Automatic detection of exonic splicing enhancers (ESEs) using SVMs (2008)
Mersch, Britta, Gepperth, Alexander, Suhai, Sándor, Hotz-Wagenblatt, Agnes
Abstract Background Exonic splicing enhancers (ESEs) activate nearby splice sites and promote the inclusion (vs. exclusion) of exons in which they reside, while being a binding site for SR proteins....
Off-target effects of siRNA specific for GFP (2008)
Tschuch, Cordula, Schulz, Angela, Pscherer, Armin, Werft, Wiebke, Benner, Axel, Hotz-Wagenblatt, Agnes, ...
Abstract Background Gene knock down by RNAi is a highly effective approach to silence gene expression in experimental as well as therapeutic settings. However, this widely used methodology entails...
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes (2008)
Münk, Carsten, Beck, Thomas, Zielonka, Jörg, Hotz-Wagenblatt, Agnes, Chareza, Sarah, Battenberg, Marion, ...
Abstract Background Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species...
New miRNAs cloned from neuroblastoma (2008)
Afanasyeva, Elena A, Hotz-Wagenblatt, Agnes, Glatting, Karl-Heinz, Westermann, Frank
Abstract Background MicroRNAs (miRNAs) are a novel class of gene expression regulators implicated in cancer biology. Neuroblastoma (NB) is an embryonal tumour consisting of neural crest-derived...
Automatic annotation tools (2007)
Coral Del Val, Mechthild Falkenhahn, Karl-heinz Glatting, Agnes Hotz-wagenblatt, Barbara Pardon, Sndor Suhai
The aim of a high-quality annotation is to identify the key genome features- in particular, the genes and their products in order to bridge the considerable gap between large-scale data-collection...
Mersch, Britta, Sela, Noa, Ast, Gil, Suhai, Sándor, Hotz-Wagenblatt, Agnes
Abstract Background Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called exonization ), or the...
Sela, Noa, Mersch, Britta, Gal-Mark, Nurit, Lev-Maor, Galit, Hotz-Wagenblatt, Agnes, Ast, Gil
Abstract Background Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome...
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs (2006)
Del Val, Coral, Kuryshev, Vladimir, Glatting, Karl-Heinz, Ernst, Peter, Hotz-Wagenblatt, Agnes, Poustka, Annemarie, ...
Abstract Background The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient...
Bmc Bioinformatics, Coral Del Val, Vladimir Yurjevich Kuryshev, Karl-heinz Glatting, Peter Ernst, Agnes Hotz-wagenblatt, ...
Software CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Estannotator: a tool for high throughput est annotation (2003)
Agnes Hotz-wagenblatt, Thomas Hankeln, Peter Ernst, Karl-heinz Glatting, Erwin R. Schmidt, Sándor Suhai
In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information....
ESTAnnotator: a tool for high throughput EST annotation (2003)
Hotz-Wagenblatt, Agnes, Hankeln, Thomas, Ernst, Peter, Glatting, Karl-Heinz, Schmidt, Erwin R., Suhai, Sándor
In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information....
ESTAnnotator: a tool for high throughput EST annotation
Hotz-Wagenblatt, Agnes, Hankeln, Thomas, Ernst, Peter, Glatting, Karl-Heinz, Schmidt, Erwin R., Suhai, Sándor
In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information....
Jelcic, Ilijas, Hotz-Wagenblatt, Agnes, Hunziker, Andreas, Zur Hausen, Harald, De Villiers, Ethel-Michele
We report the isolation of 24 novel genotypes of TT viruses from a surgically removed spleen of a patient with Hodgkin's disease. The sequence analysis of our 24 isolates revealed the remarkable...
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Del Val, Coral, Kuryshev, Vladimir Yurjevich, Glatting, Karl-Heinz, Ernst, Peter, Hotz-Wagenblatt, Agnes, Poustka, Annemarie, ...
ESTAnnotator: a tool for high throughput EST annotation
Hotz-Wagenblatt, Agnes, Hankeln, Thomas, Ernst, Peter, Glatting, Karl-Heinz, Schmidt, Erwin R., Suhai, Sándor
In high throughput sequence analysis, it is often necessary to combine the results of contemporary bioinformatics tools, because no individual tool alone computes all the requested information....
Jelcic, Ilijas, Hotz-Wagenblatt, Agnes, Hunziker, Andreas, Zur Hausen, Harald, De Villiers, Ethel-Michele
We report the isolation of 24 novel genotypes of TT viruses from a surgically removed spleen of a patient with Hodgkin's disease. The sequence analysis of our 24 isolates revealed the remarkable...
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Del Val, Coral, Kuryshev, Vladimir Yurjevich, Glatting, Karl-Heinz, Ernst, Peter, Hotz-Wagenblatt, Agnes, Poustka, Annemarie, ...
New miRNAs cloned from neuroblastoma
Afanasyeva, Elena A, Hotz-Wagenblatt, Agnes, Glatting, Karl-Heinz, Westermann, Frank
Pepperkok, Rainer, Hotz-Wagenblatt, Agnes, König, Norbert, Girod, Andreas, Bossemeyer, Dirk, Kinzel, Volker
The catalytic (C) subunit of protein kinase A functions both in the cytoplasm and the nucleus. A major charge variant representing about one third of the enzyme in striated muscle results from...
Functions, structure, and read-through alternative splicing of feline APOBEC3 genes
Münk, Carsten, Beck, Thomas, Zielonka, Jörg, Hotz-Wagenblatt, Agnes, Chareza, Sarah, Battenberg, Marion, ...
APOBEC3 (A3, Apolipoprotein B mRNA-editing catalytic polypeptide 3) genes in the genome of domestic cat (Felis catus) were identified and characterized
Sela, Noa, Mersch, Britta, Gal-Mark, Nurit, Lev-Maor, Galit, Hotz-Wagenblatt, Agnes, Ast, Gil
Analysis of transposed elements in the human and mouse genomes reveals many effects on the transcriptomes, including a higher level of exonization of Alu elements than other elements.