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Dr. Jan Grau

Teaching

summer semester 2011

• Algorithmen auf Sequenzen II (Übung)
• Spezielle Probleme der Bioinformatik (Übung)

summer semester 2010

• Expressionsdatenanalyse I (Übung)
• Spezielle Probleme der Bioinformatik (Übung)

winter semester 2009/2010

• Algorithmen der Bioinformatik II (Übung)

summer semester 2009

• Spezielle Probleme der Bioinformatik, exercise course (Stud.IP)
• Algorithmen auf Sequenzen IB (Stud.IP)

winter semester 2008/2009

• Applied Bioinformatics using Perl and R (exercise course)
• Applied Bioinformatics using Perl and R (exercise course) at Stud.IP
• Bioinformatics algorithms II (exercise course)
• Bioinformatics algorithms II (exercise course) at Stud.IP

Previous semesters

• Archive of the group’s lessons

Applications and libraries

• Jstacs (Java framework for statistical analysis and classification of biological sequences)    
• LaTeXlet - a LaTeX taglet for Javadoc

Scientific focus

• discriminative models for predicting transcription factor binding sites and splice sites
• differential approaches for de-novo discovery of cis-regulatory modules
• prediction of nucleosome positioning
• prediction of miRNA targets

Publications

Irad E. Ben-Gal, Ayala Shani, Andre Gohr, Jan Grau, S. Arviv, Armin Shmilovici, Stefan Posch, Ivo Grosse: Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics 21(11): 2657-2666 (2005)

Jan Grau, Irad E. Ben-Gal, Stefan Posch, Ivo Grosse: VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. Nucleic Acids Research 34(Web-Server-Issue): 529-533 (2006)

Stefan Posch, Jan Grau, Andre Gohr, Irad E. Ben-Gal, Alexander E. Kel, Ivo Grosse: Recognition of cis-Regulatory Elements with Vombat. J. Bioinformatics and Computational Biology 5(2b): 561-577 (2007)

Jens Keilwagen, Jan Grau, Stefan Posch, Ivo Grosse: Recognition of splice sites using maximum conditional likelihood. LWA 2007: 67-72

Jan Grau, Jens Keilwagen, Ivo Grosse, Stefan Posch: On the relevance of model orders to discriminative learning of Markov models. LWA 2007: 61-66

Jan Grau, Jens Keilwagen, Alexander E. Kel, Ivo Grosse, Stefan Posch: Supervised Posteriors for DNA-motif Classification. German Conference on Bioinformatics 2007: 123-134

Patrick Römer, Tina Strauss, Simone Hahn, Heidi Scholze, Robert Morbitzer, Jan Grau, Ulla Bonas, and Thomas Lahaye: Recognition of AvrBs3-Like Proteins Is Mediated by Specific Binding to Promoters of Matching Pepper Bs3Alleles. Plant Physiology: 150(4):1697-1712 (2009)

Jens Keilwagen, Jan Grau, Stefan Posch, and Ivo Grosse: Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis.BMC Bioinformatics: 11(1):149 (2010)

Jens Keilwagen, Jan Grau, Stefan Posch, Marc Strickert, and Ivo Grosse: Unifying generative and discriminative learning principles. BMC Bioinformatics: 11(1):98 (2010)

Stefan Posch, Jan Grau, André Gohr, Jens Keilwagen and Ivo Grosse: Probabilistic approaches to transcription factor binding site prediction. In I. Ladunga, editor,Computational Biology of Transcription Factor Binding, Methods in Molecular Biology. Humana Press: 674:97 (2010)

Jan Grau: Discriminative Bayesian principles for predicting sequence signals of gene regulation. PhD thesis, Martin Luther University Halle–Wittenberg, April 2010.

Jan Grau, Daniel Arend, Ivo Grosse, Artemis G. Hatzigeorgiou, Jens Keilwagen, Manolis Maragkakis, Claus Weinholdt, and Stefan Posch: Predicting miRNA targets utilizing an extended profile HMM. In D. Schomburg and A. Grote, editors, German Conference on Bioinformatics, volume P-173 of Lecture Notes in Informatics (LNI) - Proceedings, pages 81–91, Bonn (2010)

Jens Keilwagen, Jan Grau, Ivan A Paponov, Stefan Posch, Marc Strickert, and Ivo Grosse: De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Computational Biology, 7(2):e1001070 (2011)

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