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MOTIVATION Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically(More)
LitInspector is a literature search tool providing gene and signal transduction pathway mining within NCBI's PubMed database. The automatic gene recognition and color coding increases the readability of abstracts and significantly speeds up literature research. A main challenge in gene recognition is the resolution of homonyms and rejection of identical(More)
Genome-based prediction of genetic values is expected to overcome shortcomings that limit the application of QTL mapping and marker-assisted selection in plant breeding. Our goal was to study the genome-based prediction of test cross performance with genetic effects that were estimated using genotypes from the preceding breeding cycle. In particular, our(More)
Rapid and uniform seed germination is a crucial prerequisite for crop establishment and high yield levels in crop production. A disclosure of genetic factors contributing to adequate seed vigor would help to further increase yield potential and stability. Here we carried out a genome-wide association study in order to define genomic regions influencing seed(More)
S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct submissions is also available. S/MARt(More)
BACKGROUND The importance of maize for human and animal nutrition, but also as a source for bio-energy is rapidly increasing. Maize yield is a quantitative trait controlled by many genes with small effects, spread throughout the genome. The precise location of the genes and the identity of the gene networks underlying maize grain yield is unknown. The(More)
Ridge regression with heteroscedastic marker variances provides an alternative to Bayesian genome-wide prediction methods. Our objectives were to suggest new methods to determine marker-specific shrinkage factors for heteroscedastic ridge regression and to investigate their properties with respect to computational efficiency and accuracy of estimated(More)
The performance of hybrids can be predicted with gene expression data from their parental inbred lines. Implementing such prediction approaches in breeding programs promises to increase the efficiency of hybrid breeding. The objectives of our study were to compare the accuracy of prediction models employing multiple linear regression (MLR), partial least(More)
Introgression libraries are valuable resources for QTL detection and breeding, but their development is costly and time-consuming. Selection strategies for the development of introgression populations with a limited number of individuals and high-throughput (HT) marker assays are required. The objectives of our simulation study were to design and compare(More)
Introgression libraries can be used to make favorable genetic variation of exotic donor genotypes available in the genetic background of elite breeding material. Our objective was to employ a combination of the Dunnett test and a linear model analysis to identify favorable donor alleles in introgression lines (ILs) that carry long or multiple donor(More)