13 Result(s)

Article

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention

Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in ge...

Fabian Hausmann, Stefan Kurtz in Algorithms for Molecular Biology (2021)

Article

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research

A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obta...

Malte Mader, Ronald Simon, Stefan Kurtz in Journal of Clinical Bioinformatics (2014)

Article

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structu...

Fernando Meyer, Stefan Kurtz, Michael Beckstette in BMC Bioinformatics (2013)

Article

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction ...

Giorgio Gonnella, Stefan Kurtz in BMC Bioinformatics (2012)

Article

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarr...

Malte Mader, Ronald Simon, Sascha Steinbiss… in Journal of Clinical Bioinformatics (2011)

Article

Structator: fast index-based search for RNA sequence-structure patterns

The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence...

Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will… in BMC Bioinformatics (2011)

Article

CoCoNUT: an efficient system for the comparison and analysis of genomes

Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and so...

Mohamed I Abouelhoda, Stefan Kurtz, Enno Ohlebusch in BMC Bioinformatics (2008)

Article

Efficient computation of absent words in genomic sequences

Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are ma...

Julia Herold, Stefan Kurtz, Robert Giegerich in BMC Bioinformatics (2008)

Article

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic g...

David Ellinghaus, Stefan Kurtz, Ute Willhoeft in BMC Bioinformatics (2008)

Article

Optimising oligonucleotide array design for ChIP-on-chip

Fiona Nielsen, Stefan Graef, **nmin Zhang, Stefan Kurtz… in BMC Bioinformatics (2007)

Article

Fast index based algorithms and software for matching position specific scoring matrices

In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes ...

Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz in BMC Bioinformatics (2006)

Article

Versatile and open software for comparing large genomes

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provi...

Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot… in Genome Biology (2004)

Article

Comparative genomics of Arabidopsisand maize: prospects and limitations

The completed Arabidopsis genome seems to be of limited value as a model for maize genomics. In addition to the expansion of repetitive sequences in maize and the lack of genomic micro-colinearity, maize-specific...

Volker Brendel, Stefan Kurtz, Virginia Walbot in Genome Biology (2002)