List of Publications

                     (Philipp Bucher)

Hentschel, C., Irminger, J.-C., Bucher, P., & Birnstiel, M.L.
   (1980). Sea urchin histone mRNA termini are located in
   gene regions downstream from putative regulatory regions.
   Nature 285, 147-151.

Brahms, S., Vergne, J., Brahms, J.G., DiCapua, E., Bucher, P.
   & Koller, T. (1982). Natural DNA sequences can form left-
   handed helices in low salt solution under conditions of
   topological constraint. J. Mol. Biol. 162, 473-493.

Clerc, R.G., Bucher, P. Strub, K., & Birnstiel, M.L. (1983).
   Transcription of a cloned Xenopus laevis H4 histone gene
   in the homologous frog oocyte system depends on an evo-
   lutionary conserved sequence motif in the -50 region.
   Nucl. Acids Res. 11, 8641-8657.

Bucher, P. & Bryan, B. (1984). Signal Search Analysis: A new
   method to localize and characterize functionally important
   DNA sequences. Nucl. Acids Res. 12, 287-315.

Bucher, P. & Trifonov, E.N. (1986). Compilation and analysis
   of eukaryotic POL II promoter sequences. Nucl. Acids
   Res. 14, 10009-10026.

Bucher, P. & Trifonov, E.N. (1987). On Nussinov's compilation
   of eukaryotic transcription initiation sites. J. Theor.
   Biol. 126, 373-375.

Bucher, P. & Trifonov, E.N. (1988). CCAAT box revisited -
   bidirectionality, location and context. J. Biomol. Struct.
   Dyn. 5, 1231-1236.

Bucher, P. (1988- ). The Eukaryotic Promoter Database of the
   Weizmann Institute of Science. EMBL Nucleotide Sequence
   Data Library, release 15- . Postfach 10.2209, D-6900
   Heidelberg.

Bucher, P. (1988). Taxonomic range of eukaryotic POL II
   promoter elements. Mol. Gen. (Life Sci. Adv.) 7, 73-77.

Bucher, P. (1990). Weight matrix descriptions of four eukaryotic
   RNA polymerase II promoter elements derived from 502
   unrelated promoters. J. Mol. Biol. 212, 563-578.

Bucher, P. & Yagil, G. (1991). Occurrence of polypurine:poly-
   pyrimidine tracts in eukaryotic and prokaryotic genes.
   DNA Sequence 1, 157-172.

Karlin, S., Bucher, P., Brendel, V. & Altschul, S.F. (1991).
   Statistical methods and insights for protein and DNA
   sequences.  Ann. Rev.  Biophys. Biophys. Chem. 20, 175-203.

Schachtel, G.A., Bucher, P., Mocarski, E.S., Blaisdell, B.E.
   & Karlin, S. (1991). Evidence for selective evolution in
   codon usage in conserved amino acid segments of human
   alphaherpesvirus proteins. J. Mol. Evol. 33, 483-494.

Karlin, S., Brendel, V. & Bucher, P. (1992). Significant
   similarity and dissimilarity in homologous proteins. Mol.
   Biol. Evol. 9, 152-167.

Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E.
   & Karlin, S. (1992). Methods and algorithms for statistical
   analysis of protein sequences. Proc. Natl. Acad. Sci.
   USA 89, 2002-2006.

Lattion, A.-L., Espel. E., Reichenbach, P., Fromental, C.,
   Bucher, P., Israel, A., Baeuerle, P., Rice, N.R. & Nabholz,
   M. (1992).  Characterization of a new tissue-specific
   transcription factor binding to the simian virus 40 enhancer
   TC-II (NF-kappaB) element. Mol. Cell. Biol. 12, 5217-5227.

Karlin, S. & Bucher P. (1992). Correlation analysis of amino
   acid usage in protein classes. Proc. Natl. Acad. Sci. USA 89,
   12165-12169.

Karlin, S., Blaisdell, B.E. & Bucher, P. (1992). Quantile
   distributions of amino acid usage in protein classes.
   Protein Eng. 5, 729-738.

Luethy, R., Xenarios, I. & Bucher, P. (1994). Improving the
   sensitivity of the sequence profile method. Prot. Sci 3,
   139-146.

Bucher, P. & Bairoch A. (1994). A generalized profile syntax for
   biomolecular sequence motifs and its function in automatic
   sequence interpretation. In:Proceedings Second International
   Conference on Intelligent Systems for Molecular Biology
   (Altman, R., Brutlag, D., Karp, P., Lathrop, R.  & Searls,
   D., Eds.), pp 53-61, AAAI Press, Menlo Park, CA.

Bairoch, A. & Bucher, P. (1994). PROSITE, recent developments. Nucl.
   Acids Res. 22, 3583-3589.

Hofmann, K. & Bucher, P. (1995). The rsp5-domain is shared by proteins
   of diverse functions. FEBS Lett. 358, 153-157.

Spereisen, P., Wang, S.M., Soldaini, E., Pla, M., Rusterholz, C.,
   Bucher, P., Corthesy, P., Reichenbach, P. & Nabholz, M. (1995).
   Mouse interleukin-2 receptor alpha gene expression. Interleukin-1
   and interleukin-2 control transcription via distinct cis-acting
   elements. J. Biol. Chem. (10743-10753). 

Nabholz, M., Soldaini, E., Sperisen, P., Pla, M., Wang, S.-M.,
   MacDonald, H.R., Reichenbach, P., Beermann, F. & Bucher, P. (1995).
   The cis-acting elements controlling mouse IL-2Ralpha transcription. 
   Immonuobiol. 193, 259-262.

Hofmann, K. & Bucher, P. (1995). The FHA domain: a putative nuclear
   signalling domain found in protein kinases and transcription factors.
   Trends Biochem. Sci. 20, 347-349

Bucher, P., Karplus, K., Moeri, N., Hofmann, K. (1996). A flexible motif
   search technique based on generalized profiles. Computers Chem. 20, 3-23.

Hofmann, K. & Bucher, P. (1996). The UBA domain: a sequence motif
   present in multiple enzyme classes of the ubiquitination pathway.  
   Trends Biochem. Sci. 21, 172-173. 

Bairoch, A, Bucher, P. and Hofmann, K. (1996). The PROSITE database,
   its status in 1995. Acids Res. 24, 189-196.

Maryanski, J.L., Jongeneel, C.V., Bucher, P., Casanova, J.-L. 
   & 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.

Walker, P.R., Wilson, A., Bucher, P. & Maryanski, J.L. (1996). Memory TCR 
   repertoires analyzed long-term reflect those selected during the primary
   response. Int. Immunology 8, 1131-1138. 

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. 

Bucher, P., Ficket, J.W. & Hatzigeorgiou, A. (1996). Computational analysis
   of transcriptiotnal regulatory elements - A field in flux.
   Comput. Appl. Biosci. 12, 361-362.

Lecine, P., Algarte, M., Rameil, P., Beadling, C., Bucher, P., Nabholz, M. 
   &  Imbert, J. (1996). ELF-1 and STAT5 bind to a critical element in a
   new enhancer of the human interleukin-2 receptor alpha gene. Mol. Cell.
   Biol. 16, 6829-6840. 

Bork, P., Hofmann, K., Bucher, P., Neuwald, A.F., Altschul, S.F. &
   Koonin, E.V. (1997). A superfamily of conserved domains in DNA
   damage-responsive cell cycle checkpoint proteins. FASEB J. 11, 68-76.

Bairoch A., Bucher, P., and Hofmann, K. (1997). The PROSITE database, its
   status in 1997. Nucl. Acids Res. 25, 217-221.

Weimbs, T., Low, S.H., Chapin, S., Mostov, K.E., Bucher, P. & Hofmann, K.
   (1997). A conserved domain is present in different families of vesicular
   fusion proteins: A new superfamily Proc. Natl. Acad. Sci. USA 94, 3046-3051.

Hofmann, K., Tschopp, J. & Bucher, P. (1997). The CARD domain: a new apoptotic
   signaling motif. Trends Biochem. Sci. 22, 155-156.

Duret, L., and Bucher, P. (1997). Searching for regulatory elements in human
   non-coding sequences. Curr. Opin. Struct. Biol. 7, 399-406.

Baumgartmer, S., Hofmann, K., Chiquet-Ehrismann, R., and
   Bucher, P. (1998). The discoidin domain family revisited: new
   members from prokaryotes and homology-based fold prediction.
   Protein Sci. 7, 1626-1631. 

Cavin Perier, R., Junier, T., and Bucher, P. (1998). The Eukaryotic
   Promoter Database EPD. Nucl. Acids Res. 26, 353-357. 

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. 4, 195-208. 

Junier, T. and Bucher, P. (1998). SEView: a Java applet for
   browsing molecular sequence data. In: Silico Biol. 1, 3. 

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, 4. 

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. 

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. 

Cavin Perier, R.C., Junier, T., Bonnard, C., and Bucher, P. (1999).
   The eukaryotic promoter database (EPD): recent developments.
   Nucleic Acids Res. 27, 307-309. 

Hofmann, K., Bucher, P., Falquet, L., and Bairoch, A. (1999). The
   PROSITE database, its status in 1999. Nucleic Acids Res. 27,
   215-219. 

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), AAAI Press, ed, Menlo Park, pp 138-148.

Bucher, P. (1999). Regulatory elements and expression profiles.
   Curr. Opin.Struct. Biol. 9, 400-407. 

Bucher, P. (1999). Gene feature identification. In: Genetics
   databases, M.J. Bishop ed., (Academic Press, London), 135-164. 

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. Proc. Natl. Acad. Sci. U.S.A. 97, 8473-8478. 

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. 

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. 

Cavin Perier R., Praz V., Junier T., Bonnard C., and Bucher P.
   (2000). The eukaryotic promoter database (EPD). Nucleic Acids
   Res. 28, 302-303. 

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M,
   Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L,
   Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D,
   Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM,
   Pagni M, Servant F, Sigrist CJ, Zdobnov EM; The InterPro
   Consortium (2000). InterPro--an integrated documentation resource
   for protein families, domains and functional sites. Bioinformatics
   16:1145-1150.

Deutsch S, Iseli C, Bucher P, Antonarakis SE, Scott HS (2000). A cSNP
   map and database for human chromosome 21. Genome Res. 11, 300-307.

Ehret GB, Reichenbach P, Schindler U, Horvath CM, Fritz S, Nabholz M,
   Bucher P. (2000). DNA binding specificity of different STAT proteins.
   Comparison of in vitro specificity with natural target sites.
   J. Biol. Chem. 276, 6675-6688.

Maryanski JL, Attuil V, Hamrouni A, Mutin M, Rossi M, Aublin A,
   Bucher P. (2001). Individuality of Ag-selected and preimmune TCR
   repertoires. Immunol Res. 23(1):75-84.

Pagni M, Iseli C, Junier T, Falquet L, Jongeneel V, Bucher P. (2001) 
   trEST, trGEN and Hits: access to databases of predicted protein
   sequences. Nucleic Acids Res. 29:148-151.