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....
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...
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...
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...
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...
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...
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...
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...
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...
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...
Abnormal T lymphocyte development induced by targeted overexpression of IkappaB alpha (1997)
Esslinger, C. W., Wilson, A., Sordat, B., Beermann, F., Jongeneel, C. V.
A role in thymic maturation for factors of the NF-kappaB family has long been suspected, but not yet proven. Transgenic mice with a lymphocyte-specific defect in NF-kappaB activation were produced by...
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...
Nedospasov, S. A., Hirt, B., Shakhov, A. N., Dobrynin, V. N., Kawashima, E., Accolla, R. S., ...
We have isolated clones containing the gene for tumor necrosis factor (TNF-alpha) from a mouse genomic library. Four out of five clones containing the TNF-alpha gene also hybridized to a human...
Jongeneel, C V, Briant, L, Udalova, I A, Sevin, A, Nedospasov, S A, Cambon-Thomsen, A
We have identified three polymorphic microsatellites (which we call TNFa, TNFb, and TNFc) within a 12-kilobase region of the human major histocompatibility complex (MHC) that includes the tumor...
Structure of replicating herpes simplex virus DNA.
Jongeneel, C V, Bachenheimer, S L
We have investigated the molecular anatomy of the herpes simplex virus replicative intermediates by cleavage with the restriction endonuclease BglII. We find that in populations of multiply infected...
Pathogenicity of fibroblast- and lymphocyte-specific variants of minute virus of mice.
Kimsey, P B, Engers, H D, Hirt, B, Jongeneel, C V
We tested two strains of the minute virus of mice (MVM) for pathogenic effects and patterns of infection in laboratory mice. The two strains differ in their ability to infect differentiated cultured...
A precise map of splice junctions in the mRNAs of minute virus of mice, an autonomous parvovirus.
Jongeneel, C V, Sahli, R, McMaster, G K, Hirt, B
We have determined the exact splicing patterns of the mRNAs of the minute virus of mice by a combination of cDNA sequencing and S1 nuclease protection analysis. There are four virus-specific mRNA...
Albrecht, H, Shakhov, A N, Jongeneel, C V
In a cotransfection assay, the human T-cell leukemia virus type I Tax1 gene product specifically activated transcription from the mouse tumor necrosis factor alpha promoter. The activation patterns...
Analysis of tumor necrosis factor promoter responses to ultraviolet light.
Bazzoni, F, Kruys, V, Shakhov, A, Jongeneel, C V, Beutler, B
Ultraviolet (UV) light induces the biosynthesis of chloramphenicol acetyltransferase (CAT) in the skin of mice bearing the CATTNF reporter transgene. Moreover, nuclear run-on assays indicate that UV...
Jongeneel, C V, Quackenbush, E J, Ronco, P, Verroust, P, Carrel, S, Letarte, M
We have previously reported that the amino acid sequence of the common acute lymphoblastic leukemia antigen (CALLA, CD10) translated from a normal human kidney cDNA clone is identical to that of...
Nedospasov, S A, Hirt, B, Shakhov, A N, Dobrynin, V N, Kawashima, E, Accolla, R S, ...
We have isolated clones containing the gene for tumor necrosis factor (TNF-alpha) from a mouse genomic library. Four out of five clones containing the TNF-alpha gene also hybridized to a human...
Replication of herpes simplex virus type I DNA in permeabilized infected cells.
Jongeneel, C V, Bachenheimer, S L
Herpes simplex type 1 (HSV)-infected Vero cells can be permeabilized by a combination of hypotonic shock and a mild emulsifier, gum arabic. Permeabilized cells will incorporate triphosphate...
Jongeneel, C V, Briant, L, Udalova, I A, Sevin, A, Nedospasov, S A, Cambon-Thomsen, A
We have identified three polymorphic microsatellites (which we call TNFa, TNFb, and TNFc) within a 12-kilobase region of the human major histocompatibility complex (MHC) that includes the tumor...
Structure of replicating herpes simplex virus DNA.
Jongeneel, C V, Bachenheimer, S L
We have investigated the molecular anatomy of the herpes simplex virus replicative intermediates by cleavage with the restriction endonuclease BglII. We find that in populations of multiply infected...
Pathogenicity of fibroblast- and lymphocyte-specific variants of minute virus of mice.
Kimsey, P B, Engers, H D, Hirt, B, Jongeneel, C V
We tested two strains of the minute virus of mice (MVM) for pathogenic effects and patterns of infection in laboratory mice. The two strains differ in their ability to infect differentiated cultured...
A precise map of splice junctions in the mRNAs of minute virus of mice, an autonomous parvovirus.
Jongeneel, C V, Sahli, R, McMaster, G K, Hirt, B
We have determined the exact splicing patterns of the mRNAs of the minute virus of mice by a combination of cDNA sequencing and S1 nuclease protection analysis. There are four virus-specific mRNA...
Albrecht, H, Shakhov, A N, Jongeneel, C V
In a cotransfection assay, the human T-cell leukemia virus type I Tax1 gene product specifically activated transcription from the mouse tumor necrosis factor alpha promoter. The activation patterns...
Analysis of tumor necrosis factor promoter responses to ultraviolet light.
Bazzoni, F, Kruys, V, Shakhov, A, Jongeneel, C V, Beutler, B
Ultraviolet (UV) light induces the biosynthesis of chloramphenicol acetyltransferase (CAT) in the skin of mice bearing the CATTNF reporter transgene. Moreover, nuclear run-on assays indicate that UV...
Jongeneel, C V, Quackenbush, E J, Ronco, P, Verroust, P, Carrel, S, Letarte, M
We have previously reported that the amino acid sequence of the common acute lymphoblastic leukemia antigen (CALLA, CD10) translated from a normal human kidney cDNA clone is identical to that of...
Nedospasov, S A, Hirt, B, Shakhov, A N, Dobrynin, V N, Kawashima, E, Accolla, R S, ...
We have isolated clones containing the gene for tumor necrosis factor (TNF-alpha) from a mouse genomic library. Four out of five clones containing the TNF-alpha gene also hybridized to a human...
Replication of herpes simplex virus type I DNA in permeabilized infected cells.
Jongeneel, C V, Bachenheimer, S L
Herpes simplex type 1 (HSV)-infected Vero cells can be permeabilized by a combination of hypotonic shock and a mild emulsifier, gum arabic. Permeabilized cells will incorporate triphosphate...
Abnormal TNF production in prediabetic BB rats is linked to defective CD45R expression.
Rothe, H, Schuller, I, Richter, G, Jongeneel, C V, Kiesel, U, Diamantstein, T, ...
The genetic basis and diabetes association of aberrant tumour necrosis factor-alpha (TNF-alpha) production by activated peritoneal macrophages in diabetes-prone (dp) biobreeding (BB) rats was...