Martin-Luther-Universität Halle-Wittenberg

Dr. Jan Grau

Kontakt

Jan Grau
Institut für Informatik
Martin-Luther-Universität Halle-Wittenberg

Raum 4.12
Von-Seckendorff-Platz 1
06120 Halle

Telefon: +49-345-55-24768
Telefax: +49-345-55-27039

Postanschrift:
Jan Grau
Institut für Informatik
Martin-Luther-Universität Halle-Wittenberg
06099 Halle

Tag cloud of paper abstracts until 2015

Tag cloud of paper abstracts until 2015

Lehre

Wintersemester 2015/2016

Sommersemester 2015

Wintersemester 2014/2015

Sommersemester 2014

Wintersemester 2013/2014

Sommersemester 2013

Wintersemester 2012/2013

Sommersemester 2011

Sommersemester 2010

Wintersemester 2009/2010

Sommersemester 2009

Wintersemester 2008/2009

Frühere Veranstaltungen

Anwendungen und Bibliotheken

Forschungsinteressen

  • Statistische Analyse von Transcription activator-like Effektoren (TALEs) und deren Zielgenen (DFG-Projekt)
  • Vorhersage der off-targets von TALE-Nukleasen
  • diskriminative Modelle zur Vorhersage von Transkriptionsfaktor-Bindungsstellen und Spleißstellen
  • diskriminative Methoden zur de-novo-Suche von Bindemotiven und cis-regulatorischen Modulen
  • Abhängigkeiten in DNA-Bindestellen
  • Analyse von ChIP-seq-/-exo- und Protein-Binding-Microarray-Daten
  • Vorhersage der Positionierung von Nukleosomen
  • Vorhersage von miRNA-Zielen

Publikationen

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 Bs3 Alleles. 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. Dissertation, Martin-Luther-Universität 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)

Jan Grau, Jens Keilwagen, André Gohr, Berit Haldemann, Stefan Posch, and Ivo Grosse: Jstacs: A java framework for statistical analysis and classification of biological sequences. Journal of Machine Learning Research, 13(Jun):1967–1971, (2012)

Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch, and Jens Boch: Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput Biol, 9(3):e1002962, 03 2013.

Jan Grau, Jens Keilwagen, André Gohr, Ivan A. Paponov, Stefan Posch, Michael Seifert, Marc Strickert, and Ivo Grosse: Dispom: A discriminative de-novo motif discovery tool based on the Jstacs library. Journal of Bioinformatics and Computational Biology, 11(1), 2013.

Jan Grau, Jens Boch, and Stefan Posch: TALENoffer: genome-wide TALEN off-target prediction. Bioinformatics, 29(22):2931–2932, 2013.

Jan Grau, Stefan Posch, Ivo Grosse, and Jens Keilwagen: A general approach for discriminative de novo motif discovery from high-throughput data. Nucleic Acids Research, 41(21):e197, 2013.

Annekatrin Richter, Jana Streubel, Christina Blücher, Boris Szurek, Maik Reschke, Jan Grau, and Jens Boch: A TAL effector repeat architecture for frameshift binding. Nature Communications, 5, 2014.

Jens Keilwagen, Ivo Grosse, and Jan Grau: Area under precision-recall curves for weighted and unweighted data. PLoS ONE, 9(3):e92209, 2014.

Jan Grau, Ivo Grosse, and Jens Keilwagen. PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R. doi:10.1093/bioinformatics/btv153   . Bioinformatics, 2015.

J. Keilwagen and J. Grau. Varying levels of complexity in transcription factor binding motifs. doi:10.1093/nar/gkv577    Nucleic Acids Research, 2015.

Oliver A Müller, Jan Grau, Sabine Thieme, Heike Prochaska, Norman Adlung, Anika Sorgatz, and Ulla Bonas. Genome-Wide Identification and Validation of Reference Genes in Infected Tomato Leaves for Quantitative RT-PCR Analyses. PLOS ONE 10(8):E0136499, 2015.

Jan Grau, Ivo Grosse, Stefan Posch, Jens Keilwagen. Motif clustering with implications for transcription factor interactions. doi:10.7287/peerj.preprints.1302v1   . German Conference on Bioinformatics 2015, University Alliance Ruhr, Dortmund, 2015.

Martin Nettling, Hendrik Treutler, Jan Grau, Jens Keilwagen, Stefan Posch, and Ivo Grosse. DiffLogo: a comparative visualization of sequence motifs. BMC Bioinformatics 16(387), 2015.

Jan Grau, Maik Reschke, Annett Erkes, Jana Streubel, Richard D. Morgan, Geoffrey G. Wilson, Ralf Koebnik, and Jens Boch. AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of tales from Xanthomonas genomic sequences. Scientific Reports 6 21077, 2016.

Jens Keilwagen, Michael Wenk, Jessica L. Erickson, Martin H. Schattat, Jan Grau, and Frank Hartung. Using intron position conservation for homology-based gene prediction. Nucleic Acids Research, 2016.

Vorträge

Motif clustering with implications for transcription factor interactions. German Conference on Bioinformatics 2015, Dortmund.

Varying levels of complexity in transcription factor binding motifs (highlight talk). German Conference on Bioinformatics 2015, Dortmund.

A general approach for de novo motif discovery from high-throughput data (highlight talk), German Conference on Bioinformatics 2014, Bielefeld

A general approach for de novo motif discovery from high-throughput data, Symposium on Novel Applications of Deep Sequencing in Medicine, Genomics, and Biodiversity Research 2014, Halle

Discriminative de novo motif discovery from high-throughput data (invited), CSC ChIP- and DNase-seq data analysis workshop, 2014, Helsinki, Finnland

Computational prediction of TALEN & CRISPR off-targets (invited), 2014, TALEN & CRISPR TRAINING SCHOOL, Halle

TALEs and Motifs: Bioinformatics with a focus on sequence analysis (invited), 2014, Institute of Plant Biochemistry, Halle

The Jstacs library and its application to de-novo motif discovery (invited), 2013, JCB Workshop “Bioinformatics meets Biodiversity”, Jena

TALEs of virulence and biotechnology (highlight talk), German Conference on Bioinformatics 2013, Göttingen

Computational prediction of TAL effector target sites, 2013, Meeting on Gene Regulation and Information Theory, Halle

Neue Einblicke in die Biologie von TAL-Effektor-Zielsequenzen mittels rechnergestützter Vorhersagen (invited), 2013, Julius Kühn institute, Quedlinburg

De-Novo Discovery of Differentially Abundant DNA Binding Sites Including Their Positional Preference (highlight talk), German Conference on Bioinformatics 2011, Weihenstephan

Predicting miRNA targets utilizing an extended profile HMM, German Conference on Bioinformatics 2010, Braunschweig

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