Dr. Holger Klein

Research Interests:

• gene regulation & tissue specificity
• clustering & co-occurrence of transcription factor binding sites
• transcription factor interactions
• prediction of regulatory regions
• next-generation sequencing; ChIP-Seq, RNA-Seq, resequencing
• protein binding microarrays

Short Vita:

• Since May 2011
  Bioinformatics Scientist at Institute for Molecular Biology (IMB), Mainz
• 2009-2011:
  Bioinformatics Scientist (next generation sequencing) at MicroDiscovery, Berlin
• 2006-2009:
  Member of the International Research Training Group (IRTG) "Genomics and Systems Biology of Molecular Networks" , Berlin
• 2003-2009:
  Member of the Computational Molecular Biology Group at the Max Planck Institute for Molecular Genetics, Berlin.
• 2001 and 2002-2003:
  Bioinformatician at Science-Factory, Cologne
• 2001-2002:
  Research Assistant in the Moult group at the Center for Advanced Research in Biotechnology (CARB), Rockville, MD, USA.
• 2001:
  Research Assistant in the Faigle/Schrader-group at the Center for Applied Computer Science (ZAIK) at University of Cologne.
• 2000:
  Diploma in Chemistry at the Schomburg group / Department of Biochemistry at the University of Cologne.
• 1998:
  research training in the Eiras group (ferroelectric ceramics) at the Universidade Federal de São Carlos , SP, Brazil (three months).
• 1997:
  Diploma preliminary examination (Vordiplom), chemistry.
• 1993:
  Abitur at the Dietrich-Bonhoeffer-Gymnasium in Bergisch Gladbach.
• at various times: freelance programming work for koeln-online, IPM Köln, JazzHausMusik, and others.

Publications:

• S. Roepcke, S. Stahlberg, H. Klein, M.H. Schulz, L. Theobald, S. Gohlke, M. Vingron, D.J. Walther
  "A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ", BMC Genomics, 2011, 12:624
• L. Hallen, H. Klein, C. Stoschek, S. Wehrmeyer, U. Nonhoff, M. Ralser, J. Wilde, C. Röhr, MR Schweiger, K. Zatloukal, M. Vingron, H. Lehrach, Z. Konthur, S. Krobitsch
  "The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2", Human Molecular Genetics, 2011, Vol. 20, No. 1, 104-114
• S. Kielbasa, H. Klein, H. Roider, M. Vingron, N. Bluethgen
  "TransFind - Predicting transcriptional regulators for gene sets", Nucl. Acids Res. (2010) 38 (suppl 2), W275-W280. - Link to TransFind Webserver.
• H. Klein
  "Co-occurrence of Transcription Factor Binding Sites", PhD thesis, submitted to Free University of Berlin, 2009; Referees: Prof. Dr. M. Vingron, Prof. Dr. HP Herzel (HU Berlin).
  pdf available at FU EDoc Server; local copy:pdf
• U.J. Pape, H. Klein, M. Vingron
  "Statistical detection of co-operative transcription factors with similarity adjustment", In Beyer, A., Schroeder, M. (eds), Lecture Notes in Informatics: Proc. of German Conference on Bioinformatics (GCB), 2008, 96-105, and Bioinformatics, Vol 25, No. 16, 2103-2109, (2009). (abstract / pdf)
• H. Klein, M. Vingron
  "Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions", Genome Informatics, Vol. 18, 109-118 (2007). (abstract / pdf)
• H. Klein, M. Vingron
  "Detection of preferentially co-occuring transcription factor binding sites", Proceedings of the 5th Bioinformatics Research and Education Workshop (BREW 2005) (pdf)

• H. Klein
  "Characterization of protein-protein complex interfaces", master's thesis, University of Cologne, (Diplomarbeit, German), Advisor: Prof. Dr. D. Schomburg.
• R.G. Mendes, E.B. Araújo, H. Klein, J. A. Eiras,
  "Synthesis Of Strontium Barium Niobate Ferroelectric Thin Films By An Alternative Chemical Method" Journal of Materials Science Letters 18(23) 1941-1943 (1999). (pdf)
• R.G. Mendes, E.B. Araújo, H. Klein, J.A. Eiras,
  "Synthesis and Characterization of Strontium Barium Niobate (SBN) Ferroelectric Thin Films", Bol. Soc. Esp. Ceram Y Vidrio 38(5), 455-457 (1999). (pdf)

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