Brendan Osberg

Max Planck Institute for Molecular Genetics | MOLGEN

DNA methylation-based classification of brain tumors has emerged as a powerful and indispensable diagnostic technique. Initial implementations have used methylation microarrays for data generation, but different sequencing approaches are increasingly used. Most current classifiers, however, rely on a fixed methylation feature space, rendering them...

Acute coronary syndrome (ACS) remains a major cause of worldwide mortality. The syndrome occurs when blood flow to the heart muscle is decreased or blocked, causing muscle tissues to die or malfunction. There are three main types of ACS: Non-ST-elevation myocardial infarction, ST-elevation myocardial infarction, and unstable angina. The treatment d...

In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between differe...

In bioinformatics, as well as other computationally intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between differe...

In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or f...

Adsorption-desorption processes are ubiquitous in physics, chemistry, and biology. Models usually assume hard particles, but within the realm of soft matter physics the adsorbing particles are compressible. A minimal 1D model reveals that softness fundamentally changes the kinetics: Below the desorption time scale, a logarithmic increase of the par...

The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches hi...

Recent genome-wide maps of nucleosome positions in different eukaryotes revealed patterns around transcription start sites featuring a nucleosome-free region flanked by a periodic modulation of the nucleosome density. For Saccharomyces cerevisiae, the average in vivo pattern was previously shown to be quantitatively described by a "nucleosome gas"...

Nucleosome positioning along DNA is neither random nor precisely regular. Genome-wide maps of nucleosome positions in various eukaryotes have revealed a common pattern around transcription start sites, involving a nucleosome-free region flanked by a periodic pattern in the average nucleosome density. We take a quantitative mathematical description...

Recent genome-wide maps of nucleosome positions in different eukaryotes have revealed a common pattern around transcription start sites, involving a nucleosome-free region flanked by a pronounced periodic pattern in the average nucleosome density. For the yeast S. cerevisiae, a gas of hard rods, known as Tonks gas and equivalent to the statistical...

Carbon dioxide and nitrous oxide are investigated at pressures up to 50 GPa and 1000 K using ab initio methods. In this pressure-temperature range, both materials have a number of stable molecular structures. We demonstrate that the constituent molecules in these structures do not undergo significant changes and that the proposed phases are consist...

Recently, several methods have been proposed for measuring the magnetic fields produced by weak electric currents using magnetic resonance imaging (MRI), including a theoretically described technique for source localization of current dipoles using signal phase. We have investigated whether these results can be replicated experimentally using 4.0 T...

In this essay I explore two arguments against commercial surrogacy, based on commodification and exploitation respectively. I adopt a consequentialist framework and argue that commodification arguments must be grounded in a resultant harm to either child or surrogate, and that a priori arguments which condemn the practice for puritanical reasons ca...

The phase diagram of nitrous oxide (N2O) is investigated up to 50 GPa and 1000 K using first principles theory. The calculated stability and properties of numerous crystalline structures are compared with experimental results. We identify the structure of phase II of N2O. On the basis of its stability with respect to orthorhombic deformations, an e...