Previous Projects
Post-Doc
Roslin Institute, Roslin, Scotland.
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The project is financed by a post-doctoral fellowship from Knut and Alice Wallenbergs foundation. I am
involved in several subprojects during my time at Roslin Institute. |
Mapping of epistatic QTL in Experimental Populations:We reanalyzed data from several QTL mapping projects managed by Paul
Hocking and Dave Burt at Roslin Institute, Gudrun Brockmann at FBN in Germany
and Robert W Williams
at University of Tennessee. The work was done to evaluate the importance of
epistasis in regulating a wide range of mult-factorial traits. For these
analyses, we used an SGI Origin 3000 supercomputer at CSAR. |
Efficient numerical methods for multi-dimensional genome-scans:The project implemented and evaluated new numerical methods for mapping of
multiple QTL. The methods were shown to improve the power of QTL mapping by,
in a numerically efficient way, perform multidimensional searches for QTL in
the genome. The project was conducted in collaboration with Kajsa Ljungberg and Sverker Holmgren at the Department
of Information Technology at Uppsala University, Sweden. |
Methodology for dissecting the genetic regulation of gene-expression:In this project, we explored the properties of statistical methods used for dissection of the genetic regulation of gene-expression (“Genetical Genomics”). We used experimental data from the first publicly available dataset of this kind as well as simulated data to evaluate existing methods and propose new analytical strategies for this. |
PhD Student
Dept
of Animal Breeding and Genetics, SLU, Uppsala, Sweden.
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My thesis presents and discusses the use
of various genetic models, high performance computing, global optimization
algorithms and statistical methods for mapping Quantitative Trait Loci (QTL).
The aim of the work was to develop statistically powerful and computationally
efficient methods to detect genomic loci affecting multifactorial traits, and
use the methods use to analyse experimental data. Imprinting is an epigenetic phenomena which causes differential expression
of alleles based on their parental origin. A genetic model handling
imprinting was used during QTL mapping in an experimental Wild Boar x Large
White intercross. The analyses revealed a paternally imprinted QTL with large
effect on the development of muscle mass [1]. Parallel computing algorithms for interval mapping and randomization
testing in QTL mapping are described. New randomization testing schemes are
now computationally feasible due to these algorithms. Selection of
appropriate kernel algorithms for solving least squares type problems in QTL
mapping is discussed. The importance of optimization of QTL mapping software
is also illustrated [2]. A genetic algorithm was shown to be efficient in a multidimensional search
for interacting QTL. The genetic algorithm significantly decreases the
computational demand when employing simultaneous mapping of multiple QTL, and
makes randomization testing based on multidimensional searches
computationally feasible [3]. A new randomization testing
scheme based on simultaneous mapping of epistatic QTL was also proposed and
evaluated. A simulation study showed that the method increases the power to
detect epistatic QTL [4]. A large intercross was derived between Red junglefowl and White Leghorn
chickens. A number of QTL affecting growth was revealed using the newly
developed method for simultaneous mapping of epistatic QTL pairs. In total,
21 QTL were identified, and eleven of these were only detected by the new simultaneous
mapping method. Epistasis was shown to be an important component in the
genetic regulation of the growth process [5], [6]. |
Latest update: 03/07/02 14:45