Figure Is The, P. Bucher, E. N. Trifonov, Wataru Fujibuchi, Minoru Kanehisa
References
R. Apweiler, T. K. Attwood, A. Bateman, M. Biswas, P. Bucher, L. Cerutti, ...
2001 Oxford University Press Nucleic Acids Research, 2001, Vol. 29, No. 1 37--40 The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Girod, P. A., Nguyen, D. Q., Calabrese, D., Puttini, S., Grandjean, M., Martinet, D., ...
Gene transfer in eukaryotic cells and organisms suffers from epigenetic effects that result in low or unstable transgene expression and high clonal variability. Use of epigenetic regulators such as...
Indexing strategies for rapid searches of short words in genome sequences (2007)
Iseli, C., Ambrosini, G., Bucher, P., Jongeneel, C. V.
Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis....
Rambaldi, D., Felice, B., Praz, V., Bucher, P., Cittaro, D., Guffanti, A.
BACKGROUND: The Affymetrix technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. However, changes in gene expression levels are not...
Retelska, D., Beaudoing, E., Notredame, C., Jongeneel, C. V., Bucher, P.
ABSTRACT: BACKGROUND: The comparison of complete genomes has revealed surprisingly large numbers of conserved non-protein-coding (CNC) DNA regions. However, the biological function of CNC remains...
Schmid, C. D., Sengstag, T., Bucher, P., Delorenzi, M.
A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications...
Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus (2006)
Beermann, F., Kaloulis, K., Hofmann, D., Murisier, F., Bucher, P., Trumpp, A.
The secreted signaling molecule fibroblast growth factor 8 (Fgf8) is an essential component of certain embryonic signaling centers including the mid-hindbrain (isthmic) organizer, the first branchial...
Armougom, F., Poirot, O., Moretti, S., Higgins, D. G., Bucher, P., Keduas, V., ...
The APDB webserver uses structural information to evaluate the alignment of sequences with known structures. It returns a score correlated to the overall alignment accuracy as well as a local...
Jagannathan, V., Roulet, E., Delorenzi, M., Bucher, P.
HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The...
Similarities and differences of polyadenylation signals in human and fly (2006)
Retelska, D., Iseli, C., Bucher, P., Jongeneel, C. V., Naef, F.
ABSTRACT: BACKGROUND: Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich...
EPD in its twentieth year: towards complete promoter coverage of selected model organisms (2006)
Schmid, C. D., Perier, R., Praz, V., Bucher, P.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). Access to promoter...
Genolet, R., Kersten, A.H., Braissant, O., Mandard, S.J., Tan, N.S., Bucher, P., ...
In liver, the glyoxylate cycle contributes to two metabolic functions, urea and glucose synthesis. One of the key enzymes in this pathway is glyoxylate reductase/hydroxypyruvate reductase (GRHPR)...
Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts (2005)
Egener, T., Roulet, E., Zehnder, M., Bucher, P., Mermod, N.
The function of DNA-binding proteins is controlled not just by their abundance, but mainly at the level of their activity in terms of their interactions with DNA and protein targets. Moreover, the...
Genolet, R., Kersten, S., Braissant, O., Mandard, S., Tan, N. S., Bucher, P., ...
In liver, the glyoxylate cycle contributes to two metabolic functions, urea and glucose synthesis. One of the key enzymes in this pathway is glyoxylate reductase/hydroxypyruvate reductase (GRHPR)...
InterPro, progress and status in 2005 (2005)
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Sperisen, P., Schmid, C. D., Bucher, P., Zilian, O.
There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the...
Recent improvements to the PROSITE database (2004)
Hulo, N., Sigrist, C. J., Le Saux, V., Langendijk-Genevaux, P. S., Bordoli, L., Gattiker, A., ...
The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to documentation that provides useful...
Krawczyk, M., Peyraud, N., Rybtsova, N., Masternak, K., Bucher, P., Barras, E., ...
MHC class II (MHC-II) genes are regulated by an enhanceosome complex containing two gene-specific transcription factors, regulatory factor X complex (RFX) and CIITA. These factors assemble on a...
Praz, V., Jagannathan, V., Bucher, P.
The main goal of CleanEx is to provide access to public gene expression data via unique gene names. A second objective is to represent heterogeneous expression data produced by different technologies...
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension (2004)
Schmid, C. D., Praz, V., Delorenzi, M., Perier, R., Bucher, P.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple...
trome, trEST and trGEN: databases of predicted protein sequences (2004)
Sperisen, P., Iseli, C., Pagni, M., Stevenson, B. J., Bucher, P., Jongeneel, C. V.
We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these...
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz,C., Iseli,C., Jongeneel,C. V., Bucher,P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz, C., Iseli, C., Jongeneel, C. V., Bucher, P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
Reichenbach, P., Hoss, M., Azzalin, C. M., Nabholz, M., Bucher, P., Lingner, J.
Telomeres protect the eukaryotic chromosome ends from degradation and fusion. They are maintained by the ribonucleoprotein telomerase, the core of which is composed of a reverse transcriptase (TERT)...
Signal search analysis server (2003)
Ambrosini, G., Praz, V., Jagannathan, V., Bucher, P.
Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The...
Telomere maintenance in fission yeast requires an Est1 ortholog (2003)
Beernink, H. T., Miller, K., Deshpande, A., Bucher, P., Cooper, J. P.
Telomerase regulation is critical to genome maintenance yet remains poorly understood. Without telomerase's ability to synthesize telomere repeats, chromosome ends shorten progressively, as...
Godard, S., Getz, G., Delorenzi, M., Farmer, P., Kobayashi, H., Desbaillets, I., ...
The development of targeted treatment strategies adapted to individual patients requires identification of the different tumor classes according to their biology and prognosis. We focus here on the...
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz, C., Iseli, C., Jongeneel, C. V., Bucher, P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Barrell, D., Bateman, A., ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
O'Sullivan, O., Zehnder, M., Higgins, D., Bucher, P., Grosdidier, A., Notredame, C.
MOTIVATION: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a...
C. Lottaz, C. Iseli, C. V. Jongeneel, P. Bucher
Vol. 19 Suppl. 2 2003, pages ii103–ii112
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz, C., Iseli, C., Jongeneel, C. V., Bucher, P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
Numerous potentially functional but non-genic conserved sequences on human chromosome 21 (2002)
Dermitzakis, E. T., Reymond, A., Lyle, R., Scamuffa, N., Ucla, C., Deutsch, S., ...
The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is...
The PROSITE database, its status in 2002 (2002)
Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C. J., Hofmann, K., ...
PROSITE [Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219] is a method of identifying the functions of uncharacterized proteins...
Long-range heterogeneity at the 3' ends of human mRNAs (2002)
Iseli, C., Stevenson, B. J., De Souza, S. J., Samaia, H. B., Camargo, A. A., Buetow, K. H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., ...
The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for...
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data (2002)
Praz, V., Perier, R., Bonnard, C., Bucher, P.
The Eukaryotic Promoter Database (EPD) is an annotated, non-redundant collection of eukaryotic Pol II promoters, for which the transcription start site has been determined experimentally. Access to...
Nineteen additional unpredicted transcripts from human chromosome 21 (2002)
Reymond, A., Camargo, A. A., Deutsch, S., Stevenson, B. J., Parmigiani, R. B., Ucla, C., ...
The identification of all human chromosome 21 (HC21) genes is a necessary step in understanding the molecular pathogenesis of trisomy 21 (Down syndrome). The first analysis of the sequence of 21q...
Roulet, E., Busso, S., Camargo, A. A., Simpson, A. J., Mermod, N., Bucher, P.
The ability to determine the location and relative strength of all transcription-factor binding sites in a genome is important both for a comprehensive understanding of gene regulation and for...
PROSITE: a documented database using patterns and profiles as motif descriptors (2002)
Sigrist, C. J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., ...
Among the various databases dedicated to the identification of protein families and domains, PROSITE is the first one created and has continuously evolved since. PROSITE currently consists of a large...
Genetic basis for clinical expression in multiple sclerosis (2002)
Barcellos, L. F., Oksenberg, J. R., Green, A. J., Bucher, P., Rimmler, J. B., ...
Multiple sclerosis is a clinically heterogeneous demyelinating disease and an important cause of acquired neurological disability. An underlying complex genetic susceptibility plays an important role...
Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., ...
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein...
A cSNP map and database for human chromosome 21 (2001)
Deutsch, S., Iseli, C., Bucher, P., Antonarakis, S. E., Scott, H. S.
Single nucleotide polymorphisms (SNPs) are likely to contribute to the study of complex genetic diseases. The genomic sequence of human chromosome 21q was recently completed with 225 annotated genes,...
Ehret, G. B., Reichenbach, P., Schindler, U., Horvath, C. M., Fritz, S., Nabholz, M., ...
STAT transcription factors are expressed in many cell types and bind to similar sequences. However, different STAT gene knock-outs show very distinct phenotypes. To determine whether differences...
mmsearch: a motif arrangement language and search program (2001)
Junier, T., Pagni, M., Bucher, P.
This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does...
Individuality of Ag-selected and preimmune TCR repertoires (2001)
Maryanski, J. L., Attuil, V., Hamrouni, A., Mutin, M., Rossi, M., Aublin, A., ...
We have combined flow cytometry and single-cell PCR to characterize the TCRBV repertoires selected by individual mice in a model CD8 response against a defined peptide/MHC complex (CW3 170-1 79/Kd)....
trEST, trGEN and Hits: access to databases of predicted protein sequences (2001)
Pagni, M., Iseli, C., Junier, T., Falquet, L., Jongeneel, V., Bucher, P.
High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of...
Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., ...
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein...
Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., ...
MOTIVATION: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the...
Attuil, V., Bucher, P., Rossi, M., Mutin, M., Maryanski, J. L.
The low frequency of precursor cells specific for any particular antigen (Ag) makes it difficult to characterize preimmune T cell receptor (TCR) repertoires and to understand repertoire selection...
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags (2000)
Dias Neto, E., Correa, R. G., Verjovski-Almeida, S., Briones, M. R., Nagai, M. A., Da Silva, W. Jr., ...
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription-PCR using arbitrarily chosen primers will result in the preferential amplification of the...
The eukaryotic promoter database (EPD) (2000)
Perier, R. C., Praz, V., Junier, T., Bonnard, C., Bucher, P.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters for which the transcription start site has been determined experimentally. Access to...
Roulet, E., Bucher, P., Schneider, R., Wingender, E., Dusserre, Y., Werner, T., ...
Accurate prediction of transcription factor binding sites is needed to unravel the function and regulation of genes discovered in genome sequencing projects. To evaluate current computer prediction...
Iseli, C., Jongeneel, C. V., Bucher, P.
One of the problems associated with the large-scale analysis of unannotated, low quality EST sequences is the detection of coding regions and the correction of frameshift errors that they often...
Regulatory elements and expression profiles (1999)
There has been steady progress in the computational analysis of transcription control regions, but current methods of predicting the gene regulatory features of noncoding sequences are still not...
The PROSITE database, its status in 1999 (1999)
Hofmann, K., Bucher, P., Falquet, L., Bairoch, A.
The PROSITE database (http://www.expasy.ch/sprot/prosite.htm l) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can...
Maryanski, J. L., Attuil, V., Bucher, P., Walker, P. R.
The development of T cell effector and memory responses against foreign antigens (Ags) involves the activation, differentiation and proliferation of naive T cells expressing distinct Ag-specific...
The Eukaryotic Promoter Database (EPD): recent developments (1999)
Perier, R. C., Junier, T., Bonnard, C., Bucher, P.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to...
Baumgartner, S., Hofmann, K., Chiquet-Ehrismann, R., Bucher, P.
Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been...
The Eukaryotic Promoter Database EPD (1998)
Cavin Perier, R., Junier, T., Bucher, P.
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. The underlying definition of a promoter is that of a...
Hofmann, K., Bucher, P., Kajava, A. V.
Mammalian Cdc25 phosphatase is responsible for the dephosphorylation of Cdc2 and other cyclin-dependent kinases at Thr14 and Tyr15, thus activating the kinase and allowing cell cycle progression. The...
SEView: a Java applet for browsing molecular sequence data (1998)
SEView is a Java applet that represents known or predicted elements of a protein or nucleotide sequence. It replaces or supplements the textual format of databases or program output with an...
Molecular models for the two discoidin domains of human blood coagulation factor V (1998)
Villoutreix, B. O., Bucher, P., Hofmann, K., Baumgartner, S., Dahlback, B.
The PROSITE database, its status in 1997 (1997)
Bairoch, A., Bucher, P., Hofmann, K.
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of...
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins (1997)
Bork, P., Hofmann, K., Bucher, P., Neuwald, A. F., Altschul, S. F., Koonin, E. V.
Computer analysis of a conserved domain, BRCT, first described at the carboxyl terminus of the breast cancer protein BRCA1, a p53 binding protein (53BP1), and the yeast cell cycle checkpoint protein...
Searching for regulatory elements in human noncoding sequences (1997)
Important progress has been made in the past two years in the identification of Pol II promoters. For most other regulatory elements, however, current biological knowledge is still insufficient to...
Weimbs, T., Low, S. H., Chapin, S. J., Mostov, K. E., Bucher, P., Hofmann, K.
We have analyzed conserved domains in t-SNAREs [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors in the target membrane], proteins that are believed to be involved...
A flexible motif search technique based on generalized profiles (1996)
Bucher, P., Karplus, K., Moeri, N., Hofmann, K.
A flexible motif search technique is presented which has two major components: (1) a generalized profile syntax serving as a motif definition languaje; and (2) a motif search method specifically...
The PROSITE database, its status in 1995 (1996)
Bairoch, A., Bucher, P., Hofmann, K.
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of...
A flexible motif search technique based on generalized profiles (1996)
Bucher, P., Karplus, K., Moeri, N., Hofmann, K.
A flexible motif search technique is presented which has two major components: (1) a generalized profile syntax serving as a motif definition language; and (2) a motif search method specifically...
Emery, P., Strubin, M., Hofmann, K., Bucher, P., Mach, B., Reith, W.
The RFX DNA binding domain is a novel motif that has been conserved in a growing number of dimeric DNA-binding proteins, having diverse regulatory functions, in eukaryotic organisms ranging from...
Lecine, P., Algarte, M., Rameil, P., Beadling, C., Bucher, P., Nabholz, M., ...
The interleukin 2 receptor alpha-chain (IL-2R alpha) gene is a key regulator of lymphocyte proliferation. IL-2R alpha is rapidly and potently induced in T cells in response to mitogenic stimuli....
Maryanski, J. L., Jongeneel, C. V., Bucher, P., Casanova, J. L., Walker, P. R.
Taking advantage of a potent MHC class I-restricted response that allows the identification of antigen-selected CD8 T cells directly ex vivo, we characterized the antigen-specific T cell repertoires...
Memory TCR repertoires analyzed long-term reflect those selected during the primary response (1996)
Walker, P. R., Wilson, A., Bucher, P., Maryanski, J. L.
Normal T cell repertoire selection and evolution in antigen-specific responses is poorly understood. We have recently described an MHC class I-restricted response characterized by an overwhelming...
The rsp5-domain is shared by proteins of diverse functions (1995)
A novel, unusually small, and highly conserved domain of modular intracellular proteins is described. The domain was first recognized as three repeats in the yeast rsp5 gene product and named...
The cis-acting elements controlling mouse IL-2R alpha transcription (1995)
Nabholz, M., Soldaini, E., Sperisen, P., Pla, M., Wang, S. M., MacDonald, H. R., ...
Sperisen, P., Wang, S. M., Soldaini, E., Pla, M., Rusterholz, C., Bucher, P., ...
We have shown that interleukin-1 (IL-1) and IL-2 control IL-2 receptor alpha (IL-2R alpha) gene transcription in CD4-CD8- murine T lymphocyte precursors. Here we map the cis-acting elements that...
The cis-acting elements controlling mouse IL-2R alpha transcription (1995)
Nabholz, M., Soldaini, E., Sperisen, P., Pla, M., Wang, S. M., MacDonald, H. R., ...
A general syntax for expressing biomolecular sequence motifs is described, which will be used in future releases of the PROSITE data bank and in a similar collection of nucleic acid sequence motifs...
PROSITE: recent developments (1994)
PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences.
Improving the sensitivity of the sequence profile method (1994)
Luthy, R., Xenarios, I., Bucher, P.
The sequence profile method (Gribskov M, McLachlan AD, Eisenberg D, 1987, Proc Natl Acad Sci USA 84:4355-4358) is a powerful tool to detect distant relationships between amino acid sequences. A...
Methods and algorithms for statistical analysis of protein sequences (1992)
Brendel, V., Bucher, P., Nourbakhsh, I. R., Blaisdell, B. E., Karlin, S.
We describe several protein sequence statistics designed to evaluate distinctive attributes of residue content and arrangement in primary structure. Considered are global compositional biases, local...
Quantile distributions of amino acid usage in protein classes (1992)
Karlin, S., Blaisdell, B. E., Bucher, P.
A comparative study of the compositional properties of various protein sets from both cellular and viral organisms is presented. Invariants and contrasts of amino acid usages have been discerned for...
Significant similarity and dissimilarity in homologous proteins (1992)
Karlin, S., Brendel, V., Bucher, P.
Common practice emphasizes significant sequence similarities between different members of protein families. These similarities presumably reflect on evolutionary conservation of structurally and...
Correlation analysis of amino acid usage in protein classes (1992)
We present a comparative study of residue usage correlations of various organism protein sets of diverse phylogenetic species and of open reading frames of several large human viral genomes. Our...
Lattion, A. L., Espel, E., Reichenbach, P., Fromental, C., Bucher, P., Israel, A., ...
We have biochemically and functionally characterized a new transcription factor, NP-TCII, which is present in nuclei from unstimulated T and B lymphocytes but is not found in nonhematopoietic cells....
Occurrence of oligopurine.oligopyrimidine tracts in eukaryotic and prokaryotic genes (1991)
A program to analyse the length and frequency distribution of specific base tracts in genomic sequences is described. The frequency of oligopurine.oligopyrimidine tracts (R.Y. tracts) in a data base...
Schachtel, G. A., Bucher, P., Mocarski, E. S., Blaisdell, B. E., Karlin, S.
The genomes of human viruses herpes simplex 1 (HSV1) and varicella zoster (VZV), although similar in biology, largely concordant in gene order, and identical in many amino acid segments, differ...
Optimized weight matrices defining four major eukaryotic promoter elements, the TATA-box, cap signal, CCAAT-, and GC-box, are presented; they were derived by comparative sequence analysis of 502...
CCAAT box revisited: bidirectionality, location and context (1988)
The so-called CCAAT box is believed to be a major promoter element of higher eukaryotes though it is ill-defined being deduced from very limited sequence data. The comprehensive computer analysis of...
Compilation and analysis of eukaryotic POL II promoter sequences (1986)
A representative set of 168 eukaryotic POL II promoters has been compiled from the EMBL library and subjected to computer signal search analysis. Application of this technique to E. coli promoters as...
The generation of "signal search data" represents a general method of describing the common properties of a set of DNA sequences presumed to be functionally analogous. Besides the detailed...
Clerc, R. G., Bucher, P., Strub, K., Birnstiel, M. L.
A cloned Xenopus laevis H4 histone gene has been expressed in the X.laevis oocyte nucleus. The homologous histone H4 gene can be correctly and efficiently expressed in the frog oocyte even in...
Hentschel, C., Irminger, J. C., Bucher, P., Birnstiel, M. L.
S1 nuclease mapping of the Psammechinus miliaris embryonic histone mRNAs locates the 5' termini in or adjacent to a short sequence homology (5'pyCATTCpu3') downstream from the putative RNA polymerase...
MENKEN, U., WIEGAND, V., BUCHER, P., MEESMANN, W.
Acute occlusions of the left circumflex coronary artery were performed in open-chest dogs. A control group (n = 19) was compared with three groups (total n = 17) pretreated once daily with different...
Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., ...
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein...
Methods and algorithms for statistical analysis of protein sequences.
Brendel, V, Bucher, P, Nourbakhsh, I R, Blaisdell, B E, Karlin, S
We describe several protein sequence statistics designed to evaluate distinctive attributes of residue content and arrangement in primary structure. Considered are global compositional biases, local...
Correlation analysis of amino acid usage in protein classes.
We present a comparative study of residue usage correlations of various organism protein sets of diverse phylogenetic species and of open reading frames of several large human viral genomes. Our...
The PROSITE database, its status in 1995.
Bairoch, A, Bucher, P, Hofmann, K
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of...
The PROSITE database, its status in 1997.
Bairoch, A, Bucher, P, Hofmann, K
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of...
The Eukaryotic Promoter Database EPD.
Cavin Périer, R, Junier, T, Bucher, P
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. The underlying definition of a promoter is that of a...
The PROSITE database, its status in 1999.
Hofmann, K, Bucher, P, Falquet, L, Bairoch, A
The PROSITE database (http://www.expasy.ch/sprot/prosite.htm l) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can...
The Eukaryotic Promoter Database (EPD): recent developments.
Périer, R C, Junier, T, Bonnard, C, Bucher, P
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to...
A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity.
Emery, P, Strubin, M, Hofmann, K, Bucher, P, Mach, B, Reith, W
The RFX DNA binding domain is a novel motif that has been conserved in a growing number of dimeric DNA-binding proteins, having diverse regulatory functions, in eukaryotic organisms ranging from...
Lécine, P, Algarté, M, Rameil, P, Beadling, C, Bucher, P, Nabholz, M, ...
The interleukin 2 receptor alpha-chain (IL-2R alpha) gene is a key regulator of lymphocyte proliferation. IL-2R alpha is rapidly and potently induced in T cells in response to mitogenic stimuli....
Lécine, P, Algarté, M, Rameil, P, Beadling, C, Bucher, P, Nabholz, M, ...
PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences.
The generation of "signal search data" represents a general method of describing the common properties of a set of DNA sequences presumed to be functionally analogous. Besides the detailed...
Clerc, R G, Bucher, P, Strub, K, Birnstiel, M L
A cloned Xenopus laevis H4 histone gene has been expressed in the X.laevis oocyte nucleus. The homologous histone H4 gene can be correctly and efficiently expressed in the frog oocyte even in...
Compilation and analysis of eukaryotic POL II promoter sequences.
A representative set of 168 eukaryotic POL II promoters has been compiled from the EMBL library and subjected to computer signal search analysis. Application of this technique to E. coli promoters as...
Lattion, A L, Espel, E, Reichenbach, P, Fromental, C, Bucher, P, Israël, A, ...
We have biochemically and functionally characterized a new transcription factor, NP-TCII, which is present in nuclei from unstimulated T and B lymphocytes but is not found in nonhematopoietic cells....
Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., ...
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein...
Methods and algorithms for statistical analysis of protein sequences.
Brendel, V, Bucher, P, Nourbakhsh, I R, Blaisdell, B E, Karlin, S
We describe several protein sequence statistics designed to evaluate distinctive attributes of residue content and arrangement in primary structure. Considered are global compositional biases, local...
Correlation analysis of amino acid usage in protein classes.
We present a comparative study of residue usage correlations of various organism protein sets of diverse phylogenetic species and of open reading frames of several large human viral genomes. Our...
The PROSITE database, its status in 1995.
Bairoch, A, Bucher, P, Hofmann, K
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of...
The PROSITE database, its status in 1997.
Bairoch, A, Bucher, P, Hofmann, K
The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of...
The Eukaryotic Promoter Database EPD.
Cavin Périer, R, Junier, T, Bucher, P
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. The underlying definition of a promoter is that of a...
The PROSITE database, its status in 1999.
Hofmann, K, Bucher, P, Falquet, L, Bairoch, A
The PROSITE database (http://www.expasy.ch/sprot/prosite.htm l) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can...
The Eukaryotic Promoter Database (EPD): recent developments.
Périer, R C, Junier, T, Bonnard, C, Bucher, P
The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to...
A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity.
Emery, P, Strubin, M, Hofmann, K, Bucher, P, Mach, B, Reith, W
The RFX DNA binding domain is a novel motif that has been conserved in a growing number of dimeric DNA-binding proteins, having diverse regulatory functions, in eukaryotic organisms ranging from...
Lécine, P, Algarté, M, Rameil, P, Beadling, C, Bucher, P, Nabholz, M, ...
The interleukin 2 receptor alpha-chain (IL-2R alpha) gene is a key regulator of lymphocyte proliferation. IL-2R alpha is rapidly and potently induced in T cells in response to mitogenic stimuli....
Lécine, P, Algarté, M, Rameil, P, Beadling, C, Bucher, P, Nabholz, M, ...
PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences.
The generation of "signal search data" represents a general method of describing the common properties of a set of DNA sequences presumed to be functionally analogous. Besides the detailed...
Clerc, R G, Bucher, P, Strub, K, Birnstiel, M L
A cloned Xenopus laevis H4 histone gene has been expressed in the X.laevis oocyte nucleus. The homologous histone H4 gene can be correctly and efficiently expressed in the frog oocyte even in...
Compilation and analysis of eukaryotic POL II promoter sequences.
A representative set of 168 eukaryotic POL II promoters has been compiled from the EMBL library and subjected to computer signal search analysis. Application of this technique to E. coli promoters as...
Lattion, A L, Espel, E, Reichenbach, P, Fromental, C, Bucher, P, Israël, A, ...
We have biochemically and functionally characterized a new transcription factor, NP-TCII, which is present in nuclei from unstimulated T and B lymphocytes but is not found in nonhematopoietic cells....
HLA-DR2 Dose Effect on Susceptibility to Multiple Sclerosis and Influence on Disease Course
Barcellos, L. F., Oksenberg, J. R., Begovich, A. B., Martin, E. R., Schmidt, S., Vittinghoff, E., ...
Models of disease susceptibility in multiple sclerosis (MS) often assume a dominant action for the HLA-DRB1*1501 allele and its associated haplotype (DRB1*1501-DQB1*0602 or DR2). A robust and...
Improving the sensitivity of the sequence profile method.
Lüthy, R., Xenarios, I., Bucher, P.
The sequence profile method (Gribskov M, McLachlan AD, Eisenberg D, 1987, Proc Natl Acad Sci USA 84:4355-4358) is a powerful tool to detect distant relationships between amino acid sequences. A...
Baumgartner, S., Hofmann, K., Chiquet-Ehrismann, R., Bucher, P.
Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been...