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Ambrosini, G., Praz, V., Jagannathan, V., and Bucher, P. (2003). Signal search analysis server. Nucleic Acids Res 31, 3618-3620. More info
Beernink, H. T., Miller, K., Deshpande, A., Bucher, P., and Cooper, J. P. (2003). Telomere maintenance in fission yeast requires an est1 ortholog. Curr Biol 13, 575-580. More info
Godard, S., Getz, G., Delorenzi, M., Farmer, P., Kobayashi, H., Desbaillets, I., Nozaki, M., Diserens, A. C., Hamou, M. F., Dietrich, P. Y., Regli, L., Janzer, R. C., Bucher, P., Stupp, R., de Tribolet, N., Domany, E., and Hegi, M. E. (2003). Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res 63, 6613-25. More info
Lottaz, C., Iseli, C., Jongeneel, C. V., and Bucher, P. (2003). Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 19 Suppl 2, II103-II112. More info
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R. R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S. E., Pagni, M., Peyruc, D., Ponting, C. P., Selengut, J. D., Servant, F., Sigrist, C. J., Vaughan, R., and Zdobnov, E. M. (2003). The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31, 315-318. More info
O'Sullivan, O., Zehnder, M., Higgins, D., Bucher, P., Grosdidier, A., and Notredame, C. (2003). APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics 19 Suppl 1, I215-I221. More info
Reichenbach, P., Hoss, M., Azzalin, C. M., Nabholz, M., Bucher, P., and Lingner, J. (2003). A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed. Curr Biol 13, 568-574. More info
Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C. J., Hofmann, K., and Bairoch, A. (2002). The PROSITE database, its status in 2002. Nucleic Acids Res 30, 235-238. More info
Iseli, C., Stevenson, B. J., de Souza, S. J., Samaia, H. B., Camargo, A. A., Buetow, K. H., Strausberg, R. L., Simpson, A. J., Bucher, P., and Jongeneel, C. V. (2002). Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res 12, 1068-1074. More info
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Praz, V., Cavin-Périer, R., Bonnard, C., and Bucher, P. (2002). The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res 30, 322-324. More info
Reymond, A., Camargo, A. A., Deutsch, S., Stevenson, B. J., Parmigiani, R. B., Ucla, C., Bettoni, F., Rossier, C., Lyle, R., Guipponi, M., de Souza, S., Iseli, C., Jongeneel, C. V., Bucher, P., Simpson, A. J., Antonarakis, S. E. (2002). Nineteen additional unpredicted transcripts from human chromosome 21. Genomics 79, 824-832. More info
Roulet, E., Busso, S., Camargo, A. A., Simpson, A. J., Mermod, N., and Bucher, P. (2002). High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 20, 831-835. More info
Sigrist, C. J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., and Bucher, P. (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3, 265-274. More info
Deutsch, S., Iseli, C., Bucher, P., Antonarakis, S.E., and Scott, H.S. (2001). A cSNP Map and Database for Human Chromosome 21.Genome Res. 11, 300-307. More info
Ehret, G.B., Reichenbach, P., Schindler, U., Horvath, C.M., Fritz, S., Nabholz, M., and Bucher, P. (2001). DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites.J. Biol. Chem. 276, 6675-6688. More info
Green, A. J., Barcellos, L. F., Rimmler, J. B., Garcia, M. E., Caillier, S., Lincoln, R. R., Bucher, P., Pericak-Vance, M. A., Haines, J. L., Hauser, S. L., and Oksenberg, J. R. (2001). Sequence variation in the transforming growth factor-ß1 (TGFB1) gene and multiple sclerosis susceptibility. J Neuroimmunol 116, 116-124.
Hofmann, K., and Falquet, L. (2001). A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems. Trends Biochem Sci 26, 347-350. More info
Maryanski, J. L., Attuil, V., Hamrouni, A., Mutin, M., Rossi, M., Aublin, A., and Bucher, P. (2001). Individuality of Ag-selected and preimmune TCR repertoires. Immunol Res 23, 75-84. More info
Pagni, M., Iseli, C., Junier, T., Falquet, L., Jongeneel, V., and Bucher, P. (2001). trEST, trGEN and Hits: access to databases of predicted protein sequences.Nucleic Acids Res. 29, 148-151. More info
Junier, T., Pagni, M., and Bucher, P. (2001). Mmsearch: a motif arrangement language and search program. Bioinformatics 17, 1234-1235. More info
Apweiler, R., T. K. Attwood, et al. (2000). InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16, 1145-50. More info
Attuil, V., Bucher, P., Rossi, M., Mutin, M., and Maryanski, J. L. (2000). Comparative T cell receptor repertoire selection by antigen after adoptive transfer: A glimpse at an antigen-specific preimmune repertoire [In Process Citation]. Proc. Natl Acad. Sci. U.S.A 97, 8473-8478. More info
Cavin-Périer, R., Praz, V., Junier, T., Bonnard, C., and Bucher, P. (2000). The eukaryotic promoter database (EPD). Nucleic Acids Res. 28, 302-303. More info
Dias Neto, E., Garcia Correa, R., Verjovski-Almeida, S., Briones, M. R., Nagai, M. A., da Silva, W., Jr., Zago, M. A., Bordin, S., Costa, F. F., Goldman, G. H., Carvalho, A. F., Matsukuma, A., Baia, G. S., Simpson, D. H., Brunstein, A., de Oliveira, P. S., Bucher, P., Jongeneel, C. V., O'Hare, M. J., Soares, F., Brentani, R. R., Reis, L. F., de Souza, S. J., and Simpson, A. J. (2000). Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc. Natl Acad. Sci. U.S.A 97, 3491-3496. More info
Greasley, P. J., Bonnard, C., and Amati, B. (2000). Myc induces the nucleolin and BN51 genes: possible implications in ribosome biogenesis. Nucleic Acids Res. 28, 446-453. More info
Junier, T., and Pagni, M. (2000). Dotlet: diagonal plots in a web browser. Bioinformatics 16, 178-179. More info
Roulet, E., Bucher, P., Schneider, R., Wingender, E., Dusserre, Y., Werner, T., and Mermod, N. (2000). Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J. Mol. Biol. 297, 833-848. More info
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Iseli, C., Jongeneel, C.V., and Bucher, P. (1999). ESTScan: a program for detecting, evaluating and reconstructing potential coding regions in EST sequences. In ISMB '99 (Proceedings of the 7th International Conference on intelligent systems for molecular biology), Menlo Park ed. (AAAI Press), pp. 138-148.
Maryanski, J.L., Attuil, V., Bucher, P., and Walker, P.R. (1999). A quantitative, single-cell PCR analysis of an antigen-specific TCR repertoire selected during an in vivo CD8 response: direct evidence for a wide range of clone sizes with uniform tissue distribution. Mol. Immunol. 36, 745-753.
Boutonnet, N.S., Kajava, A.V., and Rooman, M.J. (1998). Structural classification of abb and bba supersecondary structure units in proteins. Proteins 30, 193-212.
Cavin Perier, R., Junier, T., and Bucher, P. (1998). The Eukaryotic Promoter Database EPD. Nucl. Acids Res. 26, 353-357.
Gagnebin, J., Kovar, H., Kajava, A.V., Estreicher, A., Jug, G., Monnier, P., and Iggo, R. (1998). Use of transcription reporters with novel p53 binding sites to target tumour cells expressing endogenous or virally transduced p53 mutants with altered sequence-specificity. Oncogene 16, 685-690.
Hofmann, K., and Bucher P. (1998). The PCI domain: a common theme in three multiprotein complexes. Trends Biochem. Sci. 23, 204-205.
Hofmann, K., Bucher, P., and Kajava, A. J. (1998). A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain. J. Mol. Biol. 282, 195-208.
Junier, T. and Bucher, P. (1998). SEView: a Java applet for browsing molecular sequence data. In: Silico Biol. 1, 13-20.
Kajava, A.V. (1998). Structural diversity of leucine-rich repeat proteins. J. Mol. Biol. 277, 519-527.
Karamyshev, A.L., Karamysheva, Z.N., Kajava, A.V., Ksenzenko, V.N., and Nesmeyanova, M.A. (1998). Processing of Escherichia coli alkaline phosphatase: role of the primary structure of the signal peptide cleavage region. J. Mol. Biol. 277, 859-870.
Rehn, M., Pihlajaniemi, T., Hofmann, K., and Bucher, P. (1998). The frizzled motif: in how many different protein families does it occur? Trends Biochem. Sci. 23, 415-417.
Roulet, E., Fisch, I., Junier, T., Bucher, P., and Mermod, N. (1998). Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA. In: Silico Biol. 1, 21-28.
Tiktopulo, E.I., and Kajava, A.V. (1998). Denaturation of type I collagen fibrils is an endothermic process accompanied by a noticeable change in the partial heat capacity. Biochemistry 37, 8147-8152.
Tomiuk, S., Hofmann, K., Nix, M., Zumbansen, M., and Stoffel, W. (1998). Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling? Proc. Natl. Acad. Sci. U.S.A 95, 3638-3643.
Tschopp, J., Thome, M., Hofmann, K., and Meinl, E. (1998). The fight of viruses against apoptosis. Curr. Opin. Genet. Dev. 8, 82-87.
Villoutreix, B. O., Bucher, P., Hofmann, K., Baumgartner, S., and Dahlback, B. (1998). Molecular models for the two discoidin domains of human blood coagulation factor V. J. Mol. Model. 4, 268-275.
Becker, K., Schneider, P., Hofmann, K., Mattmann, C., and Tschopp, J. (1997). Interaction of Fas(Apo-1/CD95) with proteins implicated in the ubiquitination pathway. FEBS Lett 412, 102-106.
Bodmer, J. L., Burns, K., Schneider, P., Hofmann, K., Steiner, V., Thome, M., Bornand, T., Hahne, M., Schroter, M., Becker, K., Wilson, A., French, L. E., Browning, J. L., MacDonald, H. R., and Tschopp, J. (1997). TRAMP, a novel apoptosis-mediating receptor with sequence homology to tumor necrosis factor receptor 1 and Fas(Apo-1/CD95). Immunity 6, 79-88.
Bork, P., Hofmann, K., Bucher, P., Neuwald, A. F., Altschul, S. F., and Koonin, E. V. (1997). A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. Faseb J 11, 68-76.
Bucher, P. (1997). [Description of eukaryotic promoters in the EPD database]. Mol Biol (Mosk) 31, 616-625.
Bucher, P., Corthésy, P., Imbert, J., and Nabholz, M. (1997). A conserved IL-2 responsive enhancer in the IL-2R a gene. Immunobiology 198, 136-143.
Duret, L., and Bucher, P. (1997). Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol 7, 399-406.
Gallegos, M. T., Schleif, R., Bairoch, A., Hofmann, K., and Ramos, J. L. (1997). Arac/XylS family of transcriptional regulators. Microbiol Mol Biol Rev 61, 393-410.
Hofmann, K., Bucher, P., and Tschopp, J. (1997). The CARD domain: a new apoptotic signalling motif. Trends Biochem Sci 22, 155-156.
Irmler, M., Hofmann, K., Vaux, D., and Tschopp, J. (1997). Direct physical interaction between the Caenorhabditis elegans 'death proteins' CED-3 and CED-4. FEBS Lett 406, 189-190.
Irmler, M., Thome, M., Hahne, M., Schneider, P., Hofmann, K., Steiner, V., Bodmer, J. L., Schroter, M., Burns, K., Mattmann, C., Rimoldi, D., French, L. E., and Tschopp, J. (1997). Inhibition of death receptor signals by cellular FLIP. Nature 388, 190-195.
Lupas, A., Baumeister, W., and Hofmann, K. (1997). A repetitive sequence in subunits of the 26S proteasome and 20S cyclosome (anaphase-promoting complex). Trends Biochem Sci 22, 195-196.
Nesmeyanova, M. A., Karamyshev, A. L., Karamysheva, Z. N., Kalinin, A. E., Ksenzenko, V. N., and Kajava, A. V. (1997). Positively charged lysine at the N-terminus of the signal peptide of the Escherichia coli alkaline phosphatase provides the secretion efficiency and is involved in the interaction with anionic phospholipids. FEBS Lett 403, 203-207.
Schmidt, S., Hofmann, K., and Simanis, V. (1997). Sce3, a suppressor of the Schizosaccharomyces pombe septation mutant cdc11, encodes a putative RNA-binding protein. Nucl Acids Res 25, 3433-3439.
Schmidt, S., Sohrmann, M., Hofmann, K., Woollard, A., and Simanis, V. (1997). The Spg1p GTPase is an essential, dosage-dependent inducer of septum formation in Schizosaccharomyces pombe. Genes Dev 11, 1519-1534.
Schneider, P., Bodmer, J. L., Thome, M., Hofmann, K., Holler, N., and Tschopp, J. (1997). Characterization of two receptors for TRAIL. FEBS Lett 416, 329-334.
Schneider, P., Thome, M., Burns, K., Bodmer, J. L., Hofmann, K., Kataoka, T., Holler, N., and Tschopp, J. (1997). TRAIL receptors 1 (DR4) and 2 (DR5) signal FADD-dependent apoptosis and activate NF-kB. Immunity 7, 831-836.
Schultz, J., Ponting, C. P., Hofmann, K., and Bork, P. (1997). SAM as a protein interaction domain involved in developmental regulation. Protein Sci 6, 249-253.
Terskikh, A. V., Le Doussal, J. M., Crameri, R., Fisch, I., Mach, J. P., and Kajava, A. V. (1997). "Peptabody": a new type of high avidity binding protein. Proc Natl Acad Sci U S A 94, 1663-1668.
Terskikh, A.V., Potekhin, S.A., Melnik, T.N., and Kajava, A.V. (1997). Mutation Gln54Leu of the conserved polar residue in the interfacial coiled coil position (d) results in sigificant stabilization of the original structure of the COMP pentamerization domain. Lett. Pept. Sci. 4, 297-304.
Thome, M., Schneider, P., Hofmann, K., Fickenscher, H., Meinl, E., Neipel, F., Mattmann, C., Burns, K., Bodmer, J. L., Schroter, M., Scaffidi, C., Krammer, P. H., Peter, M. E., and Tschopp, J. (1997). Viral FLICE-inhibitory proteins (FLIPs) prevent apoptosis induced by death receptors. Nature 386, 517-521.
Wang, Y., Okamoto, M., Schmitz, F., Hofmann, K., and Sudhof, T. C. (1997). Rim is a putative Rab3 effector in regulating synaptic-vesicle fusion. Nature 388, 593-598.
Weimbs, T., Low, S. H., Chapin, S. J., Mostov, K. E., Bucher, P., and Hofmann, K. (1997). A conserved domain is present in different families of vesicular fusion proteins: a new superfamily. Proc Natl Acad Sci U S A 94, 3046-3051.
Bairoch, A., Bucher, P., and Hoffmann, K. (1996). The Prosite database, its status in 1995. Nucl Acids Res 24, 189-196.
Betz, A., Telemenakis, I., Hofmann, K., and Brose, N. (1996). Mammalian Unc-13 homologues as possible regulators of neurotransmitter release. Biochem Soc Trans 24, 661-666.
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Bucher, P., and Hofmann, K. (1996). A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system. Ismb 4, 44-51.
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Emery, P., Strubin, M., Hofmann, K., Bucher, P., Mach, B., and Reith, W. (1996). A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity. Mol Cell Biol 16, 4486-4494.
Hofmann, K., and Bucher, P. (1996). The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway. Trends Biochem Sci 21, 172-173.
Kajava, A. V. (1996). Modeling of a five-stranded coiled-coil structure for the assembly domain of the cartilage oligomeric matrix protein. Proteins 24, 218-226.
Lecine, P., Algarte, M., Rameil, P., Beadling, C., Bucher, P., Nabholz, M., and Imbert, J. (1996). Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor a gene. Mol Cell Biol 16, 6829-6840.
Maryanski, J. L., Jongeneel, C. V., Bucher, P., Casanova, J.-L., and Walker, P. R. (1996). Single-cell PCR analysis of TCR repertoires selected by antigen in vivo : a high magnitude CD8 response is comprised of very few clones. Immunity 4, 47-55.
Tschopp, J., and Hofmann, K. (1996). Cytotoxic T cells : more weapons for new targets? Trends Microbiol 4, 91-94.
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