- SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elementsBritta Mersch
Department of Molecular Biophysics, German Cancer Research Center DKFZ, Heidelberg, Germany
BMC Genet 8:78. 2007..Thus, exonizations can have negative effects for the transcriptome of an organism...
- Evolutionary optimization of sequence kernels for detection of bacterial gene startsBritta Mersch
Abteilung Molekulare Biophysik, German Cancer Research Center, 69120 Heidelberg, Germany
Int J Neural Syst 17:369-81. 2007..The resulting kernels lead to higher classification rates, and the adapted parameters reveal the importance of particular triplets for classification, for example of those occurring in the Shine-Dalgarno Sequence...
- Automatic detection of exonic splicing enhancers (ESEs) using SVMsBritta Mersch
Department of Molecular Biophysics, German Cancer Research Center DKFZ, Im Neuenheimer Feld 580, Heidelberg, Germany
BMC Bioinformatics 9:369. 2008..Identifying SR protein-binding sites in human DNA sequences by machine learning techniques is a formidable task, since the exon sequences are also constrained by their functional role in coding for proteins...
- Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptomeNoa Sela
Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
Genome Biol 8:R127. 2007..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 and the mouse transcriptome...
- Gradient-based optimization of kernel-target alignment for sequence kernels applied to bacterial gene start detectionChristian Igel
Institut fur Neuroinformatik, Ruhr Universitat Bochum, Bochum, Germany
IEEE/ACM Trans Comput Biol Bioinform 4:216-26. 2007..The power of this new, general model selection procedure and the benefits of fitting kernels to problem classes are demonstrated by adapting oligo kernels for bacterial gene start detection...