Xenopus Laevis, Alexander Sczyrba, Ag Praktische Informatik, ...
am 30.03.2007 verteidigt und genehmigt.
Distinguishing isoforms and paralogs on the protein level (2008)
Bmc Bioinformatics, Michael Spitzer, Stefan Lorkowski, Paul Cullen, Er Sczyrba, Georg Fuellen, ...
Research article
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI (2008)
Lamprecht, Anna-Lena, Margaria, Tiziana, Steffen, Bernhard, Sczyrba, Alexander, Hartmeier, Sven, Giegerich, Robert
Abstract Background PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using...
Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server (2008)
Sczyrba, Alexander, Konermann, Susanne, Giegerich, Robert
Conferences in computational biology continue to provide tutorials on classical and new methods in the field. This can be taken as an indicator that education is still a bottleneck in our field's...
IsoSVM – Distinguishing isoforms and paralogs on the protein level (2006)
Spitzer, Michael, Lorkowski, Stefan, Cullen, Paul, Sczyrba, Alexander, Fuellen, Georg
Abstract Background Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein...
Collections of Expressed Sequence Tags (ESTs) provide the most extensive available survey of the transcriptome of an organism and with it evidence for the existence of genes. They are indispensable...
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis (2005)
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H, Giegerich, Robert, Altmann, Curtis R
Abstract Background Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts...
Genlight: Interactive high-throughput sequence analysis and comparative genomics (2004)
Beckstette, Michael, Mailänder, Jens T., Marhöfer, Richard J., Sczyrba, Alexander, Ohlebusch, Enno, Giegerich, Robert, ...
With rising numbers of fully sequenced genomes the importance of comparative genomics is constantly increasing. Although several software systems for genome comparison analyses do exist, their...
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, Giegerich, Robert
e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable...
AGenDA: gene prediction by cross-species sequence comparison (2004)
Taher, Leila, Rinner, Oliver, Garg, Saurabh, Sczyrba, Alexander, Morgenstern, Burkhard
Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By...
AltAVisT: Comparing alternative multiple sequence alignments (2003)
Morgenstern, Burkhard, Goel, Sachin, Sczyrba, Alexander, Dress, Andreas
Summary: We introduce a WWW-based tool that is able to compare two alternative multiple alignments of a given sequence set. Regions where both alignments coincide are color-coded to visualize the...
RNA-related tools on the Bielefeld Bioinformatics Server (2003)
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, Giegerich, Robert
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, ...
Article may be found at: http://www.nature.com/ng/journal/v27/n3/pdf/ng0301_337.pdf
Gopal, Shuba, Schroeder, Mark, Pieper, Ursula, Sczyrba, Alexander, Aytekin-Kurban, Gulriz, Bekiranov, Stefan, ...
Article may be found at: http://www.nature.com/ng/journal/v27/n3/pdf/ng0301_337.pdf
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region (2000)
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
RNA-related tools on the Bielefeld Bioinformatics Server
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, Giegerich, Robert
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
Our challenge in annotating the 2.91-Mb Adh region of the Drosophila melanogaster genome was to identify genetic and genomic features automatically, completely, and precisely within a 6-week period....
AGenDA: gene prediction by cross-species sequence comparison
Taher, Leila, Rinner, Oliver, Garg, Saurabh, Sczyrba, Alexander, Morgenstern, Burkhard
Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By...
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, Giegerich, Robert
e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable...
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H, Giegerich, Robert, Altmann, Curtis R
IsoSVM – Distinguishing isoforms and paralogs on the protein level
Spitzer, Michael, Lorkowski, Stefan, Cullen, Paul, Sczyrba, Alexander, Fuellen, Georg
RNA-related tools on the Bielefeld Bioinformatics Server
Sczyrba, Alexander, Krüger, Jan, Mersch, Henning, Kurtz, Stefan, Giegerich, Robert
We present four tools for the analysis of RNA secondary structure. They provide animated visualization of multiple structures, prediction of potential conformational switching, structure comparison...
MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region
Gaasterland, Terry, Sczyrba, Alexander, Thomas, Elizabeth, Aytekin-Kurban, Gulriz, Gordon, Paul, Sensen, Christoph W.
Our challenge in annotating the 2.91-Mb Adh region of the Drosophila melanogaster genome was to identify genetic and genomic features automatically, completely, and precisely within a 6-week period....
AGenDA: gene prediction by cross-species sequence comparison
Taher, Leila, Rinner, Oliver, Garg, Saurabh, Sczyrba, Alexander, Morgenstern, Burkhard
Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By...
Krüger, Jan, Sczyrba, Alexander, Kurtz, Stefan, Giegerich, Robert
e2g is a web-based server which efficiently maps large expressed sequence tag (EST) and cDNA datasets to genomic DNA. It significantly extends the volume of data that can be mapped in reasonable...
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba, Alexander, Beckstette, Michael, Brivanlou, Ali H, Giegerich, Robert, Altmann, Curtis R