Mika Gustafsson,

Ph. d. student in Applied Mathematical Physics

ITN, Linköpings universitet

Contents

Short presentation

I work as a Ph. D. student at the Department of Science and Technology (ITN), Linköping University/ Campus Norrköping, Sweden with Michael Hörnquist and Jesper Tegner as supervisors. My main research interest regards computational systems biology.

Personal

My Master thesis in theoretical physics at Linköping University is titled "Coherent waves in DNA within the Peyrard-Bishop model" and is about mobility of nonlinear coherent waves in a heterogenous extension to the Peyrard-Bishop model of DNA dynamics.
I have also done a master thesis in mathematics at the mathematics departement at the Stockholm University, which is about game theory with the particular example of simplified poker problems. It is mainly written in swedish (apart from an abstract) and is called "Spelteori: En studie av hur pokerproblemet delvis lösts".

Research

My main project has been focused on genetic networks. The primary goal has been to see what can be learned from inferred linear genetic networks on a genomic-scale, i.e., assuming a linear relationship between the gene activity and gene expression levels. The project has resulted in one accepted paper in IEEE/ACM Transactions on Computational Biology and Bioinformatics together with Michael Hörnquist and Anna Lombardi.

We also have one paper in manuscript together with Jesper Tegner, and some posters presented as some conferences (ICSB 2003, Reglermöte 2004, Bioinformatics 2004 and Complex Systems 2004, and DIMACS 2005). Another ongoing project is to study topological properties of existing networks. In a project (in manuscript) together with MH and AL we investigate some properties of communities (dense subgraphs). Another key interest is to investigate whether communities in biological networks are linked to functional modules, i.e., robust gene sets that fulfil a specific function.

Publications

Conference contributions:

· Outdegrees, motifs and modules in a gene-to-gene regulatory network at DIMACS workshop 2005 in New Jersey (poster)

· Community structure in gene-to-gene networks at Bioinformatics 2004 in Linköping (poster)

· Combination of gene clustering enhances biological validity at Reglermöte 2004 in Göteborg (paper and poster)

· Large-scale reverse engineering by the Lasso, poster at ICSB03 in St. Louis (abstract and poster)

Papers:

· Constructing and analyzing a large-scale gene-to-gene regulatory network – LASSO-constrained inference and biological validation (with Michael Hörnquist and Anna Lombardi). Accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Comparison and validation of community structures in complex networks (with Michael Hörnquist and Anna Lombardi). Submitted to Physica A.

Presentations:

Gene network dynamics in yeast; communities (motifs) and hubs. Presented at the 6^th Swedish Bioinformatics Workshop (SBW2005), November 2005.
Coherence of network modules in the Internet. Presented at the internal ITN conference August 2005.
Biological analysis of LASSO inferred network. Presented at a lab. meeting at IFM for the Computational biology group in April 2005.
Biological validation of a large-scale reconstructed network. Presented at a lab. meeting at IFM for the Computational biology group in April 2004.
Large-scale Reverse Engineering by the LASSO. Presented at the workshop Cellular networks in Norrköping in December 2003.

Location:    Department of Science and Technology
                   Linköpings universitet, Campus Norrköping
                   S-601 74 Norrköping
                   Sweden

Office:         Spetsen 5202

Phone:        +46 11 363464

E-mail:          mikgu@itn.liu.se