Reichwald, Kathrin, Lauber, Chris, Nanda, Indrajit, Kirschner, Jeanette, Hartmann, Nils, Schories, Susanne, ...
Abstract Background The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal...
Accurate prediction of NAGNAG alternative splicing (2009)
Sinha, Rileen, Nikolajewa, Swetlana, Szafranski, Karol, Hiller, Michael, Jahn, Niels, Huse, Klaus, ...
Alternative splicing (AS) involving NAGNAG tandem acceptors is an evolutionarily widespread class of AS. Recent predictions of alternative acceptor usage reported better results for acceptors...
Comparative analysis of sequence features involved in the recognition of tandem splice sites (2008)
Bortfeldt, Ralf, Schindler, Stefanie, Szafranski, Karol, Schuster, Stefan, Holste, Dirk
Abstract Background The splicing of pre-mRNAs is conspicuously often variable and produces multiple alternatively spliced (AS) isoforms that encode different messages from one gene locus....
Schindler, Stefanie, Szafranski, Karol, Hiller, Michael, Ali, Gul, Palusa, Saiprasad G, Backofen, Rolf, ...
Abstract Background Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However,...
Support Vector Machines for Predicting microRNA Hairpins (2008)
Karol Szafranski, Molly Megraw, Martin Reczko, Artemis G. Hatzigeorgiou
Abstract- microRNAs (miRNAs) are 20-22 nt noncoding RNAs which are rapidly emerging as crucial regulators of gene expression in plants and animals. Identification of the hairpins which yield mature...
Selection against tandem splice sites affecting structured protein regions (2008)
Hiller, Michael, Szafranski, Karol, Huse, Klaus, Backofen, Rolf, Platzer, Matthias
Abstract Background Alternative selection of splice sites in tandem donors and acceptors is a major mode of alternative splicing. Here, we analyzed whether in-frame tandem sites leading to subtle...
Assessing the fraction of short-distance tandem splice sites under purifying selection (2008)
Hiller, Michael, Szafranski, Karol, Sinha, Rileen, Huse, Klaus, Nikolajewa, Swetlana, Rosenstiel, Philip, ...
Many alternative splice events result in subtle mRNA changes, and most of them occur at short-distance tandem donor and acceptor sites. The splicing mechanism of such tandem sites likely involves the...
Szafranski, Karol, Schindler, Stefanie, Taudien, Stefan, Hiller, Michael, Huse, Klaus, Jahn, Niels, ...
Abstract Background Despite some degeneracy of sequence signals that govern splicing of eukaryotic pre-mRNAs, it is an accepted rule that U2-dependent introns exhibit the 3' terminal dinucleotide AG....
TassDB: a database of alternative tandem splice sites (2007)
Hiller, Michael, Nikolajewa, Swetlana, Huse, Klaus, Szafranski, Karol, Rosenstiel, Philip, Schuster, Stefan, ...
Subtle alternative splice events at tandem splice sites are frequent in eukaryotes and substantially increase the complexity of transcriptomes and proteomes. We have developed a relational database,...
Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More? (2006)
Michael Hiller, Karol Szafranski, Rolf Backofen, Matthias Platzer
Phylogenetically widespread alternative splicing at unusual GYNGYN donors (2006)
Hiller, Michael, Huse, Klaus, Szafranski, Karol, Rosenstiel, Philip, Schreiber, Stefan, Backofen, Rolf, ...
Abstract Background Splice donor sites have a highly conserved GT or GC dinucleotide and an extended intronic consensus sequence GTRAGT that reflects the sequence complementarity to the U1 snRNA....
Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, ...
Subtle alternative splice events at tandem splice sites are frequent in eukaryotes and substantially increase the complexity of transcriptomes and proteomes. We have developed a relational database,...
tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression (2006)
Szafranski, Karol, Jahn, Niels, Platzer, Matthias
Summary: The program tuple_plot identifies and visualizes local similarities between two genomic sequences, typically 100 kb or longer, by applying the well-known dotplot principle. A dictionary of...
The Dictyosteliumgenome encodes numerous RasGEFs with multiple biological roles (2005)
Wilkins, Andrew, Szafranski, Karol, Fraser, Derek J, Bakthavatsalam, Deenadayalan, Müller, Rolf, Fisher, Paul R, ...
Abstract Background Dictyostelium discoideum is a eukaryote with a simple lifestyle and a relatively small genome whose sequence has been fully determined. It is widely used for studies on cell...
DictyMOLD-a Dictyostelium discoideum genome browser database (2005)
Felder, Marius, Szafranski, Karol, Lehmann, Rüdiger, Eichinger, Ludwig, Noegel, Angelika A., Platzer, Matthias, ...
Summary: With the Dictyostelium Genome Project nearing completion, we initiated the construction of a data repository for all Dictyostelium discoideum genomic data. Up to now this database, called...
Dictymold - a Dictyostelium discoideum genome browser database (2005)
Felder, Marius, Szafranski, Karol, Lehmann, Rüdiger, Eichinger, Ludwig, Noegel, Angelika A., Platzer, Matthias, ...
Summary: With the Dictyostelium Genome Project nearing completion, we initiated the construction of a data repository for all Dictyostelium discoideum genomic data. Up to now this database, called...
Taudien, Stefan, Galgoczy, Petra, Huse, Klaus, Reichwald, Kathrin, Schilhabel, Markus, Szafranski, Karol, ...
Abstract Background Defensins are important components of innate immunity to combat bacterial and viral infections, and can even elicit antitumor responses. Clusters of defensin (DEF) genes are...
Bmc Genomics, Stefan Taudien, Petra Galgoczy, Klaus Huse, Kathrin Reichwald, Markus Schilhabel, ...
Research article Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
Die Transposons im Genom von Dictyostelium discoideum (2003)
Im Rahmen eines Genomsequenzierungsprojekts für Dictyostelium discoideum wurde der Genomgehalt an Transposons eingehend untersucht. Laut Analyse existieren mindestens 18 Transposonspezies mit einem...
Die Transposons im Genom von Dictyostelium discoideum / (2002)
Jena, Universiẗat, Diss., 2002 (Nicht für den Austausch).
The Complex Repeats of Dictyostelium discoideum (2001)
Glöckner, Gernot, Szafranski, Karol, Winckler, Thomas, Dingermann, Theodor, Quail, Michael A., Cox, Edward, ...
The Complex Repeats of Dictyostelium discoideum (2001)
Glöckner, Gernot, Szafranski, Karol, Winckler, Thomas, Dingermann, Theodor, Quail, Michael A., Cox, Edward, ...
The Complex Repeats of Dictyostelium discoideum (2001)
Glöckner, Gernot, Szafranski, Karol, Winckler, Thomas, Dingermann, Theodor, Quail, Michael A., Cox, Edward, ...
The Complex Repeats of Dictyostelium discoideum
Glöckner, Gernot, Szafranski, Karol, Winckler, Thomas, Dingermann, Theodor, Quail, Michael A., Cox, Edward, ...
In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species....
Taudien, Stefan, Galgoczy, Petra, Huse, Klaus, Reichwald, Kathrin, Schilhabel, Markus, Szafranski, Karol, ...
The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles
Wilkins, Andrew, Szafranski, Karol, Fraser, Derek J, Bakthavatsalam, Deenadayalan, Müller, Rolf, Fisher, Paul R, ...
A survey of the Dictyostelium genome reveals at least 25 RasGEFs, all of which appear to be expressed at some point in development. Disruption of several of these novel RasGEFs reveals that many have...
Hiller, Michael, Huse, Klaus, Szafranski, Karol, Jahn, Niels, Hampe, Jochen, Schreiber, Stefan, ...
Aberrant or modified splicing patterns of genes are causative for many human diseases. Therefore, the identification of genetic variations that cause changes in the splicing pattern of a gene is...
Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?
Hiller, Michael, Szafranski, Karol, Backofen, Rolf, Platzer, Matthias
The Complex Repeats of Dictyostelium discoideum
Glöckner, Gernot, Szafranski, Karol, Winckler, Thomas, Dingermann, Theodor, Quail, Michael A., Cox, Edward, ...
In the course of determining the sequence of the Dictyostelium discoideum genome we have characterized in detail the quantity and nature of interspersed repetitive elements present in this species....
Taudien, Stefan, Galgoczy, Petra, Huse, Klaus, Reichwald, Kathrin, Schilhabel, Markus, Szafranski, Karol, ...
The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles
Wilkins, Andrew, Szafranski, Karol, Fraser, Derek J, Bakthavatsalam, Deenadayalan, Müller, Rolf, Fisher, Paul R, ...
A survey of the Dictyostelium genome reveals at least 25 RasGEFs, all of which appear to be expressed at some point in development. Disruption of several of these novel RasGEFs reveals that many have...
Hiller, Michael, Huse, Klaus, Szafranski, Karol, Jahn, Niels, Hampe, Jochen, Schreiber, Stefan, ...
Aberrant or modified splicing patterns of genes are causative for many human diseases. Therefore, the identification of genetic variations that cause changes in the splicing pattern of a gene is...
Alternative Splicing at NAGNAG Acceptors: Simply Noise or Noise and More?
Hiller, Michael, Szafranski, Karol, Backofen, Rolf, Platzer, Matthias
Phylogenetically widespread alternative splicing at unusual GYNGYN donors
Hiller, Michael, Huse, Klaus, Szafranski, Karol, Rosenstiel, Philip, Schreiber, Stefan, Backofen, Rolf, ...
Computational and experimental evidence is given for alternative splicing at the unusual GYNGYN motif in several species, enabling in most cases subtle protein variations.
TassDB: a database of alternative tandem splice sites
Hiller, Michael, Nikolajewa, Swetlana, Huse, Klaus, Szafranski, Karol, Rosenstiel, Philip, Schuster, Stefan, ...
Subtle alternative splice events at tandem splice sites are frequent in eukaryotes and substantially increase the complexity of transcriptomes and proteomes. We have developed a relational database,...
Selection against tandem splice sites affecting structured protein regions
Hiller, Michael, Szafranski, Karol, Huse, Klaus, Backofen, Rolf, Platzer, Matthias
Szafranski, Karol, Schindler, Stefanie, Taudien, Stefan, Hiller, Michael, Huse, Klaus, Jahn, Niels, ...
TG dinucleotides functioning as alternative 3' splice sites were identified and experimentally verified in 36 human genes.
Schindler, Stefanie, Szafranski, Karol, Hiller, Michael, Ali, Gul Shad, Palusa, Saiprasad G, Backofen, Rolf, ...
Comparative analysis of sequence features involved in the recognition of tandem splice sites
Bortfeldt, Ralf, Schindler, Stefanie, Szafranski, Karol, Schuster, Stefan, Holste, Dirk
Assessing the fraction of short-distance tandem splice sites under purifying selection
Hiller, Michael, Szafranski, Karol, Sinha, Rileen, Huse, Klaus, Nikolajewa, Swetlana, Rosenstiel, Philip, ...
Many alternative splice events result in subtle mRNA changes, and most of them occur at short-distance tandem donor and acceptor sites. The splicing mechanism of such tandem sites likely involves the...
Reichwald, Kathrin, Lauber, Chris, Nanda, Indrajit, Kirschner, Jeanette, Hartmann, Nils, Schories, Susanne, ...
A genomic analysis of the annual fish Nothobranchius furzeri, a vertebrate with the shortest known life span in captivity and which may provide a new model organism for aging research.
Accurate prediction of NAGNAG alternative splicing
Sinha, Rileen, Nikolajewa, Swetlana, Szafranski, Karol, Hiller, Michael, Jahn, Niels, Huse, Klaus, ...
Alternative splicing (AS) involving NAGNAG tandem acceptors is an evolutionarily widespread class of AS. Recent predictions of alternative acceptor usage reported better results for acceptors...