Bioinformatics and Structural Proteomics

Henning Stehr*, Seon-Hi J. Jang*, Jose M. Duarte, Christoph Wierling, Hans Lehrach, Michael Lappe, Bodo M.H. Lange (2011) "The structural impact of cancer-associated mutations in oncogenes and tumor suppressors" Molecular Cancer , accepted / to appear

Corinna Vehlow, Henning Stehr, Matthias Winkelmann, Jose M. Duarte, Lars Petzold, Juliane Dinse and Michael Lappe (2011) "CMView: Interactive contact map visualization and analysis" Bioinformatics doi: 10.1093/bioinformatics/btr163

Achim Leutz, Ole Pless, Michael Lappe, Gunnar Dittmar and Elisabeth Kowenz-Leutz (2011) "Crosstalk between phosphorylation and multi-site arginine/lysine methylation in C/EBPs" TRANSCRIPTION Volume 2, Issue 1, (open access)

Henning Stehr, Michael Lappe (2010) "Prediction of Native Contacts, 3D Structures and Model Quality Using Consensus Contacts" Critical assessment of methods for protein structure prediction (CASP9) - Abstract Book

M.Parthiban, S. Susdalzew, S. Belsare, H. Stehr, M. Winkelmann, C. L. Sargent, E. Michalsky, M. Schneider, R. Preissner and M. Lappe (2010). "Homology Modeling of Protein Structure using Fragment/Profile based search method in CASP9" Critical assessment of methods for protein structure prediction (CASP9) - Abstract Book

Bernd Timmermann, Martin Kerick, Christina Roehr, Axel Fischer, Melanie Isau, Stefan T. Boerno, Andrea Wunderlich, Christian Barmeyer, Petra Seemann, Jana Koenig, Michael Lappe, Andreas W. Kuss, Masoud Garshasbi, Lars Bertram, Kathrin Trappe, Martin Werber, Bernhard G. Herrmann, Kurt Zatloukal, Hans Lehrach, Michal R. Schweiger (2010) "Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis" PLoS ONE 5(12): e15661. doi:10.1371/journal.pone.0015661 (open access)

Jose M. Duarte, R. Sathyapriya, Henning Stehr, Ioannis Filippis, Michael Lappe (2010) "Optimal contact definition for reconstruction of Contact Maps" BMC Bioinformatics 2010, 11:283. doi:10.1186/1471-2105-11-283

Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak and Dan M. Bolser (2010) "PDBWiki: added value through community annotation of the Protein Data Bank" Database Vol. 2010:baq009; doi:10.1093/database/baq009

R. Sathyapriya, Jose M Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe (2009) "Defining an Essence of Structure Determining Residue Contacts in Proteins" PLoS Computational Biology 5(12): e1000584. doi:10.1371/journal.pcbi.1000584

Michael Lappe, Ganesh Bagler, Ioannis Filippis, Henning Stehr, Jose M. Duarte, Rajagopal Sathyapriya (2009) "Designing evolvable libraries using multi-body potentials" Current Opinion in Biotechnology doi:10.1016/j.copbio.2009.07.008

Sylvain Daujat, Thomas Weiss, Fabio Mohn, Ulrike C Lange, Celine Ziegler-Birling, Ulrike Zeissler, Michael Lappe, Dirk Schubeler, Maria-Elena Torres-Padilla, Robert Schneider (2009). "H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming" Nature Structural and Molecular Biology, doi:10.1038/nsmb.1629

Tijana Milenkovic, Ioannis Filippis, Michael Lappe, Natasa Przulj (2009). "Optimized Null Model for Protein Structure Networks" PLoS ONE 4(6): e5967. doi:10.1371/journal.pone.0005967

Dan M Bolser, Ioannis Filippis, Henning Stehr, Jose Duarte and Michael Lappe (2008). "Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys" BMC Structural Biology 2008, 8:53 doi:10.1186/1472-6807-8-53

Patrick Slama, Ioannis Filippis and Michael Lappe (2008). "Detection of protein catalytic residues at high precision using local network properties" BMC Bioinformatics 2008, 9:517 doi:10.1186/1471-2105-9-517

Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C (2008) "Estimating the size of the human interactome" Proc Natl Acad Sci U S A. 2008 May 13;105(19):6959-64. doi: 10.1073/pnas.0708078105

Jain, B.J. and Lappe, M. (2007). "Joining Softassign and Dynamic Programming for the Contact Map Overlap Problem" Springer Lecture Notes in Computer Science, S. Hochreiter and R. Wagner (Eds.): BIRD 2007, LNBI 4414, pp. 410-423. [Full text]

Paszkiewicz, K. H., Sternberg, M. J. & Lappe, M. (2006). Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics 22, 1353-8. [Full text]

Lappe, M. and L. Holm (2005). "Algorithms for protein interaction networks"
Biochem Soc Trans 33(3): 530-34. [Full text]

Park, D., S. Lee, et al. (2005). "Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)."
Bioinformatics 21(15): 3234-40. [Full text]

Gong, S., G. Yoon, et al. (2005). "PSIbase: a database of Protein Structural Interactome map (PSIMAP)."
Bioinformatics 21(10): 2541-43. [Full text]

Lappe, M. and L. Holm (2004). "Unraveling protein interaction networks with near-optimal efficiency."
Nat Biotechnol 22(1): 98-103. [Full text]

Hermjakob, H., L. Montecchi-Palazzi, et al. (2004). "The HUPO PSI's Molecular Interaction format - a community standard for the representation of protein interaction data."
Nat Biotechnol 22(2): 177-183. [Full text]

Heger, A., M. Lappe, et al. (2003). "Accurate detection of very sparse sequence motifs."
Seventh annual international conference on Computational molecular biology RECOMB 2003: 139-47 [Full text]

Schlitt, T., K. Palin, et al. (2003). "From gene networks to gene function."
Genome Res 13(12): 2568-76 [Full text]

Lappe, M., J. Park, et al. (2001). "Generating protein interaction maps from incomplete data: application to fold assignment."
Bioinformatics 17 Suppl 1: S149-56 [Full text]

Park, J., M. Lappe, et al. (2001). "Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast."
J Mol Biol 307(3): 929-38 [Full text]

Dietmann, S., J. Park, et al. (2001). "A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3."
Nucleic Acids Res 29(1): 55-7. [Full text]