biological information systems group (bis)

• Scientific:
  
  • Analysis of disease related biological networks
  • microRNA mediated regulatory systems
  • Self-organizing systems, disorder effects on mesoscopic scales
• Computing:
  
  • Semantic Web technologies for systems biology
  • Massive parallel semantic information processing of unstructured text
  • Cloud computing, scalable distributed systems

IT background:

RDBMS application development (Oracle, PostgreSQL, ...), development of component and service oriented architectures (SOA) based on JEE / Web Services, Hadoop/HBase

• Group manager biological information systems at MIPS
• Teamleader of a middleware third level support group at debis Systemhaus / T-Systems (Information and Communication Technologies)
• Trainee at debis Systemhaus Munich
• Postdoc at Dutch Polymer Institute / TU Eindhoven; Subject: Passive emmissive liquid crystalline displays
• PhD in chemistry in Marburg; Subject: polymer and liquid crystalline (yes they exist too) light emitting diodes
• Study of chemistry in Stuttgart and Marburg

• Mewes HW, Wachinger B, Stümpflen V.
  Perspectives of a Systems Biology of the Synapse: How to Transform an Indefinite Data Space into a Model
  Pharmacopsychiatry 43(S1): S2-S8, 2010.
  DOI: 10.1055/s-0030-1249666
• Schmidt T, Mewes HW, Stümpflen V.
  A novel putative miRNA target enhancer signal
  PLoS One 4(7):e6473, 2009.
  PMID: 19649282
• Barnickel T, Weston J, Collobert R, Mewes HW, Stümpflen V.
  Large scale application of neural network based semantic role labeling for automated relation extraction from biomedical texts
  PLoS One 4(7):e6393, 2009.
  PMID: 19636432
• Mewes, HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer K, Muensterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T.
  MIPS: Analysis and annotation of genome information in 2007.
  Nuc Acids Res. 36(Database issue):D196-201, 2008.
  PMID: 1815829
• Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stümpflen V, Frishman D.
  DIMA 2.0 predicted and known domain interactions.
  Nucleic Acids Res 36(Database issue):D651-5, 2008.
  PMID: 1799999
• Rattei T, Tischler P, Arnold R; Hamberger F, Krebs J, Krumsiek J, Wachinger, B, Stuempflen V, Mewes HW.
  SIMAP: structuring the network of protein similarities
  Nuc Acids Res 36(Database issue):D289-92, 2008.
  PMID: 1803761
• Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Wägele B, Schmidt T, Noubibou Doudieu O, Stümpflen V, Mewes HW.
  CORUM: the Comprehensive Resource of Mammalian Protein Complexes
  Nuc Acids Res 36(Database issue):D646-50, 2008.
  PMID: 1796509
• Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.
  Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions.
  BMC Biol. 5(1):44, 2007.
  PMID: 1792502
• Stümpflen V, Barnickel T, Nenova K.
  Large Scale Knowledge Representation of Distributed Biomedical Information Scaling Topic Maps
  Lecture Notes in Artificial Intelligence 4999: 116-127, TMRA, 2007
• Stümpflen V, Mewes HW.
  Neue Informationstechnologien zur Nutzung biologischer Daten.
  Biospektrum, 03, 2007, p. 281-28
• Oesterheld M, Mewes HW, Stuempflen V.
  Analysis of integrated biomolecular networks using a generic network analysis suite.
  J Int Bio. 4(3), 2007.
• Pagel P, Strack N, Oesterheld M, Stümpflen V, Frishman D.
  Computational prediction of domain interactions.
  Methods Mol Biol 396:3-16, 2007.
  PMID: 18025682
• Stümpflen, V, Gregory R, Nenova, K.
  From Biological Data to Biological Knowledge
  Lecture Notes in Artificial Intelligence 4438: 62-66, TMRA, 2006
• Dietmann S, Aguilar D, Mader M, Oesterheld M, Ruepp A, Stuempflen V, Mewes HW.
  Resources and Tools for Investigating Biomolecular Networks in Mammals
  Curr Pharm Des 12(29):3723-3724, 2006.
• Güldener U, Münsterkötter M, Mannhaupt G, Haase D, Oesterheld M, Stumpflen V, Mewes, HW, Adam, G.
  FGDB: A comprehensive fungal genome resource on the plant pathogen Fusarium graminearum
  Nucl Acids Res 34(Database issue):D456-8, 2006.
  PMID: 16381910
• Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V.
  MPact: the MIPS protein interaction resource on yeast.
  Nucl Acids Res 34(Database issue):D436-41, 2006.
  PMID: 16381906
• Mewes HW, Frishman D, Mayer K, Münsterkötter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V.
  MIPS: analysis and annotation of proteins from whole genomes in 2005
  Nucl Acids Res 34(suppl_1):D169-D172, 2006.
  PMID: 16381839
• Pagel P, Oesterheld M, Stuempflen V, Frishman D.
  The DIMA web resource -- exploring the protein domain network
  Bioinformatics 22(8):997-8, 2006.
  PMID: 16481337
• Rattei T, Arnold R, Tischler P, Lindner D, Stumpflen V, Mewes HW.
  SIMAP: the similarity matrix of proteins
  Nucl Acids Res 34(Database issue):D252-6, 2006.
  PMID: 16381858
• Ruepp A, Doudieu ON, Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Skornia C, Wanka S, Rattei T, Pagel P, Riley L, Frishman D, Surmeli D, Tetko I, Oesterheld M, Stümpflen V and Mewes HW.
  The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context
  Nucl Acids Res 34(Database issue):D568-71, 2006.
  PMID: 16381934
• Arnold R, Rattei T, Tischler P, Truong M, Stuempflen V, Mewes, HW.
  SIMAP-The similarity matrix of proteins
  Bioinformatics 21: ii42-ii46, 2005.
  PMID: 16204123
• Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D.
  The MIPS mammalian protein-protein interaction database.
  Bioinformatics. 21(6):832-4, 2005
  PMID: 15531608
• Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stümpflen V, Warfsmann J and Ruepp A.
  MIPS: analysis and annotation of proteins from whole genomes.
  Nucleic Acids Res 32 Database issue:D41-4, 2004.
  PMID: 14681354
• Karlowski WM, Schoof H, Janakiraman V, Stümpflen V and Mayer KF.
  MOsDB: an integrated information resource for rice genomics.
  Nucleic Acids Res 31(1):190-2, 2003.
  PMID: 12519979
• "On track to provide convenient genome data: The MIPS Comprehensive Yeast Genome Database". Güldener U., Münsterkötter M., Stümpflen V., Kastenmüller G., Mewes HW. YEAST 20: S334-S334 Suppl. 1, JUL 2003
• "Thermo-reversible gelation of liquid crystals using di-benzylidene-D-sorbitol". Janssen, Rob H. C.; Stümpflen, Volker; Van Boxtel, Marysia C. W.; Bastiaansen, Cees W. M.; Broer, Dirk J.; Tervoort, Theo A.; Smith, Paul.; Macromolecular Symposia (2000), 154(Polymers in Display Applications), 117-126.
• "Thermo-Reversible Liquid-Crystal Gels: Towards a New Processing Route for Twisted Nematic Displays". R. H. C. Janssen, V. Stümpflen, D. J. Broer, C. W. M. Bastiaansen, T. A. Tervoort and P. Smith; Jap. J. Appl. Phys., 39, 2721 (2000)
• "Electrically Controlled Light Scattering from Thermoreversible Liquid-Crystal Gels". R. H. C. Janssen, V. Stümpflen, D. J. Broer, C. W. M. Bastiaansen, T. A. Tervoort and P. Smith; J. Appl. Phys., 88, 161 (2000)
• "Structural analysis of PPX prepared by vapor phase pyrolysis of (2,2)paracyclophane". C. Schmidt, V. Stümpflen, J. H. Wendorff, A. Hasenhindl, W. Gronski, M. Ishaque, A. Greiner; Acta Polymerica, 1998, 49(5), 232
• "Rigid Stars: Properties and Functions". W. Heitz, C. Meckel-Jonas, R. Neuhaus, M. D. Roth, V. Stümpflen, J. H. Wendorff; Polymers for Adv. Technologies, 1998, 9, 549
• "Columnar discotics for light emitting diodes". V. Stümpflen, I. H. Stapff, J.H. Wendorff; Proceedings-of-the-SPIE-The-International-Society-for-Optical-Engineering (USA), 1998, 3281, 164
• "Multi-layer light emitting diodes based on columnar discotics". I.H. Stapff, V. Stümpflen, J.H. Wendorff, D.B. Spohn, D. Möbius; Liq. Cryst., 1997, 33(4), 613
• "Light emitting diodes based on a discotic main chain polymer". Th. Christ, V. Stümpflen, J.H. Wendorff; Macromol. Chem. Rapid Commun., 1997, 18, 93
• "Columnar discotics for light emitting diodes". Th. Christ, B. Glüsen, A. Greiner, A. Kettner, R. Sander, V. Stümpflen, V. Tsukruk, J.H. Wendorff; Adv. Mat., 1997, 9, 48
• "Analysis of light emitting diodes by X-ray reflectivity investigations". Th. Christ, F. Geffart, A. Kettner, G. Lüssem, O. Schäfer, V. Stümpflen, V.V. Tsukruk, J.H. Wendorff; Thin Solid Films, 1997, 302, 214
• "Multicoloured chromophores for white light emitting diodes". Th. Christ, A. Greiner, R. Sander, V. Stümpflen, J.H. Wendorff; Adv. Mat., 1997, 9, 219
• Unterlechner C; Christ T; Sander R; Stümpflen V; Heitz W; Wendorff JH: Controlled bathochromic shift of the emission maximum of tri-(stilbene)-amine dyes for the application in organic led devices. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 1997, Vol 213, p 374.
• "Poly (p-phenylenevinylene) by chemical vapor deposition: Synthesis, structural evaluation, glass transition, electroluminescence and photoluminescence". O. Schäfer, J. Pommerehne, W. Gus, H. Vestweber, H.-Y. Tak, H. Bässler, G. Lüssem, B. Schartel, C. Schmidt, V. Stümpflen, J.H. Wendorff, S. Spiegel, C. Müller, A. Greiner; Synth. Metals, 1996, 82, 1
• "Synthesis, properties und guest host systems of triphenylamine based oligo (arylenevinylene)s: Advanced materials for LED-applications". R.Sander, V.Stümpflen, J.H.Wendorff, A.Greiner; Macromolecules, 1996, 29, 7705
• "Rigid Star-Shaped Multipodes: Molecules Designed for Molecular Reinforcement". B.Schartel, V.Stümpflen, J.Wendling, J.H.Wendorff; Colloid Polym. Sci.,1996, 274, 911
• "Rigid Cross-Shaped Multipodes: Molecules Designed for Molecular Reinforcement". B.Schartel, V.Stümpflen, J.Wendling, J.H.Wendorff; Polymers for Applied Technologies, 1996, 7, 160
• "Polarized Electroluminescence in Liquid Crystalline Main Chain Polymers Containing Arylene Vinylene Units". R. Festag, A. Greiner, G. Lüssem, C. Schmidt, V. Stümpflen, J.H. Wendorff; 1995, in "Organic Thin Films for Photonics Applications", Vol. 21 OSA Technical Digest Series (Optical Society of America, Washington D.C.), p. 448-451

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