Utz Pape

New Website:

Research Interests:

• DNA Motifs: Statistics for DNA Motifs: enrichment, co-occurences, similarity, clustering, and modules. See our website MoSta for solutions of some of these problems.
• Word Counting Approaches: Since many statistics of DNA motifs can be transformed to word counting problems, understanding and extending existing approaches is crucial.

Publications:

• Statistical detection of co-operative transcription factors with similarity adjustment
  Utz J. Pape, Holger Klein and Martin Vingron
  In Beyer, A., Schroeder, M. (eds), Lecture Notes in Informatics: Proc. of German Conference on Bioinformatics (GCB), 2008, 96-105,
  and accepted by Bioinformatics, 2009. [Try the approach online]
• Statistics for Transcription Factor Binding Sites
  PhD Thesis at the Max-Planck-Institute for Molecular Genetics, Free University of Berlin and the International Max-Planck Research School, 2008.
• Statistics for Co-Occurrence of DNA Motifs
  Utz J. Pape and Martin Vingron
  In Chiquet, J., Glaz, J., Limnios, N., Moyal, P. (eds), Proc. of the International Workshop for Applied Probability (IWAP), 2008.
• Compound Poisson approximation of DNA motif counts on both strands
  Utz J. Pape, Sven Rahmann, Fengzhu Sun and Martin Vingron
  Journal of Computational Biology, 2008, 15 (6).
• Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes
  M. Toenjes, M. Schueler, S. Hammer, U.J. Pape, J.J. Fischer, F. Berger, M. Vingron and S. Sperling
  Molecular BioSystems, 2008, 4 (6), 589-598.
• Natural Similarity Measures between Position Frequency Matrices with an Application to Clustering
  Utz J. Pape, Sven Rahmann and Martin Vingron
  Bioinformatics, 2008, 24 (3), pp. 350 - 357. [Read the article!] [Try the approach online]
• A new statistical model to select target sequences bound by transcription factors
  Utz J. Pape, Steffen Grossmann, Stefanie Hammer, Silke Sperling and Martin Vingron
  Genome Informatics, 2006, 17 (1), pp. 134 - 140.
• A gene expression map of Arabidopsis development
  Markus Schmid, Timothy S. Davison, Stefan R. Henz, Utz J. Pape, Monika Demar, Martin Vingron, Bernhard Schölkopf, Detlef Weigel and Jan U. Lohmann
  Nature Genetics, 2005, 37 (5), pp. 501 - 506.
• Estimation of Genetic Regulatory Networks with Aggregated Bayesian Networks
  Master's thesis at Max-Planck-Institute for Molecular Genetics (Dep. Computational Molecular Biology) and the Free University of Berlin, 2004.
• Differentiation in the tissues of the zebrafish
  Bachelor's thesis at Max-Planck-Institute for Molecular Genetics (Dep. Computational Molecular Biology) and the Free University of Berlin, 2003.

Teaching:

• WS 2008:
  • Algorithmic Computational Biology
• SS 2008:
  • Systems Biology
• WS 2007/08:
  • Probability and Statistics for Sequence Analysis
  • Softwarepraktikum Simulation of Distributions and Monte-Carlo Methods
• SS 2007:
  • Seminar zu aktuellen Themen der Bioinformatik / Discussion of brand new research articles from Recomb 07
  • Softwarepraktikum Gene-Expression and Regulation
  • Seminar Gene-Expression and Regulation
• WS 2006/07: Algorithmic Bioinformatics
• WS 2005/06: Gene Expression Analysis [Lecture Notes about Expression Networks and Microarrays]
• SS 2005: Statistics (using R and Bioconductor)
• WS 2004/05: Algorithmic Bioinformatics
• WS 2002/03: Algorithms and Data Structures

Short CV:

I started working for the Max-Planck-Institute for Molecular Genetics in 2001 at the Lehrach Department. Then, I worked as a tutor for bioinformatics for the Free University of Berlin until I changed back to the Max-Planck-Institute to the Department Computational Biology. In summer 2003, I finished my Bachelor thesis. The year after, I graduated as Master of Science. After my visit of the VIB Institute for Plant Systems Biology in Belgium in summer 2004, I have been employed by the Free University of Berlin. Then, I was doing my PhD for Bioinformatics at the Max-Planck-Institute for Molecular Genetics with Prof. Dr. Martin Vingron as supervisor. In addition, I was a student of the International Max-Planck Research School for Computational Biology and Scientific Computing in Berlin.

After visiting the group of Prof. Fengzhu Sun at the University of Southern California for half a year in 2006, I obtained my PhD in October 2008.

Address

Utz Pape
Max Planck Institute for Molecular Genetics	Email:  pape [at] molgen.mpg.de
Computational Molecular Biology (Abt. Vingron)	Fon:    ++49 (30) 8413-1171
Ihnestrasse 63-73	Fax:    ++49 (30) 8413-1152
14195 Berlin, Germany