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Classification of expression profiles to predict disease characteristics of for example cancer is a common application in high-throughput gene and protein expression research. Cross-validation is often used to optimize design of classifiers, with the aim to construct an optimal single classifier. In this work, we explore if classification performance can be improved by aggregating classifiers into

Unraveling functional and ancestral relationships between proteins as well as structure-prediction procedures require powerful protein-alignment methods. A structure-alignment method is presented where the problem is mapped onto a cost function containing both fuzzy (Potts) assignment variables and atomic coordinates. The cost function is minimized by using an iterative scheme, where at each step

Meristems continually supply new cells for post-embryonic plant development and coordinate the initiation of new organs, such as leaves and flowers. Meristem function is regulated by a large and interconnected dynamic system that includes transcription networks, intercellular protein signalling, polarized transport of hormones and a constantly changing cellular topology. Mathematical modelling, in

Morphogenesis during multicellular development is regulated by intercellular signaling molecules as well as by the mechanical properties of individual cells. In particular, normal patterns of organogenesis in plants require coordination between growth direction and growth magnitude. How this is achieved remains unclear. Here we show that in Arabidopsis thaliana, auxin patterning and cellular growt

Many small proteins fold in a two-state manner, the rate-limiting step being the passage of the free-energy barrier separating the unfolded state from the native one. The free-energy barrier is, however, weak or absent for the fastest-folding proteins. Here a simple diffusion picture for such proteins is discussed. It is tested on a model protein that makes a three-helix bundle. Assuming the motio

Pharmacogenomics is the application of genomic technologies to drug discovery and development, as well as for the elucidation of the mechanisms of drug action on cells and organisms. DNA microarrays measure genome-wide gene expression patterns and are an important tool for pharmacogenomic applications, such as the identification of molecular targets for drugs, toxicological studies and molecular d

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

We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described

Tack vare kikare, teleskop och spektroskop har vi kunnat blicka längre ut i Universum än som någonsin hade varit möjligt med bara ögonen. På samma sätt finns det ett helt Universum åt andra hållet. Bland celler, molekyler, ände ner till atomer. Men nere i atomvärlden är det inte teleskop som behövs. Nej, där tar vi hjälp av de fiffiga små neutronerna själva.Thanks to binoculars, telescopes and spectroscopes, we have been able to look further out into the Universe than would ever have been possible with the naked eye. In the same way, there is a whole Universe in the other direction. Among cells, molecules, and down to atoms. But down in the nuclear world, telescopes are not needed. No, there we take the help of the small neutrons themselves.

The enlargement of the EU towards the CEE pointed and leaned towards democratization. Two of the countries that were on the path of democratization was the Czech Republic and Hungary. However, as time has gone by Czech Republic and Hungary that once were on the path of democratization has now suffered a Democratic Backslide. Czech Republic with Andrej Babiš as Prime Minister followed by Viktor Orb

In this thesis, the consequences of extending the internal symmetries of the standard model with a complex singlet scalar field, are investigated in terms of dark matter phenomenology and the possibility of primordial gravitational wave detection utilizing space based laser interferometry. The scalar potential of the model is constructed with a Z2 symmetry, which allows for the retainment of a lin

In this study, inspired by the work of Nakazato and Kitahara (1980 Prog. Theor. Phys. 64 2261), we consider the theoretical problem of tracer particle diffusion in an environment of diffusing hardcore interacting crowder particles. The tracer particle has a different diffusion constant from the crowder particles. Based on a transformation of the generating function, we provide an exact formal expa

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore ap

A method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional probabilities rather than minimizing energy functions, is based upon a different and very efficient multisequence Monte Carlo scheme. By construction, the method ensures that the

Folding properties of a two-dimensional toy protein model containing only two amino acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entir

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