Sökresultat

A general method is discussed, the δ-test, which establishes functional dependencies given a table of measurements. The approach is based on calculating conditional probabilities from data densities. Imposing the requirement of continuity of the underlying function the obtained values of the conditional probabilities carry information on the variable dependencies. The power of the method is illust

This talk presents some results relevant for lattice QCD at higher order in ChPT. First we discuss the finite volume corrections at two loops for the quark condensate as well as a Luscherlike finite volume formula for it. The latter allows for an alternative determination of meson sigma terms. The second set of results presented here are the calculations at two loops in partially quenched chiral p

The mechanisms of protein folding and aggregation are investigated by computer simulations of all-atom and reduced models with sequence-based potentials. A quasi local Monte Carlo update is developed in order to efficiently sample proteins in the folded phase. A small helical protein, the B-domain of staphylococcal protein A, is studied using a reduced model. In the thermodynamically favoured topo

High-throughput technologies have led to an explosion in the availability of data at the genome scale. Such data provide important information about cellular processes and causes of human diseases, as well as for drug discovery. Deciphering the biologically relevant results from these data requires comprehensive analytical methods. In this dissertation, we present methods for gene and protein expr

Background Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microarrays in the context of such pathways. Results We use pathways compiled from the TRANSPATH/TRANSFAC databases and the literature, and three publicly available cancer microarray da

Background. Recent studies have associated the transcription factors, Oct4, Sox2 and Nanog as parts of a self-regulating network which is responsible for maintaining embryonic stem cell properties -- self renewal and pluripotency. In addition, mutual antagonism between two of these and other master regulators have been shown to regulate lineage determination. In particular, an excess of Cdx2 over

Possible consequences of the production of small black holes at the LHC for different scenarios with large extra dimensions are investigated. The effects from black hole production on some standard jet observables are examined, concentrating on the reduction of the QCD cross section. It is found that black hole production of partons interacting on a short enough distance indeed seem to generate a

We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein modifications. The method's focus is to globally detect mass differences, not to assign peptide sequences or modifications to individual spectra. The Mass Distance Fingerprint is calculated from high accuracy measured peptide masses. For the da

The authors studied the temperature-induced unfolding of ubiquitin by all-atom Monte Carlo simulations. The unfolding behavior is compared with that seen in previous simulations of the mechanical unfolding of this protein, based on the same model. In mechanical unfolding, secondary-structure elements were found to break in a quite well-defined order. In thermal unfolding, the authors saw somewhat

We demonstrate how to generalize two of the most well-known random graph models, the classic random graph, and random graphs with a given degree distribution, by the introduction of hidden variables in the form of extra degrees of freedom, color, applied to vertices or stubs (half-edges). The color is assumed unobservable, but is allowed to affect edge probabilities. This serves as a convenient me

The majority of microarray studies focus on analysis of gene expression differences between various specimens or conditions. However, the causes of this variability from one cancer to another, from one sample to another and from one gene to another often remain unknown. In this study, we present a systematic procedure for finding genes whose expression levels are altered due to an intrinsic or ext