Appel, R. D., MSight: an LC-MS image analysis software, Fourth HUPO annual meeting, Munich, Germany, August 2005

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

  • Wirapati, P., Flores, S., Delorenzi, M., SwissBrod: Swiss Breast Oncology Gene-Expression Database, MGED8 (Microarray Gene Expression Data Society), Bergen, Norway, September 2005

  • Yip, Y. L., Kumar, A., Tutorial: Online Cancer Information Resources: From Clinics to Biology The Medical Informatics Europe (MIE) congress 2005, Geneva, Switzerland, September 2005

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


  • Other


  • Bairoch, A., Apweiler, R., Wu, C. H., 2005, UniProt knowledgebase: Swiss-Prot and TrEMBL user manual, Swiss Institute of Bioinformatics and European Bioinformatics Institute, 6.0 (August )

  • Bairoch, A., Axelsen, K., 2005, The ENZYME nomenclature database user manual, Swiss Institute of Bioinformatics, 37, (March)

  • Bairoch, A., Hulo, N., Sigrist, C. J. A., 2005, The PROSITE database of protein families and domains user manual Swiss Institute of Bioinformatics, 19, (April)

  • Dobrokhotov, P., 2005, Bio-text Mining - An approach to assist information retrieval in Swiss-Prot medical annotation. , Thèse de doctorat ès sciences, mention interdisciplinaire (Université de Genève)

  • Gattiker, A., 2005, Development of methods for automated annotation of prokaryotic proteomes Thèse de doctorat ès sciences, mention bioinformatique (Université de Genève)

  • Hernandez, D., 2005, 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)

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

  • Rebholz-Schuhman, D., Veuthey, A.-L., Blaske, C., Hahn, U., Future of text-mining and its relation with database annotations, Workshop on Biomedical Ontologies and Text Processing ECCB'05, Madrid, Spain, September 28th (panel discussion)

  • Yip, Y. L., Kumar, A., Tutorial: Online Cancer Information Resources: From Clinics to Biology The Medical Informatics Europe (MIE) congress 2005, Geneva, Switzerland, September 2005

Other:


Protein Spotlight: 2005 issues, edited by Vivienne Baillie Gerritsen
  • Hazel? Blue? Greenish-brown? Black? (54)
  • The taste experience (55)
  • Forbidden fruit (56)
  • Flower power (57)
  • Tintin's blight (58)
  • Lipid freight (59)
  • The life of a whiff (60)
  • No one nose (61)
  • Shackled sperm (62)
  • The color of the rose (63)
  • A grey matter (64)
  • The thread of life (65)

Protéines à la Une : 2005 issues, edited by Marie Anne Phélouzat, Anne Estreicher and Séverine Altairac
  • Un prix Nobel pour le flair de deux savants (14)
  • In vino veritas (15)
  • Alzheimer: quand la personnalité s'égare (16)

Protein Snapshots: 2005 issues, edited by Vivienne Baillie Gerritsen and Séverine Altairac
  • HFE protein (January)
  • Beta-arrestin 2 and pde4, Protein Snapshot (February)
  • Semidwarf-1 protein, Protein Snapshot (March)
  • Contalukin-G protein (April)
  • Brachyury protein (May)
  • Cannabinoid receptor 2 protein (June)
  • HvAPX1 protein (July)
  • Sonic hedgehog protein (August)
  • The cry proteins (September)
  • The trp channels (October)
  • Adenosine deaminase (November)
  • Neuraminidase (December)

Instantanés du mois: 2005 issues, edited by Vivienne Baillie Gerritsen and Séverine Altairac
  • La protéine HFE (janvier)
  • La bêta-arrestine 2 et la pde 4 (février)
  • La protéine semidwarf-1 (mars)
  • La protéine contalukine-G (avril)
  • La protéine brachyury (mai)
  • Le récepteur cannabinoïde 2 (juin)
  • La protéine HvAPX1 (juillet)
  • La protéine sonic hedgehog (août)
  • Les protéines cry  (septembre)
  • Les canaux trp (octobre)
  • L’adénosine déaminase (novembre)
  • La neuraminidase (décembre)

 

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