Bioinformatics in Quantitative Biology
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Dr. Christoph Dieterich
87: Timoféeff-Ressovsky-Haus (Genomzentrum)
Raum: 1.11
Tel. 9406-4235
Bioinformatics in Quantitative Biology
Emerging technologies in nucleic acids sequencing, mass spectrometry and imaging revolutionise the field of Systems Biology. For the first time, a holistic quantification of biological systems at the level of genes, mRNAs, proteins and metabolites is in reach. We develop computational methods and analysis strategies to exploit these data sources for a better understanding of biological systems.
Biological Systems are defined by components, component interactions and dynamics thereof. Current and feature projects concentrate on identifying components, predicting interactions and studying system dynamics in an evolutionary context.
Projects
Motifs, Modules and Long-range interactions in Gene regulation
The readout of a static genome is directly regulated by interactions of proteins and nucleic acids (DNA / RNA). We work on defining sequence motifs and on generic sequence segmentation methods to identify factor binding sites by integrating signals such as sequence conservation, chromatin state and motif descriptions. We also support experimentalists by software tools (e.g. for chromosome conformation capture experiments)
Dieterich, C. et al. (2002), 'Annotating regulatory DNA based on man-mouse genomic comparison.', Bioinformatics 18 Suppl 2, S84—S90.
Dieterich, C. & Sommer, R. J. (2008), 'A Caenorhabditis motif compendium for studying transcriptional gene regulation.', BMC Genomics 9, 30.
Fröhler, S. & Dieterich, C. (2009), '3PD: Rapid design of optimal primers for chromosome conformation capture assays.', BMC Genomics 10(1), 635.
Nematode Omics – The Evolution of Parasitism
We would like to understand how changes in gene content, gene sequence and gene regulation lead to the emergence of evolutionary novelties. Nematodes are ideal to study the impact of the aforementioned changes. Comparative analyses of ecologically diverse nematodes are beginning to reveal molecular mechanisms by which parasites arise and how they evolve.
Dieterich, C. et al. (2008), 'The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism.', Nat Genet 40(10), 1193—1198.
Dieterich, C. & Sommer, R. J. (2009), 'How to become a parasite - lessons from the genomes of nematodes.', Trends Genet 25(5), 203--209.
Gene Order Evolution
Whole genome gene order evolution in metazoans was initially considered as a random process. This view had to be revised in the light of results from sequencing dozens of metazoan genomes. We develop gene order alignment software, to identify genomic regions of conserved synteny over large sets of diverging species. We also try to reconstruct the evolutionary history of genome rearrangement events.
Rödelsperger, C. & Dieterich, C. (2008), 'Syntenator: Multiple gene order alignments with a gene-specific scoring function.', Algorithms Mol Biol 3, 14.
Rödelsperger, C. & Dieterich, C. (2010), 'CYNTENATOR: Progressive gene order alignment of 17 vertebrate genomes.', PLOS ONE accepted