Current Projects
Associate Professor,
Linnaeus Centre for Bioinformatics
Uppsala University,
Uppsala, Sweden
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My researcher position is financed by a fellowship from Knut and Alice Wallenbergs foundation. A
sample of my completed and ongoing projects while at LCB are given below: |
Efficient methods for QTL mapping:
We develop general, high-precision methods for detection of genes
underlying multifactorial traits. The aim is to extract knowledge of interactions
between multiple genes and present the results in an intuitive way. We have earlier proposed a number of efficient algorithms for mapping QTL
using fixed-effect genetic models. Our main focus at present is, however, on
random-effect (“variance-component”) methods. Funded by a grant from FORMAS, Lars Rönnegård is working as a
Post-Doc focusing on developing new variance component models for QTL mapping
in experimental populations. Funded by the LCB and Ulf Gyllensten
at the Department of Genetics and Pathology, Francois Besnier is developing
efficient methods for estimation of IBD-matrices for use in QTL mapping. |
New genetic models for epistasis
We develop new genetic
models for detection of genes underlying complex traits. The aim is to
propose models for obtaining high power as well as consistent and
biologically relevant estimates of marginal and interaction effects in
epistatic QTL analyses. This work is funded by the LCB, has resulted in a new
combined statistical and functional model for epistasis (the NOIA-model) and
is the main focus of Jose Alvarez-Castro’s Post-Doc project.
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Mapping of QTL in Experimental
Populations:
We are always interested in applying our methods to experimental data.
Both in order to evaluate their properties when they are developed, but also
to explore the genetic background of agriculturally, medically and
evolutionary interesting traits. Examples of current collaborations include
work on metabolic and disease traits in several experimental populations of
domestic animals from the group of Leif
Andersson at the Department of Medical Biochemistry and Microbiology,
Uppsala University, on the genetics underlying heterosis in Maize with
Jianbing Yan and colleagues at the National Maize Improvement Center of
China, China Agricultural University, Beijing and studying the genetics
underlying behavior with the group of Roger Butlin at University of Leeds.
For these analyses, we use high performance computing resources from UPPMAX in Uppsala and the National Supercomputing Center in Linköping,
Sweden. |
Numerical methods in QTL mapping:
We will develop, implement and evaluate new numerical methods for variance
component mapping of QTL. The proposed methods will improve the numerical stability
and efficiency of variance component estimation methods needed in QTL
mapping. These improvements will allow numerically efficient,
multi-dimensional searches for interacting QTL using variance component based
methods. The project is performed in collaboration with Kateryna Mishchenko and Sverker Holmgren at the Department
of Information Technology at Uppsala University, Sweden. |
Computational methods in QTL mapping:
We implement and
evaluate new parallelization paradigms for use in genetic analyses of complex
traits. The aim is to identify the most appropriate computer platform for
performing these analyses, both in terms of throughput and cost efficiency. The project is performed in collaboration with Mahen Jayawardena and Sverker Holmgren at the Department
of Information Technology at Uppsala University, Sweden.
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Implications of genetic architecture in
QTL mapping and evolution:
We explore the implications of various
genetic architectures involving epistasis on complex trait phenotypic
evolution. In a Post-Doc project funded by FORMAS,
Arnaud le Rouzic is exploring how network architectures affect the dynamics
and plasticity of phenotypic evolution under various types of selection.
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Theoretical studies of link between
biological and statistical epistasis:
We explore the relationship between
biological genetic interactions in gene regulatory networks and their
statistical signature in QTL mapping studies. This work is a collaboration
with Arne Gjuvsland and Stig
Omholt at Cigene, Norway.
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Latest update: 06/07/28 07:41