Roland Krause

Roland Krause
Max-Planck-Institute for Molecular Genetics
Department Vingron
Computational Molecular Biology
Ihnestr. 73
D-14195 Berlin
Tel. +49 30 8413 1153
roland.krause@molgen.mpg.de
  1. Research
  2. Biography
  3. Publications
  4. Teaching

Projects

Structure and evolution of protein-protein interactions

How were protein complexes shaped by the evolution of binding interfaces and the gain and loss of proteins? Joint, unpublished work in collaboration with Shamil Sunyaev, Harvard Medical School.

Evolution of multi-domain proteins

Reconstruction of phylogenies of multi-domain proteins as networks.

Definition, detection, and functions of protein complexes

Functional and structural characterization of the modularity of biological networks.

Translation in prokaryotes

Joint work with Knud Nierhaus and Markus Pech, Charite.

Education

Dr. sc. hum. in Biochemistry, University of Heidelberg (2004)
Dipl. Ingenieur (FH) in Biotechnology, University of Applied Sciences, Mannheim( 1998)

Biography

2008–2012 Free University of Berlin and
Max Planck Institute for Molecular Genetics. Research Fellow.
2005–2008 Max Planck Institute for Molecular Genetics, Berlin. Research Fellow.
2004 European Molecular Biology Laboratory, Heidelberg. Postdoc.
2004 University of California, Institute for Pure and Applied Mathematics. Visiting Fellow.
2000–2004 Cellzome AG, Heidelberg. Graduate student.
1997–2000 Lion Bioscience AG, Heidelberg. Software engineer.

Publications

  1. Chang WC, Vakati S, Krause R, Eulenstein O: Exploring Biological Interaction Networks With Tailored Weighted Quasi-Bicliques. BMC Bioinformatics Updated, expanded version of a contribution to ISBRA11. To appear.
  2. Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R: Cocos: Constructing multi-domain protein phylogenies. PLoS Currents 9;3:RRN1240 (2011) [PubMed|full text, OA]
  3. Pett, P, Mehnert, D, Ibn-Salem, J, Eigenbrod, O, Otto, R, Knorr, S, Richter SM, Krause, R: Identification of shared components of protein complexes. German conference on bioinformatics, Freising (2011). [PDF]
  4. Wiedenhoeft J, Krause R, Eulenstein O: The Plexus Model for the Inference of Ancestral Multi-Domain Proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(4):890-901 (2011) [PubMed|full text]
  5. Hafemeister C, Krause R, Schliep, A: Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(6):1642–1652 (2011) [PubMed|full text]
  6. Chang WC, Vakati S, Krause R, Eulenstein O: Mining Biological Interaction Networks Using Weighted Quasi-Bicliques. ISBRA 2011. Bioinformatics Research and Applications, 428-439 (2011) [full text]
  7. Metge, F, Josten, J, Müller, M, Apelt, F, Hartmann, C, von Falkenhausen, T, Korkuc, P, Manin, J, Krause, R: Context-dependent annotation of protein domains. German conference on bioinformatics, Braunschweig (2010).
  8. Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider R: Live coverage of scientific conferences using web technologies. PLoS Computational Biology 6 (1), e1000563, 1 (2010) [PubMed|full text, OA]
  9. Lister AL, Datta RS, Hofmann O, Krause R, Kuhn M, Roth B, Schneider: R. Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009. PLoS Computational Biology 6 (1), e1000640, 1 (2010)
  10. Wiedenhoeft J, Krause R, Eulenstein O: Inferring Evolutionary Scenarios for Protein Domain Compositions ISBRA 2010. Bioinformatics Research and Applications6053, 179-190, (2010) [full text]
  11. Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S Microblogging the ISMB: a new approach to conference reporting PLoS Computational Biology 5 (1), e1000263, 11, (2009)
  12. Schliep A, Krause R: Efficient algorithms for the computational design of optimal tiling arrays. IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, 557-567 5 (2008) [full text]
  13. Tegha-Dunghu J, Neumann B, Reber S, Krause R, Erfle H, Walter T, Held M, Gruss O: EML3 is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. Journal of Cell Science 121 (10), 1718 10 (2008) [PubMed|full text, OA]
  14. Lee JS, Krause R, Schreiber J, Stein R, Mollenkopf HJ, Jeon BY, Kwak JY, Kowall J, Song, MK, Cho, NS, Kaufmann, SHE: Mutation in the transcriptional regulator PhoP contributes to avirulence of Mycobacterium tuberculosis H37Ra strain Cell Host & Microbe 3 (2), 97-103 38 (2008) [PubMed|full text]
  15. Costa I, Krause R, Opitz L, Schliep A: Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. BMC Bioinformatics 8 (Suppl 10), S3 13 (2007) [PubMed|full text, OA]
  16. Rungsarityotin W, Krause R, Schödl A, Schliep A: Identifying protein complexes directly from high-throughput TAP data with Markov random fields BMC Bioinformatics 8 (1), 482 7 (2007) [PubMed|full text]
  17. Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EEM: Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology 3 (1) 43 (2007) [PMC]
  18. Schliep A, Krause R Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach Algorithms in Bioinformatics, 383-394 2 (2007)
  19. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B et al: Proteome survey reveals modularity of the yeast cell machinery Nature 440 (7084), 631-636 1010 (2006)
  20. Chu W, Ghahramani Z, Krause R, Wild DL: Identifying protein complexes in high-throughput protein interaction screens using an infinite latent feature model. Pacific Symposium on Biocomputing 19 (2006) [PubMed|PDF]
  21. R Krause, C von Mering, P Bork, T Dandekar Shared components of protein complexes—versatile building blocks or biochemical artefacts? Bioessays 26 (12), 1333-1343 28 (2004) [PubMed|PDF]
  22. Gagneur J, Krause R, Bouwmeester T, Casari G: Modular decomposition of protein-protein interaction networks. Genome Biology 5 (8), R57 [PubMed|full text, OA ]
  23. Bettler E, Krause R, Horn F, Vriend G: NRSAS: Nuclear receptor structure analysis servers. Nucleic Acids Research 31 (13):3400-3403 (2003). [PubMed|full text]
  24. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417(6887):399-403 (2002) [PubMed|full text]
  25. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM et al: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868):141-147 (2002) [PubMed|full text]

Current courses at the Free University of Berlin (Winter semester 2011)

Upcoming EMBO course

  • EMBO Practical Course: Computational Biology.
    October 14th-20th, 2012. L'escala, Spain.
    In preparation.

Past lectures and courses

  • Algorithms in Systems Biology (2007–2011)
  • Algorithms in Bioinformatics (2008, 2010)
  • Sequence Analysis and Molecular Evolution (2010)
  • Project management in software engineering (2006, 2007, 2009–2011)

Past EMBO courses

  • EMBO Practical Course: Computational Biology. Reykjavik, Iceland (2011)
  • EMBO World Practical course Computational Biology. Shanghai, China (2009)
  • EMBO World Practical course Computational Biology, Singapore (2008)
  • EMBO World Practical course Computational Biology, Cuernavaca, Mexico (2007)

Resources

  1. Google Profile