Jakob Skou Pedersen

Assistant professor at the Bioinformatics Center at Copenhagen University. Also affiliated with The Center for Comparative Genomics at University of Copenahagen.

Contact

Mail: jsp-at-binf.ku.dk
Phone: (+45) 3532 1248

Postal address:
The Bioinformatics Centre
Department of Molecular Biology
University of Copenhagen
Ole Maaloes Vej 5
2200 Copenhagen N
Denmark

Education

2004: Ph.D., Univiersity of Aarhus, Denmark
2001: M.Sc., Univiersity of Aarhus, Denmark

Career

2007-: Assistant professor, Department of Molecular Biology, University of Copenhagen
2004-2007: Post Doc., University of California, Santa Cruz

Reseach

Structural RNA identification The conserved elements of the human genome are anlyzed for substitution patterns consistent with selection for functional RNA structure. An SCFG is used to propose secondary structures and a pair of phylogenetic models are used to separately evaluate the substitution pattern in base-paired and in unpaired regions. Figure from Pedersen et al. 2006 PLoS comp. Bio..

My reseach focuses on the development and application of comparative genomics methods based on sound models of the evolutionary pocess. A main goal of my work is therefore to better understand how different selection constraints shape the evolutinary process along the genomic sequence. Based on this, I seek to develop tractable mathematical models of the evolutionary process, which form the basis for comparative analysis methods.

Recent projects include:

• The development of comparative identification methods for protein-coding genes as well as for structural RNAs.
• Genome-wide screens for structural RNAs in vertebrates and for several consortium projects (ENCODE and Drosophila).
• Case studies of specific structural RNA predictions, which have led to exciting discoveries with experimental collaborators (e.g., HAR1 and A-to-I editing of GABRA3).

Teaching

Each third quartor I teach a couse in "Phylogenetics and Comparative Genomics" as part of the Master's Program in Bioinformatics. The course is open for everybody with a natural science degree at the bachelor level.

Publications

My publications from pubmed

Links

EvoFold program and predictions vertebrate structural RNAs
EvoFold predictions in the ENCODE regions of the human genome
EvoGene program