Biomedical subjects

Malte J Rasch

Publications and source records attributed to Malte J Rasch.

3 recordsLinked to original sources

PubMed2006

Integrating structured biological data by Kernel Maximum Mean Discrepancy.

MOTIVATION: Many problems in data integration in bioinformatics can be posed as one common question: Are two sets of observations generated by the same distribution? We propose a kernel-based statistical test for this problem, based on the fact that two distributions are different if and only if there exists at least one function having different expectation on the two distributions. Consequently we use the maximum discrepancy between function means as the basis of a test statistic. The Maximum Mean Discrepancy (MMD) can take advantage of the kernel trick, which allows us to apply it not only to vectors, but strings, sequences, graphs, and other common structured data types arising in molecular biology. RESULTS: We study the practical feasibility of an MMD-based test on three central data integration tasks: Testing cross-platform comparability of microarray data, cancer diagnosis, and data-content based schema matching for two different protein function classification schemas. In all of these experiments, including high-dimensional ones, MMD is very accurate in finding samples that were generated from the same distribution, and outperforms its best competitors. CONCLUSIONS: We have defined a novel statistical test of whether two samples are from the same distribution, compatible with both multivariate and structured data, that is fast, easy to implement, and works well, as confirmed by our experiments. AVAILABILITY: http://www.dbs.ifi.lmu.de/~borgward/MMD.

Algorithms↗

PubMed2006

A functional hypothesis for adult hippocampal neurogenesis: avoidance of catastrophic interference in the dentate gyrus.

The dentate gyrus is part of the hippocampal memory system and special in that it generates new neurons throughout life. Here we discuss the question of what the functional role of these new neurons might be. Our hypothesis is that they help the dentate gyrus to avoid the problem of catastrophic interference when adapting to new environments. We assume that old neurons are rather stable and preserve an optimal encoding learned for known environments while new neurons are plastic to adapt to those features that are qualitatively new in a new environment. A simple network simulation demonstrates that adding new plastic neurons is indeed a successful strategy for adaptation without catastrophic interference.

Adaptation, Physiological↗

PubMed2005

On the kinetic design of transcription.

We analyse a stochastic model of transcription that describes transcription initiation by promoter activation and subsequent polymerase recruitment. Explicit expressions are derived for the control of an activator on the mean mRNA number and for the mRNA noise. Both properties are strongly influenced by the kinetics of promoter activation, mRNA synthesis and degradation. Low transcriptional noise is obtained either when the transcription initiation complex has a long life-time or when its components associate and dissociate rapidly. However, the ability of an activator to regulate the mRNA level is low in the first and high in the second case. Large noise is generated when the initial activation step of the promoter is slow. In this case, transcription can be burst-like; the mRNA distribution becomes bimodal while regulability of the mean copy number is maintained.

DNA-Directed RNA Polymerases↗