Scientific publications
Research - Publications - 2007
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2007
Journal Articles – peer-reviewed

  • Alemani, D., Chopard, B., Galceran, J., Buffle, J., 2007, Study of three grid refinement methods in the Lattice Boltzmann framework for reactive-diffusive processes, Int. J. Mod. Phys. C, 18 (4), 722-731

  • Altenhoff, A. M., Walther, J. H., Koumoutsakos, P., 2007, A stochastic boundary forcing for dissipative particle dynamics, Journal of Computational Physics, 225 (1), 1125-1136

  • Alves, P. M., Viatte, S., Fagerberg, T., Michielin, O., Bricard, G., Bouzourene, H., Vuilleumier, H., Kruger, T., Givel, J. C., Levy, F., Speiser, D. E., Cerottini, J. C., Romero, P., 2007, Immunogenicity of the carcinoembryonic antigen derived peptide 694 in HLA-A2 healthy donors and colorectal carcinoma patients, Cancer Immunol Immunother, 56 (11), 1795-1805 (PubMed)

  • Amoutzias, G. D., Pichler, E. E., Mian, N., De Graaf, D., Imsiridou, A., Robinson-Rechavi, M., Bornberg-Bauer, E., Robertson, D. L., Oliver, S. G., 2007, A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network, BMC Syst Biol, 1 34 (PubMed)

  • Amoutzias, G. D., Veron, A. S., Weiner, J., 3rd, Robinson-Rechavi, M., Bornberg-Bauer, E., Oliver, S. G., Robertson, D. L., 2007, One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity, Mol Biol Evol, 24 (3), 827-835 (PubMed)

  • Arnedo, M., Taffe, P., Sahli, R., Furrer, H., Hirschel, B., Elzi, L., Weber, R., Vernazza, P., Bernasconi, E., Darioli, R., Bergmann, S., Beckmann, J. S., Telenti, A., Tarr, P. E., 2007, Contribution of 20 single nucleotide polymorphisms of 13 genes to dyslipidemia associated with antiretroviral therapy, Pharmacogenet Genomics, 17 (9), 755-764 (PubMed)

  • Axner, L., Latt, J., Hoekstra, A. G., Chopard, B., Sloot, P. M. A., 2007, Simulating Time Harmonic Flows with the Regularized L-BGK Method, Int. J. Mod. Phys. C, 18 (4), 661-666

  • Bagheri, N., Steeling, J., Doyle III, F. J., 2007, Circadian phase entrainment via nonlinear model predictive control, Int J Robust Nonlinear Control, 17 1555-1571

  • Bagheri, N., Stelling, J., Doyle, F. J., 3rd, 2007, Quantitative performance metrics for robustness in circadian rhythms, Bioinformatics, 23 (3), 358-364 (PubMed)

  • Battey, J. N., Kopp, J., Bordoli, L., Read, R. J., Clarke, N. D., Schwede, T., 2007, Automated server predictions in CASP7, Proteins, 69 Suppl 8, 68-82 (PubMed)

  • Bergmann, S., Sandler, O., Sberro, H., Shnider, S., Schejter, E., Shilo, B. Z., Barkai, N., 2007, Pre-steady-state decoding of the Bicoid morphogen gradient, PLoS Biol, 5 (2), e46 (PubMed)

  • Boettner, M., Steffens, C., von Mering, C., Bork, P., Stahl, U., Lang, C., 2007, Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes, J Biotechnol, 130 (1), 1-10 (PubMed)

  • Bonnefoi, H., Potti, A., Delorenzi, M., Mauriac, L., Campone, M., Tubiana-Hulin, M., Petit, T., Rouanet, P., Jassem, J., Blot, E., Becette, V., Farmer, P., Andre, S., Acharya, C. R., Mukherjee, S., Cameron, D., Bergh, J., Nevins, J. R., Iggo, R. D., 2007, Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial, Lancet Oncol, 8 (12), 1071-1078 (PubMed)

  • Bordoli, L., Kiefer, F., Schwede, T., 2007, Assessment of disorder predictions in CASP7, Proteins, 69 Suppl 8 129-136 (PubMed)

  • Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., Bairoch, A., 2007, UniProtKB/Swiss-Prot: The Manually Annotated Section of the UniProt KnowledgeBase, Methods Mol Biol, 406, 89-112 (PubMed)

  • Bragg, J. G., Wagner, A., 2007, Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes, Proc Biol Sci, 274 (1613), 1063-1070 (PubMed)

  • Butticaz, C., Michielin, O., Wyniger, J., Telenti, A., Rothenberger, S., 2007, Silencing of both beta-TrCP1 and HOS (beta-TrCP2) is required to suppress human immunodeficiency virus type 1 Vpu-mediated CD4 down-modulation, J Virol, 81 (3), 1502-1505 (PubMed)

  • Cannarozzi, G., Schneider, A., Gonnet, G., 2007, A phylogenomic study of human, dog, and mouse, PLoS Comput Biol, 3 (1), e2 (PubMed)

  • Chalmel, F., Rolland, A. D., Niederhauser-Wiederkehr, C., Chung, S. S., Demougin, P., Gattiker, A., Moore, J., Patard, J. J., Wolgemuth, D. J., Jegou, B., Primig, M., 2007, The conserved transcriptome in human and rodent male gametogenesis, Proc Natl Acad Sci U S A, 104 (20), 8346-8351 (PubMed)

  • Chopard, B., Ouared, R., Ruefenacht, D. A., Yilmaz, H., Boltzmann, L., 2007, Modeling of Thrombosis in Giant Aneurysms, Int. J. Mod. Phys. C, 18 (4), 712-721

  • Ciliberti, S., Martin, O. C., Wagner, A., 2007, Innovation and robustness in complex regulatory gene networks, Proc Natl Acad Sci U S A, 104 (34), 13591-13596 (PubMed)

  • Ciliberti, S., Martin, O. C., Wagner, A., 2007, Robustness can evolve gradually in complex regulatory gene networks with varying topology, PLoS Comput Biol, 3 (2), e15 (PubMed)

  • Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., MacCallum, I. et al., 2007, Evolution of genes and genomes on the Drosophila phylogeny, Nature, 450 (7167), 203-218 (PubMed)

  • Clarke, N. D., Ezkurdia, I., Kopp, J., Read, R. J., Schwede, T., Tress, M., 2007, Domain definition and target classification for CASP7, Proteins, 69 Suppl 8, 10-18 (PubMed)

  • Conradi, C., Flockerzi, D., Raisch, J., Stelling, J., 2007, Subnetwork analysis reveals dynamic features of complex (bio)chemical networks, Proc Natl Acad Sci U S A, 104 (49), 19175-19180 (PubMed)

  • Coute, Y., Hernandez, C., Appel, R. D., Sanchez, J. C., Margolles, A., 2007, Labeling of Bifidobacterium longum cells with 13C-substituted leucine for quantitative proteomic analyses, Appl Environ Microbiol, 73 (17), 5653-5656 (PubMed)

  • Derre, L., Ferber, M., Touvrey, C., Devevre, E., Zoete, V., Leimgruber, A., Romero, P., Michielin, O., Levy, F., Speiser, D. E., 2007, A novel population of human melanoma-specific CD8 T cells recognizes Melan-AMART-1 immunodominant nonapeptide but not the corresponding decapeptide, J Immunol, 179 (11), 7635-7645 (PubMed)

  • Desmedt, C., Piette, F., Loi, S., Wang, Y., Lallemand, F., Haibe-Kains, B., Viale, G., Delorenzi, M., Zhang, Y., d'Assignies, M. S., Bergh, J., Lidereau, R., Ellis, P., Harris, A. L., Klijn, J. G., Foekens, J. A., Cardoso, F., Piccart, M. J., Buyse, M., Sotiriou, C., 2007, Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series, Clin Cancer Res, 13 (11), 3207-3214 (PubMed)

  • Di Cara, A., Garg, A., De Micheli, G., Xenarios, I., Mendoza, L., 2007, Dynamic simulation of regulatory networks using SQUAD, BMC Bioinformatics, 8 462 (PubMed)

  • Feige, J. N., Gelman, L., Rossi, D., Zoete, V., Metivier, R., Tudor, C., Anghel, S. I., Grosdidier, A., Lathion, C., Engelborghs, Y., Michielin, O., Wahli, W., Desvergne, B., 2007, The endocrine disruptor monoethyl-hexyl-phthalate is a selective peroxisome proliferator-activated receptor gamma modulator that promotes adipogenesis, J Biol Chem, 282 (26), 19152-19166 (PubMed)

  • Fiechter, V., Cameroni, E., Cerutti, L., De Virgilio, C., Barral, Y., Fankhauser, C., 2008, The evolutionary conserved BER1 gene is involved in microtubule stability in yeast, Curr Genet, 53 (2), 107-115 (PubMed)

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

  • Fulci, V., Chiaretti, S., Goldoni, M., Azzalin, G., Carucci, N., Tavolaro, S., Castellano, L., Magrelli, A., Citarella, F., Messina, M., Maggio, R., Peragine, N., Santangelo, S., Mauro, F. R., Landgraf, P., Tuschl, T., Weir, D. B., Chien, M., Russo, J. J., Ju, J., Sheridan, R., Sander, C., Zavolan, M., Guarini, A., Foa, R., Macino, G., 2007, Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia, Blood, 109 (11), 4944-4951(PubMed)

  • Gaidatzis, D., van Nimwegen, E., Hausser, J., Zavolan, M., 2007, Inference of miRNA targets using evolutionary conservation and pathway analysis, BMC Bioinformatics, 8 69 (PubMed)

  • Gattiker, A., Niederhauser-Wiederkehr, C., Moore, J., Hermida, L., Primig, M., 2007, The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction, Nucleic Acids Res, 35 (Database issue), D457-462 (PubMed)

  • Gattiker, A., Rischatsch, R., Demougin, P., Voegeli, S., Dietrich, F. S., Philippsen, P., Primig, M., 2007, Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists, BMC Genomics, 8 9 (PubMed)

  • Girod, P. A., Nguyen, D. Q., Calabrese, D., Puttini, S., Grandjean, M., Martinet, D., Regamey, A., Saugy, D., Beckmann, J. S., Bucher, P., Mermod, N., 2007, Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells, Nat Methods, 4 (9), 747-753 (PubMed)

  • Gottschling, M., Stamatakis, A., Nindl, I., Stockfleth, E., Alonso, A., Bravo, I. G., 2007, Multiple evolutionary mechanisms drive papillomavirus diversification, Mol Biol Evol,
    24 (5), 1242-1258 (PubMed)

  • Grosdidier, A., Zoete, V., Michielin, O., 2007, EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization, Proteins, 67 (4),
    1010-1025 (PubMed)

  • Harrington, E. D., Singh, A. H., Doerks, T., Letunic, I., von Mering, C., Jensen, L. J., Raes, J., Bork, P., 2007, Quantitative assessment of protein function prediction from metagenomics shotgun sequences, Proc Natl Acad Sci U S A, 104 (35), 13913-13918 (PubMed)

  • Hau, J., Muller, M., Pagni, M., 2007, HitKeeper, a generic software package for hit list management, Source Code Biol Med, 2 2 (PubMed)

  • Helmuth, J. A., Burckhardt, C. J., Koumoutsakos, P., Greber, U. F., Sbalzarini, I. F., 2007, A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells, J Struct Biol, 159 (3), 347-358 (PubMed)

  • Huber, W., Carey, V. J., Long, L., Falcon, S., Gentleman, R., 2007, Graphs in molecular biology, BMC Bioinformatics, 8 Suppl 6 S8 (PubMed)

  • Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B. A., de Castro, E., Lachaize, C., Langendijk-Genevaux, P. S., Sigrist, C. J., 2008, The 20 years of PROSITE, Nucleic Acids Res, 36 (Database issue), D245-249 (PubMed)

  • Iseli, C., Ambrosini, G., Bucher, P., Jongeneel, C. V., 2007, Indexing strategies for rapid searches of short words in genome sequences, PLoS ONE, 2 (6), e579 (PubMed)

  • Itoh, T., Tanaka, T., Barrero, R. A., Yamasaki, C., Fujii, Y., Hilton, P. B., Antonio, B. A., Aono, H., Apweiler, R., Bruskiewich, R., Bureau, T., Burr, F., Costa de Oliveira, A., Fuks, G., Habara, T., Haberer, G., Han, B., Harada, E., Hiraki, A. T., Hirochika, H., Hoen, D., Hokari, H., Hosokawa, S., Hsing, Y. I., Ikawa, H., Ikeo, K., Imanishi, T., Ito, Y., Jaiswal, P., Kanno, M., Kawahara, Y., Kawamura, T., Kawashima, H., Khurana, J. P., Kikuchi, S., Komatsu, S., Koyanagi, K. O., Kubooka, H., Lieberherr, D., Lin, Y. C., Lonsdale, D., Matsumoto, T., Matsuya, A., McCombie, W. R., Messing, J., Miyao, A., Mulder, N., Nagamura, Y., Nam, J., Namiki, N., Numa, H., Nurimoto, S., O'Donovan, C., Ohyanagi, H., Okido, T., Oota, S., Osato, N., Palmer, L. E., Quetier, F., Raghuvanshi, S., Saichi, N., Sakai, H., Sakai, Y., Sakata, K., Sakurai, T., Sato, F., Sato, Y., Schoof, H., Seki, M., Shibata, M., Shimizu, Y., Shinozaki, K., Shinso, Y., Singh, N. K., Smith-White, B., Takeda, J., Tanino, M., Tatusova, T., Thongjuea, S., Todokoro, F., Tsugane, M., Tyagi, A. K., Vanavichit, A., Wang, A., Wing, R. A., Yamaguchi, K., Yamamoto, M., Yamamoto, N., Yu, Y., Zhang, H., Zhao, Q., Higo, K., Burr, B., Gojobori, T., Sasaki, T., 2007, Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana, Genome Res, 17 (2), 175-183 (PubMed)

  • Junne, T., Schwede, T., Goder, V., Spiess, M., 2007, Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology, J Biol Chem, 282 (45), 33201-33209 (PubMed)

  • Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi-Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R., Hermjakob, H., 2007, IntAct--open source resource for molecular interaction data, Nucleic Acids Res, 35 (Database issue), D561-565

  • Kopp, J., Bordoli, L., Battey, J. N., Kiefer, F., Schwede, T., 2007, Assessment of CASP7 predictions for template-based modeling targets, Proteins, 69 Suppl 8 38-56 (PubMed)

  • Koutsos, A. C., Blass, C., Meister, S., Schmidt, S., MacCallum, R. M., Soares, M. B., Collins, F. H., Benes, V., Zdobnov, E., Kafatos, F. C., Christophides, G. K., 2007, Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster, Proc Natl Acad Sci U S A, 104 (27), 11304-11309 (PubMed)

  • Kriventseva, E. V., Rahman, N., Espinosa, O., Zdobnov, E. M., 2008, OrthoDB: the hierarchical catalog of eukaryotic orthologs, Nucleic Acids Res, 36 (Database issue), D271-275 (PubMed)

  • Kuepfer, L., Peter, M., Sauer, U., Stelling, J., 2007, Ensemble modeling for analysis of cell signaling dynamics, Nat Biotechnol, 25 (9), 1001-1006 (PubMed)

  • Kuhn, A., Goldstein, D. R., Hodges, A., Strand, A. D., Sengstag, T., Kooperberg, C., Becanovic, K., Pouladi, M. A., Sathasivam, K., Cha, J. H., Hannan, A. J., Hayden, M. R., Leavitt, B. R., Dunnett, S. B., Ferrante, R. J., Albin, R., Shelbourne, P., Delorenzi, M., Augood, S. J., Faull, R. L., Olson, J. M., Bates, G. P., Jones, L., Luthi-Carter, R., 2007, Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage, Hum Mol Genet, 16 (15), 1845-1861 (PubMed)

  • Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A. O., Landthaler, M., Lin, C., Socci, N. D., Hermida, L., Fulci, V., Chiaretti, S., Foa, R., Schliwka, J., Fuchs, U., Novosel, A., Muller, R. U., Schermer, B., Bissels, U., Inman, J., Phan, Q., Chien, M., Weir, D. B., Choksi, R., De Vita, G., Frezzetti, D., Trompeter, H. I., Hornung, V., Teng, G., Hartmann, G., Palkovits, M., Di Lauro, R., Wernet, P., Macino, G., Rogler, C. E., Nagle, J. W., Ju, J., Papavasiliou, F. N., Benzing, T., Lichter, P., Tam, W., Brownstein, M. J., Bosio, A., Borkhardt, A., Russo, J. J., Sander, C., Zavolan, M., Tuschl, T., 2007, A mammalian microRNA expression atlas based on small RNA library sequencing, Cell, 129 (7), 1401-1414 (PubMed)

  • Latt, J., Chopard, B., 2007, A benchmark case for   lattice Boltzmann: turbulent dipole-wall collision, Int. J. Mod. Phys. C, 18 (4), 619-626

  • Lawson, D., Arensburger, P., Atkinson, P., Besansky, N. J., Bruggner, R. V., Butler, R., Campbell, K. S., Christophides, G. K., Christley, S., Dialynas, E., Emmert, D., Hammond, M., Hill, C. A., Kennedy, R. C., Lobo, N. F., MacCallum, M. R., Madey, G., Megy, K., Redmond, S., Russo, S., Severson, D. W., Stinson, E. O., Topalis, P., Zdobnov, E. M., Birney, E., Gelbart, W. M., Kafatos, F. C., Louis, C., Collins, F. H., 2007, VectorBase: a home for invertebrate vectors of human pathogens, Nucleic Acids Res, 35 (Database issue), D503-505 (PubMed)

  • Ledergerber, C., Dessimoz, C., 2007, Alignments with Non- overlapping Moves, Inversions and Tandem Duplications in O(n4) time, COCOON, 151-164

  • Lo Presti, L., Cockell, M., Cerutti, L., Simanis, V., Hauser, P. M., 2007, Functional characterization of Pneumocystis carinii brl1 by transspecies complementation analysis, Eukaryot Cell, 6 (12), 2448-2452 (PubMed)

  • Loi, S., Haibe-Kains, B., Desmedt, C., Lallemand, F., Tutt, A. M., Gillet, C., Ellis, P., Harris, A., Bergh, J., Foekens, J. A., Klijn, J. G., Larsimont, D., Buyse, M., Bontempi, G., Delorenzi, M., Piccart, M. J., Sotiriou, C., 2007, Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade, J Clin Oncol, 25 (10), 1239-1246  (PubMed)

  • Michalik, L., Zoete, V., Krey, G., Grosdidier, A., Gelman, L., Chodanowski, P., Feige, J. N., Desvergne, B., Wahli, W., Michielin, O., 2007, Combined simulation and mutagenesis analyses reveal the involvement of key residues for peroxisome proliferator-activated receptor alpha helix 12 dynamic behavior, J Biol Chem, 282 (13), 9666-9677 (PubMed)

  • Michelsen, K., Schmid, V., Metz, J., Heusser, K., Liebel, U., Schwede, T., Spang, A., Schwappach, B., 2007, Novel cargo-binding site in the beta and delta subunits of coatomer, J Cell Biol, 179 (2), 209-217 (PubMed)

  • Michielin, O., 2007, [Application of molecular modeling to new therapeutic cancer approaches], Bull Cancer, 94 (9), 763-768 (PubMed)

  • Moretti, S., Armougom, F., Wallace, I. M., Higgins, D. G., Jongeneel, C. V., Notredame, C., 2007, The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods, Nucleic Acids Res, 35 (Web Server issue), W645-648 (PubMed)

  • Mottaz, A., Yip, Y. L., Ruch, P., A.-L., V.-. 2007, Mapping protein information to disease terminologies, Journal of Integrative Bioinformatics, 4 (3)

  • Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P. S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A. N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J. D., Sigrist, C. J., Thomas, P. D., Valentin, F., Wilson, D., Wu, C. H., Yeats, C., 2007, New developments in the InterPro database, Nucleic Acids Res, 35 (Database issue), D224-228 (PubMed)

  • Nene, V., Wortman, J. R., Lawson, D., Haas, B., Kodira, C., Tu, Z. J., Loftus, B., Xi, Z., Megy, K., Grabherr, M., Ren, Q., Zdobnov, E. M., Lobo, N. F., Campbell, K. S., Brown, S. E., Bonaldo, M. F., Zhu, J., Sinkins, S. P., Hogenkamp, D. G., Amedeo, P., Arensburger, P., Atkinson, P. W., Bidwell, S., Biedler, J., Birney, E., Bruggner, R. V., Costas, J., Coy, M. R., Crabtree, J., Crawford, M., Debruyn, B., Decaprio, D., Eiglmeier, K., Eisenstadt, E., El-Dorry, H., Gelbart, W. M., Gomes, S. L., Hammond, M., Hannick, L. I., Hogan, J. R., Holmes, M. H., Jaffe, D., Johnston, J. S., Kennedy, R. C., Koo, H., Kravitz, S., Kriventseva, E. V., Kulp, D., Labutti, K., Lee, E., Li, S., Lovin, D. D., Mao, C., Mauceli, E., Menck, C. F., Miller, J. R., Montgomery, P., Mori, A., Nascimento, A. L., Naveira, H. F., Nusbaum, C., O'Leary, S., Orvis, J., Pertea, M., Quesneville, H., Reidenbach, K. R., Rogers, Y. H., Roth, C. W., Schneider, J. R., Schatz, M., Shumway, M., Stanke, M., Stinson, E. O., Tubio, J. M., Vanzee, J. P., Verjovski-Almeida, S., Werner, D., White, O., Wyder, S., Zeng, Q., Zhao, Q., Zhao, Y., Hill, C. A., Raikhel, A. S., Soares, M. B., Knudson, D. L., Lee, N. H., Galagan, J., Salzberg, S. L., Paulsen, I. T., Dimopoulos, G., Collins, F. H., Birren, B., Fraser-Liggett, C. M., Severson, D. W., 2007, Genome sequence of Aedes aegypti, a major arbovirus vector, Science, 316 (5832), 1718-1723 (PubMed)

  • Nguyen, H., Chopard, B., Stoll, S., 2007, Hydrodynamic properties and permeability of fractal objects, Int. J. Mod. Phys. C, 18 (4), 732-738

  • Nikolaev, S., Montoya-Burgos, J. I., Margulies, E. H., Rougemont, J., Nyffeler, B., Antonarakis, S. E., 2007, Early history of mammals is elucidated with the ENCODE multiple species sequencing data, PLoS Genet, 3 (1), e2 (PubMed)

  • Orchard, S., Jones, A. R., Stephan, C., Binz, P. A., 2007, The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006, Proteomics, 7 (7), 1006-1008 (PubMed)

  • Orchard, S., Montechi-Palazzi, L., Deutsch, E. W., Binz, P. A., Jones, A. R., Paton, N., Pizarro, A., Creasy, D. M., Wojcik, J., Hermjakob, H., 2007, Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Superieure (ENS), Lyon, France, Proteomics, 7 (19), 3436-3440 (PubMed)

  • Orchard, S., Taylor, C. F., Jones, P., Montechi-Palazzo, L., Binz, P. A., Jones, A. R., Pizarro, A., Julian, R. K., Jr., Hermjakob, H., 2007, Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA, Proteomics, 7 (3), 337-339 (PubMed)

  • Pachkov, M., Erb, I., Molina, N., van Nimwegen, E., 2007, SwissRegulon: a database of genome-wide annotations of regulatory sites, Nucleic Acids Res, 35 (Database issue), D127-131, (PubMed)

  • Pagni, M., Ioannidis, V., Cerutti, L., Zahn-Zabal, M., Jongeneel, C. V., Hau, J., Martin, O., Kuznetsov, D., Falquet, L., 2007, MyHits: improvements to an interactive resource for analyzing protein sequences, Nucleic Acids Res, 35 (Web Server issue), W433-437, (PubMed)

  • Parisi, F., Wirapati, P., Naef, F., 2007, Identifying synergistic regulation involving c-Myc and sp1 in human tissues, Nucleic Acids Res, 35 (4), 1098-1107, (PubMed)

  • Passardi, F., Theiler, G., Zamocky, M., Cosio, C., Rouhier, N., Teixera, F., Margis-Pinheiro, M., Ioannidis, V., Penel, C., Falquet, L., Dunand, C., 2007, PeroxiBase: the peroxidase database, Phytochemistry, 68 (12), 1605-1611 (PubMed)

  • Pattengale, N. D., Gottlieb, E. J., Moret, B. M., 2007, Efficiently computing the Robinson-Foulds metric, J Comput Biol, 14 (6), 724-735 (PubMed)

  • Peyer, A. K., Jung, D., Beer, M., Gnerre, C., Keogh, A., Stroka, D., Zavolan, M., Meyer, U. A., 2007, Regulation of human liver delta-aminolevulinic acid synthase by bile acids, Hepatology, 46 (6), 1960-1970 (PubMed)

  • Plattet, P., Strahle, L., le Mercier, P., Hausmann, S., Garcin, D., Kolakofsky, D., 2007, Sendai virus RNA polymerase scanning for mRNA start sites at gene junctions, Virology, 362 (2), 411-420  (PubMed)

  • Prandini, P., Deutsch, S., Lyle, R., Gagnebin, M., Delucinge Vivier, C., Delorenzi, M., Gehrig, C., Descombes, P., Sherman, S., Dagna Bricarelli, F., Baldo, C., Novelli, A., Dallapiccola, B., Antonarakis, S. E., 2007, Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance, Am J Hum Genet, 81 (2),
    252-263 (PubMed)

  • Quandt, A., Hernandez, P., Kunzst, P., Pautasso, C., Tuloup, M., Hernandez, C., Appel, R. D., 2007, Grid-based analysis of tandem mass spectrometry data in clinical proteomics, Stud Health Technol Inform, 126,13-22 (PubMed)

  • Raes, J., Korbel, J. O., Lercher, M. J., von Mering, C., Bork, P., 2007, Prediction of effective genome size in metagenomic samples, Genome Biol, 8 (1), R10 (PubMed)

  • Rambaldi, D., Felice, B., Praz, V., Bucher, P., Cittaro, D., Guffanti, A., 2007, Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data, BMC Bioinformatics, 8 Suppl 1, S17 (PubMed)

  • Randall, G., Panis, M., Cooper, J. D., Tellinghuisen, T. L., Sukhodolets, K. E., Pfeffer, S., Landthaler, M., Landgraf, P., Kan, S., Lindenbach, B. D., Chien, M., Weir, D. B., Russo, J. J., Ju, J., Brownstein, M. J., Sheridan, R., Sander, C., Zavolan, M., Tuschl, T., Rice, C. M., 2007, Cellular cofactors affecting hepatitis C virus infection and replication, Proc Natl Acad Sci U S A, 104 (31), 12884-12889 (PubMed)

  • Retelska, D., Beaudoing, E., Notredame, C., Jongeneel, C. V., Bucher, P., 2007, Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time, BMC Genomics, 8, 398 (PubMed)

  • Rougemont, J., Naef, F., 2007, Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks, Mol Syst Biol, 3, 93 (PubMed)

  • Ruch, P., Boyer, C., Chichester, C., Tbahriti, I., Geissbuhler, A., Fabry, P., Gobeill, J., Pillet, V., Rebholz-Schuhmann, D., Lovis, C., Veuthey, A. L., 2007, Using argumentation to extract key sentences from biomedical abstracts, Int J Med Inform, 76 (2-3), 195-200 (PubMed)

  • Ruch, P., Geissbuhler, A., Gobeill, J., Lisacek, F., Tbahriti, I., Veuthey, A. L., Aronson, A. R., 2007, Using discourse analysis to improve text categorization in MEDLINE, Medinfo, 12 (Pt 1), 710-715 (PubMed)

  • Runne, H., Kuhn, A., Wild, E. J., Pratyaksha, W., Kristiansen, M., Isaacs, J. D., Regulier, E., Delorenzi, M., Tabrizi, S. J., Luthi-Carter, R., 2007, Analysis of potential transcriptomic biomarkers for Huntington's disease in peripheral blood, Proc Natl Acad Sci U S A, 104 (36), 14424-14429 (PubMed)

  • Sbalzarini, I. F., 2007, Informatik und Biologie – Eine Symbiose ermöglicht neue Entdeckungen, Vierteljahresschrift der Naturforschenden Gesellschaft in Zürich, 152 (3), 63-70

  • Scarsi, M., Podvinec, M., Roth, A., Hug, H., Kersten, S., Albrecht, H., Schwede, T., Meyer, U. A., Rucker, C., 2007, Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity: a combined virtual screening and biological assay approach, Mol Pharmacol, 71 (2), 398-406 (PubMed)

  • Schmid, C. D., Bucher, P., 2007, ChIP-Seq data reveal nucleosome architecture of human promoters, Cell, 131 (5), 831-832; author reply 832-833 (PubMed)

  • Schmid, C. D., Sengstag, T., Bucher, P., Delorenzi, M., 2007, MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data, Nucleic Acids Res, 35 (Web Server issue), W201-205 (PubMed)

  • Schneider, A., Dessimoz, C., Gonnet, G. H., 2007, OMA Browser--exploring orthologous relations across 352 complete genomes, Bioinformatics, 23 (16), 2180-2182 (PubMed)

  • Schneider, A., Gonnet, G., Cannarozzi, G., 2007, SynPAM-a distance measure based on synonymous codon substitutions, IEEE/ACM Trans Comput Biol Bioinform, 4 (4), 553-560 (PubMed)

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

  • Siddharthan, R., van Nimwegen, E., 2007, Detecting regulatory sites using PhyloGibbs, Methods Mol Biol, 395 381-402 (PubMed)

  • Stamatakis, A., Auch, A. F., Meier-Kolthoff, J., Goker, M., 2007, AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa, BMC Bioinformatics, 8 405  (PubMed)

  • Stamatakis, A., Blagojevic, F., Antonopoulos, C. D., Nikolopoulos, D. S., 2007, Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell, VLSI Signal Processing Sytmes, 48 (3), 271-286

  • Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., Dougan, G., von Mering, C., Hardt, W. D., 2007, Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota, PLoS Biol, 5 (10), 2177-2189 (PubMed)

  • Stelling, J., 2007, Understandable complexity, Science STKE: pe9

  • Stevenson, B. J., Iseli, C., Panji, S., Zahn-Zabal, M., Hide, W., Old, L. J., Simpson, A. J., Jongeneel, C. V., 2007, Rapid evolution of cancer/testis genes on the X chromosome, BMC Genomics, 8 129 (PubMed)

  • Stoll, G., Rougemont, J., Naef, F., 2007, Representing perturbed dynamics in biological network models, Phys Rev E Stat Nonlin Soft Matter Phys, 76 (1 Pt 1), 011917 (PubMed)

  • Stupp, R., Pica, A., Mirimanoff, R. O., Michielin, O., 2007, [A practical guide for the management of gliomas], Bull Cancer, 94 (9), 817-822 (PubMed)

  • Sumedha, Martin, O. C., Wagner, A., 2007, New structural variation in evolutionary searches of RNA neutral networks, Biosystems, 90 (2), 475-485 (PubMed)

  • Tallada, V. A., Bridge, A. J., Emery, P. A., Hagan, I. M., 2007, Suppression of the Schizosaccharomyces pombe cut12.1 cell-cycle defect by mutations in cdc25 and genes involved in transcriptional and translational control, Genetics, 176 (1), 73-83 (PubMed)

  • Tapparel, C., Junier, T., Gerlach, D., Cordey, S., Van Belle, S., Perrin, L., Zdobnov, E. M., Kaiser, L., 2007, New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features, BMC Genomics, 8 224 (PubMed)

  • 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., 3rd, Hermjakob, H., 2007, The minimum information about a proteomics experiment (MIAPE), Nat Biotechnol, 25 (8), 887-893 (PubMed)

  • Terzer, M., Jovanovic, M., Choutko, A., Nikolayeva, O., Korn, A., Brockhoff, D., Zürcher, F., Friedmann, M., Schütz, R., Zitzler, E., Stelling, J., Panke, S., 2007, Design of a biological half adder, IET Systems Biol., 1 53-58

  • UniProt, 2007, The Universal Protein Resource (UniProt), Nucleic Acids Res, 35 (Database issue), D193-197

  • Van Nimwegen, E., 2007, Finding regulatory elements and regulatory motifs: a general probabilistic framework, BMC Bioinformatics, 8 Suppl 6 S4 (PubMed)

  • Von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, L. J., Ward, N., Bork, P., 2007, Quantitative phylogenetic assessment of microbial communities in diverse environments, Science, 315 (5815), 1126-1130 (PubMed)

  • Von Mering, C., Jensen, L. J., Kuhn, M., Chaffron, S., Doerks, T., Kruger, B., Snel, B., Bork, P., 2007, STRING 7--recent developments in the integration and prediction of protein interactions, Nucleic Acids Res, 35 (Database issue), D358-362 (PubMed)

  • Vuaroqueaux, V., Urban, P., Labuhn, M., Delorenzi, M., Wirapati, P., Benz, C. C., Flury, R., Dieterich, H., Spyratos, F., Eppenberger, U., Eppenberger-Castori, S., 2007, Low E2F1 transcript levels are a strong determinant of favorable breast cancer outcome, Breast Cancer Res, 9 (3), R33 (PubMed)

  • Wagner, A., 2007, Energy costs constrain the evolution of gene expression,
    J Exp Zoolog B Mol Dev Evol, 308 (3), 322-324 (PubMed)

  • Wagner, A., 2007, From bit to it: how a complex metabolic network transforms information into living matter, BMC Syst Biol, 1 33 (PubMed)

  • Wagner, A., 2007, Rapid detection of positive selection in genes and genomes through variation clusters, Genetics, 176 (4), 2451-2463 (PubMed)

  • Wagner, A., Wright, J., 2007, Alternative routes and mutational robustness in complex regulatory networks, Biosystems, 88 (1-2), 163-172 (PubMed)

  • Waterhouse, R. M., Kriventseva, E. V., Meister, S., Xi, Z., Alvarez, K. S., Bartholomay, L. C., Barillas-Mury, C., Bian, G., Blandin, S., Christensen, B. M., Dong, Y., Jiang, H., Kanost, M. R., Koutsos, A. C., Levashina, E. A., Li, J., Ligoxygakis, P., Maccallum, R. M., Mayhew, G. F., Mendes, A., Michel, K., Osta, M. A., Paskewitz, S., Shin, S. W., Vlachou, D., Wang, L., Wei, W., Zheng, L., Zou, Z., Severson, D. W., Raikhel, A. S., Kafatos, F. C., Dimopoulos, G., Zdobnov, E. M., Christophides, G. K., 2007, Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes, Science, 316 (5832), 1738-1743 (PubMed)

  • Weaver, D. B., Anzola, J. M., Evans, J. D., Reid, J. G., Reese, J. T., Childs, K. L., Zdobnov, E. M., Samanta, M. P., Miller, J., Elsik, C. G., 2007, Computational and transcriptional evidence for microRNAs in the honey bee genome, Genome Biol, 8 (6), R97 (PubMed)

  • Weber, W., Stelling, J., Rimann, M., Keller, B., Daoud-El Baba, M., Weber, C. C., Aubel, D., Fussenegger, M., 2007, A synthetic time-delay circuit in mammalian cells and mice, Proc Natl Acad Sci U S A, 104 (8), 2643-2648 (PubMed)

  • Wyder, S., Kriventseva, E. V., Schroder, R., Kadowaki, T., Zdobnov, E. M., 2007, Quantification of ortholog losses in insects and vertebrates, Genome Biol, 8 (11), R242 (PubMed)

  • Yao, Y., Zhao, Y., Xu, H., Smith, L. P., Lawrie, C. H., Sewer, A., Zavolan, M., Nair, V., 2007, Marek's disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1, J Virol, 81 (13), 7164-7170 (PubMed)

  • Yip, Y. L., Lachenal, N., Pillet, V., Veuthey, A. L., 2007, Retrieving mutation-specific information for human proteins in UniProt/Swiss-Prot Knowledgebase, J Bioinform Comput Biol, 5 (6), 1215-1231 (PubMed)

  • Zdobnov, E. M., Bork, P., 2007, Quantification of insect genome divergence, Trends Genet, 23 (1), 16-20 (PubMed)

  • Zhang, K. L., Mangeat, B., Ortiz, M., Zoete, V., Trono, D., Telenti, A., Michielin, O., 2007, Model structure of human APOBEC3G, PLoS ONE, 2 (4), e378 (PubMed)

  • Zoete, V., Grosdidier, A., Michielin, O., 2007, Peroxisome proliferator-activated receptor structures: ligand specificity, molecular switch and interactions with regulators, Biochim Biophys Acta, 1771 (8), 915-925 (PubMed)

  • Zoete, V., Michielin, O., 2007, Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex, Proteins, 67 (4), 1026-1047 (PubMed)

  • Zosso, D., Podvinec, M., Muller, M., Aebersold, R., Peitsch, M. C., Schwede, T., 2007, Tandem mass spectrometry protein identification on a PC grid, Stud Health Technol Inform, 126 3-12 (PubMed)
  •  

    Journal Articles – non-peer-reviewed


  • Albar, J. P., Corthals, G. L., Gil, C., James, P., Jensen, O. N., Palagi, P. M., Penque, D., 2007, Promoting Proteomics Knowledge in Europe: report on the Activities of the EuPA Education Committee 2, Proteomics, 7 (S1), 90-94

  • Book

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

  • Book Chapters

  • Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., Bairoch, A., UniProtKB/Swiss-Prot: The Manually Annotated Section of the UniProt KnowledgeBase, in  Edwards, D. (Ed.), Methods in Molecular Biology - Plant Bioinformatics. Methods and Protocols, Humana Press, 2007

  • Cannarozzi, G., Schneider, A., Gonnet, G. H., Probabilistic Ancestral Sequences Based on the Markovian Model of Evolution - Algorithms and Applications, in  Liberles, D. A. (Ed.), Ancestral Sequence Reconstruction, Oxford University Press, USA, 2007

  • González-Segredo, N., Amphiphilic fluids: mesoscopic modelling and computer simulations, in  Dillon, K. I. (Ed.), Soft Condensed Matter: New Research, Nova Science, New York, 2007

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

  • Hinz, U., Bairoch, A., The impact of 3D-structures on a protein knowledgebase, in  Sussman, J., L. and Silman, I. (Ed.), Structural Proteomics, World Scientific Publisher, 2007

  • Hoekstra, A. G., Lorenz, E., Falcone, J.-L., Chopard, B., Towards a Complex Automata Framework for Multi-Scale Modeling: Formalism and the Scale Separation Map, in  Shin, Y. and al. (Ed.), Computational Science – ICCS 2007 Beijing    Springer Verlag, Berlin/Heidelberg, 2007

  • Hoogland, C., Sanchez, J. C., F., H. D., Appel, R. D., 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

  • Kapp, E., Schütz, F., Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms, in  Coligan, J. E., Dunn, B. M., Speicher, D. W. and Wingfield, P. T. (Ed.), Current Protocols in Protein Science, John Wiley and Sons, 2007

  • Lane, L., Yip, Y. L., Boeckmann, B., Protein function analysis, in  Ye, S. Q. (Ed.), Bioinformatics: A Practical Approach, Chapman & Hall / CRC Press, 2007

  • Moret, B. M., Large-scale phylogenetic reconstruction, in  Brown, J. R. (Ed.), Comparative Genomics: Basic and Applied Research, CRC Press/Taylor & Francis, 2007

  • Palagi, P., Walther, D., Zimmermann-Ivol, C. G., Appel, R. D., Proteome imaging, in  Wilkins, M. R., Appel, R. D., Williams, K. L. and Hochstrasser, D. F. (Ed.), Proteome Research: concepts, technology and application Springer Verlag, 2007

  • Pupko, T., Doron-Faigenboim, A., Liberles, D. A., Cannarozzi, G., Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences, in  Liberles, D. A. (Ed.), Ancestral Sequence Reconstruction, Oxford University Press, USA, 2007

  • Schwede, T., Sali, A., Eswar, N., Peitsch, M. C., Protein Structure Modelin, in  Schwede, T. and Peitsch, M. C. (Ed.), Computational Structural Biology, World Scientific Publishing, 2008

  • Wagner, A., Gene networks and natural selection: Is there a network biology?, in  Pagel, M. P., A. (Ed.), Evolutionary Genomics and Proteomics, Sinauer Associates, Sunderland, MA, USA, 2007

  • Guest Edition

  • Affolter, M., Lashuel, H., Lion, N., Moniatte, M., Palagi, P. M., Quadroni, M., Sanchez, J. C., 2007, Proceedings of the Swiss Proteomics Society, 2007 Congress, Proteomics - pushing the limits (Editors)

  • Lisacek, F., Appel, R. D., 2007, Systems Biology: a loose definition, Special edition on Systems Biology in Proteomics, 7 (6), 825-827 (PubMed)

  • Conference Proceedings

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

  • Blagojevic, F., Nikolopoulos, D. S., Stamatakis, A., Antonopoulos, C. D., Dynamic multigrain parallelization on the Cell broadband engine, ACM SIGPLAN Symp. Principles & Practice of Parallel Programming PPoPP'07, 90-100, San Jose, CA, USA, March 2007

  • Blagojevic, F., Nikolopoulos, D. S., Stamatakis, A., Antonopoulos, C. D., RAxML-Cell: Parallel phylogenetic tree inference on the Cell broadband engine, 21st IEEE Int'l Parallel & Distributed Processing Symp. IPDPS'07, Long Beach, CA, USA, March 2007

  • Falcone, J.-L., Chopard, B., Understanding Signal Sequences with Machine Learning, BioEvo '07, Valence, Spain, April 2007

  • Gatfiel, D., Le Martelot, G., Kornmann, B., Stark, A., Gerlach, D., Zdobnov, E. M., Schibler, U., Cardian transcription of the miR-122 locus in mouse liver, Computational Biology Conference USGEB [Bc]2, Basel, Switzerland, March 2007

  • Gerlach, D., Junier, T., Tapparel, C., Frayard, S., Perrin, L., Kaiser, L., Zdobnov, E. M., Comparative Genomics of Human Rhinoviruses, Basel Computational Biology Conference USGEB [Bc]2, Basel, Switzerland, March 2007

  • Gerlach, D., Junier, T., Tapparel, C., Frayard, S., Perrin, L., Kaiser, L., Zdobnov, E. M., Comparative Genomics of Human Rhinoviruses, ISMB, Vienna, Austria, July 2007

  • Gerlach, D., Zdobnov, E. M., Survey of MicroRNA Genes in the Body Louse Genome, ISMB/ECCB, Vienna, Austria, July 2007

  • Kothari, M., Moret, B. M., An experimental evaluation of inversion- and transposition-based genomic distances, 3rd IEEE Symp. on Comput. Intelligence in Bioinformatics and Comput. Biol. CIBCB'07, 151-158, Honolulu, HW, USA, April 2007

  • Ott, M., Zola, J., Aluru, S., Stamatakis, A., Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L, 19th ACM/IEEE Supercomputing Conf. SC'07, Reno, USA, November 2007

  • 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., Kafetzopoulos, D., Functional specifications of an integrated proteomics information management and analysis platform, IEEE Eng Med Biol Soc 2007, 16064-16068, Lyon, France, August 2007 (PubMed)

  • Tusek, A., Müller, C. L., Supper, J., Zell, A., Kurtanjek, Z., Sbalzarini, I. F., Systems biology markup language: Case study of T-cell signal transduction network, 29th International Conference on Information Technology Interfaces, 651-656, Cavtat/Dubrovnik, Croatia, June 2007

  • Wegener, D., Sengstag, T., Sfakianakis, S., Rueping, A. A., GridR: An R-based grid-enabled tool for data analysis in ACGT, 3rd IEEE International Conference on e-Science and Grid Computing, Bangalore, India, December 2007

  • Wyder, S., Kriventseva, E. V., Zdobnov, E. M., Quantification of ortholog losses in insects and vertebrates, ISMB/ECCB, Vienna, Austria, July 2007

  • Zosso, D., Arnold, K., Schwede, T., Podvinec, M., SWISS-TANDEM: A Web-Based Workspace for MS/MS Protein Identification on PC Grids, Twentieth IEEE International Symposium on Computer-Based Medical Systems. CBMS'07, 406-411, Maribor, Slovenia, June 2007 (PubMed)

  • Abstracts & Posters

  • Ahrné, E., Masselot, A., Vaezzadeh, A., Binz, P.-A., Appel, R. D., More (and faster) ms/ms identifications: combining on-the-fly spectral library search (spectrast) and sequence database search (phenyx), HUPO 6th Annual World Congress, Seoul, South Korea, October 2007

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

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

  • Bairoch, A., The Annotation of Proteins from Pathogens in UniProtKB/Swiss-Prot : Current Status and Future Plans, International School and Conference on the Bioinformatics of African Pathogens and Disease Vectors, Nairobi, Kenya, May 2007

  • Bairoch, A., To annotate is useful, to annotate well is better, to reannotate is essential, 2nd International Biocurators Meeting’07, San José, California, USA, October 2007

  • Boeckmann, B., Protein function analysis beyond orthology prediction., Structural, functional and evolutionary genomics, Hinxton, England, July 2007

  • Boeckmann, B., Jimenez, S., Bougueleret, L., Bairoch, A., UniProt Consortium, Protein Function Annotation in UniProtKB/Swiss-Prot and its use for Automated Function Prediction., 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria,

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

  • David, F. P. A., Veuthey, A.-L., Yip, Y. L., SAALSA, a UniProtKB/Swiss-Prot curator assistant for structural data integration, The 15th Annual International Conference on Intelligent Systems for Molecular Biology/6th Annual European Conference on Computational Biology (ISMB/ECCB), Vienna, Austria, July 2007

  • Duvaud, S., Jain, E., UniProt Consortium, beta.uniprot.org: A preview of the new Web site of the UniProt consortium, SPS 6th Scientific meeting, Lausanne, Switzerland, December 2007

  • Estreicher, A., La base de données de séquences de protéine UniProtKB/Swiss-Prot : visite guidée, 20e colloque BIOTECHNOCENTRE, Seillac, France, October 2007

  • Famiglietti, M. L., Evolution of Swiss-Prot or From data to knowledge, Sociomics, Hinxton, England, June 2007

  • Fuermann, M., Pedruzzi, I., Junker, V., Laiho, K., Bairoch, A., Swiss-Prot, The Fungal Proteome Annotation in the UniProtKB/Swiss-Prot knowledgebase, ESF-EMBO Symposium – Comparative genomics of Eukaryotic Microorganisms Sant Feliu de Guixols, Spain, October 2007

  • Jimenez, S., HPI Team, UniProt Consortium, Human Proteome Initiative, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July  2007

  • Jimenez, S., HPI Team, UniProt Consortium, The Human proteomics initiative, SPS 6th Scientific meeting, Lausanne, Switzerland, December 2007

  • Junker, V., Laiho, K., Fuermann, M., Pedruzzi, I., UniProt Consortium, UniProtKB/Swiss-Prot and the annotation of microbial proteomes, 4th International Fission Yeast conference, Copenhagen, Denmark, June 2007

  • Hinz, U., Bairoch, A., Swiss-Prot Making the best of it: the role of 3D-structures in UniProtKB/Swiss-Prot, USGEB - Annual Meeting of the Swiss Societies for Experimental Biology, Basel, Switzerland, February 2007

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

  • Hochstrasser, D. F., Lescuyer, P., Moll, S., Vaezzadeh, A., Sanchez, J. C., Zimmermann, C., Appel, R. D., Clinical Proteomics & Biomarker Discovery, International Symposium on High Performance Proteomics, Dortmund, Germany, May 2007

  • Jain, E., UniProt Consortium, beta.uniprot.org: Preview of the new Web site of the UniProt consortium, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 2007

  • Jain, E., beta.uniprot.org: 5 Lessons Learned, 8th annual Bioinformatics Open Source Conference (BOSC), Vienna, Austria, July 2007

  • Lane, L., The UniProtKB/Swiss-Prot Human Proteomic Initiative (HPI) as a support for the characterization of human proteome in health and disease, Affinity Proteomics, 3rd ESF Workshop on Ligand Binders against the Human Proteome, Alpbach, Austria, March 2007

  • Lane, L., Feuermann, L., Gruaz, N., Pedruzzi, I., S., P., Schneider, M., Bairoch, Swiss-Prot, The UniProtKB/Swiss-Prot “histone code annotation project, EMBO conference on Chromatin and Epigenetics, EMBL Heidelberg, Germany, May 2007

  • Lane, L., Gateau, A., Bairoch, A., group, t. S.-P., Proteomic data integration in UniProtKB/Swiss-Prot, SPS 6th Scientific meeting, Lausanne, Switzerland, December 2007

  • Lieberherr, D., Boutet, E., Tognolli, M., Schneider, M., Bairoch, A., UniProt Consortium, Rice protein sequence annotation in UniProtKB/Swiss-Prot, Rice Annotation Project 4 (RAP4), Tsukuba, Japan, October 2007

  • Lieberherr, D., Boutet, E., Tognolli, M., Schneider, M., Bairoch, A., UniProt Consortium, Rice proteins in UniProtKB/Swiss-Prot: linking functional annotation of protein sequences to rice genome, 5th International Symposium on Rice Functional Genomics (ISRFG2007), Tsukuba, Japan, October 2007

  • Lima, T., UniProt, UniProtKB/Swiss-Prot and the annotation of microbial proteomes, Microbial genome 2007, Hinxton, England, March 2007

  • Lima, T., UniProt, UniProtKB/Swiss-Prot and the annotation of microbial proteomes, 15th International Conference on Microbial Genome, Maryland, USA, September 2007

  • Pagni, M., Hau, J., Falquet, L., MyHits underground, HitKeeper: a relational database and query language, RIBIO-EMBnet joint meeting, Malaga, Spain, June 2007
  • 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., Appel, R. D., Exploring and integrating proteomics data, BSPR/EBI 4th Annual Proteomics meeting, Hinxton, United Kingdom, July 2007

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

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

  • Schneider, M., Boutet, E., Lieberherr, D., Tognolli, M., Lane, L., Bairoch, A., Plant proteome annotation in UniProtKB/Swiss-Prot and integration of data from large scale proteomic analysis, 16th Swiss Plant Molecular and Cell Biology Conference, Les Diablerets, Switzerland, March 2007

  • Schneider, M., Boutet, E., Lieberherr, D., Tognolli, M., Lane, L., Bairoch, A., Swiss-Prot, Integration of data from large scale proteomic analysis and plant proteome annotation in UniProtKB/Swiss-Prot, USGEB - Annual Meeting of the Swiss Societies for Experimental Biology, Basel, Switzerland, February 2007

  • Tognolli, M., Boutet, E., Lieberherr, D., Schneider, M., Bairoch, A., UniProt, UniProtKB: a cental hub for plant protein research, Plant-GEMs 6, Tenerife, Canaries Islands, October 2007

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

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

  • Yip, Y. L., Mottaz, A., Ruch, P., Veuthey, A.-L., UniMed: Mapping of UniProtKB/Swiss-Prot entries to disease terminologies, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 2007

  • Yip, Y. L., Archiving single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase, HGV 2007 meeting, Sitges, Spain, September 2007

  • Yip, Y. L., Mottaz, A., Ruch, P., Veuthey, A.-L., UniProt to Mesh: Mapping proteins to disease terminologies, Bio-Ontologies SIG Workshop 2007, Vienna, Austria, July 2007


Other

Articles published in the local newspapers


  • Le moustique de la dengue décortiqué, Le Temps, 22-06-2007
    L’UNIGE a contribué au séquençage du moustique vecteur de la dengue, AGEFI, Juin 2007

     

    Children’s story

    • Baillie Gerritsen, V., Déthiollaz, S., Journey into a tiny world, Swiss-Prot group, SIB, 2007

    Protein Spotlight, 2007 issues edited by Vivienne Baillie Gerritsen:
    • Of froth and haze (78)
    • Heavy metal (79)
    • The tenuous nature of sex (80)
    • Slip siding away (81)
    • The power behind pain (82)
    • Tangled (83)
    • Journey into a tiny world (84)
    • Of fidgets and food (85)
    • Red velvet (86)
    • The dark side of RNA (87)
    • An unexpected place (88)
    • Ear of stone (89)

    Protéines à la Une: 2007 issues edited by Séverine Altairac:
    • Etre Homme ou Femme, telle est la question (20)
    • La face autiste du monde, (21)
    • Sauve qui peut (22)
    • A la lueur d'une protéine (23)

      Protein Snapshots: 2007 issues edited by Vivienne Baillie Gerritsen and Séverine Altairac:
    • Dermaseptin (January)
    • Polygalacturonase-2 (February)
    • Sodium channel protein type 9 subunit alpha (March)
    • Tyrannosaurus rex and collagen  (April)
    • Presequence protein (May)
    • FATSO (June)
    • Carbonic anhydrase (July)
    • Aquaporin (August)
    • Dardarin (September)
    • 1,2 rhamnosyltransferase (October)
    • Dofusin (November)
    • Stilbene synthase (December)

    Instantanés du mois 2007 issues edited by Vivienne Baillie Gerritsen and Séverine Altairac:

    • La dermaseptine (janvier)
    • La polygalacturonase-2 (février)
    • La sous-unité alpha type 9 du canal de sodium (mars)
    • Le tyrannosaurus rex et le collagène (avril)
    • La protéine Presequence (mai)
    • La protéine FATSO (juin)
    • L'anhydrase carbonique (juillet)
    • L'aquaporine (août)
    • La dardarine (septembre)
    • La 1,2 rhamnosyltransférase (octobre)
    • La dofusine (novembre)
    • La stilbène synthase (décembre)

     


    © SIB, 2003-2009.

      
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