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Publications 2009


Scientific Journals:

  1. E.M. Jounaux, B.B. Timm, K.M. Arndt, T.E. Exner: Improving the Interaction of Myc-Interfering Peptides with Myc Using Molecular Dynamics Simulations. J Pept Sci, 2009; 15 (1): 5-15.
  2. J.M. Mason, K.M. Müller, K.M. Arndt: Peptides Tailored to Interfere with Protein Interaction and Function. Chim Oggi, 2009; 27 (2): 47-50.
  3. J.M. Mason, U.B. Hagemann, K.M. Arndt: Role of Hydrophobic and Electrostatic Interactions in Coiled Coil Stability and Specificity. Biochemistry-us, 2009; 48 (43): 10380-10388.
  4. J. Sarmann, J. Hegermann, E. von Gromoff, S. Eimer, R. Baumeister, E. Schmidt: Caenorhabditis elegans LRK-1 and PINK-1 Act Antagonistically in Stress Response and Neurite Outgrowth. Journal of Biological Chemistry, 2009; 284 (24): 16482-16491.
  5. M. Vargiolu, D. Fusco, I. Kurelac, D. Dirnberger, R. Baumeister, I. Morra, A. Melcarne, R. Rimondini, G. Romeo, E. Bonora: The Tyrosine Kinase Receptor RET Interacts in Vivo with Aryl Hydrocarbon Receptor-Interacting Protein to Alter Survivin Availability. Journal of Clinical Endocrinology & Metabolism, 2009; 94 (7): 2571-2578.
  6. A. Fritsch, S. Spassov, S. Elfert, A. Schlosser, Y. Gache, G. Meneguzzi, L. Bruckner-Tuderman: Dominant negative effects of COL7A1 mutations can be rescued by controlled overexpression of normal collagen. J Biol Chem, 2009; VII (284): 30248-30256.
  7. A.W. Arnold, L. Bruckner-Tuderman, C. Zuger, P. Itin: Cetuximab Therapy of Metastasizing Cutaneous Squamous Cell Carcinoma in a Patient with Severe Recessive Dystrophic Epidermolysis Bullosa. Dermatology, 2009; 219 (1): 80-83.
  8. C. Franzke, L. Bruckner-Tuderman, C. Blobel: Shedding of collagen XVII/BP180 in skin depends on both ADAM10 and ADAM9. Journal of Biological Chemistry, 2009; 284 (35): 23386-23396.
  9. D. Nashan, M. Muller, M. Braun-Falco, S. Reichenberger, R. Szeimies, L. Bruckner-Tuderman: Cutaneaus metastases of visceral tumours: a review. Journal of Cancer Research and Clinical Oncology, 2009; 135 (1): 1-14.
  10. J. Kern, G. Grüninger, R. Imsak, M. Müller, H. Schumann, D. Kiritsi, S. Emmert, W. Borozdin, J. Kohlhase, L. Bruckner-Tuderman, C. Has: Forty-two novel COL7A1 mutations and the role of a frequent single nucleotide polymorphism in the MMP1 promoter in modulation of disease severity in a large European dystrophic epidermolysis bullosa cohort. British Journal of Dermatology, 2009; 161 (5): 1089-1097.
  11. J. Kern, S. Loeckermann, A. Fritsch, I. Hauser, M. Müller, O. Paul, P. Ruther, L. Bruckner-Tuderman: Mechanisms of fibroblast cell therapy for dystrophic epidermolysis bullosa: high stability of collagen VII favors long-term skin integrity. Molecular Therapy, 2009; 17 (9): 1605-1615.
  12. L. Huilaja, T. Hurskainen, H. Autio-Harmainen, R. Sormunen, H. Tu, S.C. Hofmann, T. Pihlajaniemi, L. Bruckner-Tuderman, K. Tasanen: Glycine substitution mutations cause intracellular accumulation of collagen XVII and affect its post-translational modifications. Journal of Investigative Dermatology, 2009; 129 (9): 2302-2306.
  13. N. Ishii, M. Yoshida, A. Ishida-Yamamoto, A. Fritsch, S. Elfert, L. Bruckner-Tuderman, T. Hashimoto: Some epidermolysis bullosa acquisita sera react with epitopes within the triple-helical collagenous domain as indicated by immunoelectron microscopy. British Journal of Dermatology, 2009; 160 (5): 1090-1093.
  14. O. Kautz, L. Bruckner-Tuderman, M. Müller, C. Schempp: Trigeminal trophic syndrome with extensive ulceration following herpes zoster. European Journal of Dermatology, 2009; 19 (1): 61-63.
  15. S.C. Hofmann, U. Voith, V. Schönau, L. Sorokin, L. Bruckner-Tuderman, C.-W. Franzke: Plasmin Plays a Role in the In Vitro Generation of the Linear IgA Dermatosis Antigen LADB97. Journal of Investigative Dermatology, 2009; 129 (7): 1730-1739.
  16. W. Roth, U. Reuter, C. Wohlenberg, L. Bruckner-Tuderman, T. Magin: Cytokines as Genetic Modifiers in K5-/- Mice and in Human Epidermolysis Bullosa Simplex. Human Mutation, 2009; 30 (5): 832-841.
  17. G. Cedersund, J. Roll: Systems biology: model based evaluation and comparison of potential explanations for given biological data. Febs J, 2009; 276 (4): 903-922.
  18. G. Cedersund, P. Stralfors: Putting the pieces together in diabetes research: Towards a hierarchical model of whole-body glucose homeostasis. European Journal of Pharmaceutical Sciences, 2009; 36 (1): 94-104.
  19. J. Brugard, D. Hedberg, M. Cascante, G. Cedersund, A. Gomez-Garrido, D. Maier, E. Nyman, V. Selivanov: Creating a bridge between modelica and the systems biology community. Proc Modelica conference, 2009;
  20. J. Tegner, A. Compte, C. Auffray, G. An, G. Cedersund, G. Clermont, B. Gutkin, Z. Oltvai, K. Stephan, R. Thomas, P. Villoslada: Computational disease modelling - fact or fiction? BMC Systems Biology, 2009; 3: 56.
  21. J. Dengjel, I. Kratchmarova, B. Blagoev: Receptor tyrosine kinase signaling: a view from quantitative proteomics. Mol Biosyst, 2009; 5: 1112-1121.
  22. J. Wahlstrom, J. Dengjel, O. Winqvist, I. Targoff, B. Persson, H. Duyar, H.-G. Rammensee, A. Eklund, R. Weissert, J. Grunewald: Autoimmune T cell responses to antigenic peptides presented by bronchoalveolar lavage cell HLA-DR molecules in sarcoidosis. Clinical Immunology, 2009; 133 (3): 353-363.
  23. M. Feuchtinger, S. Christ, B. Preuss, J. Dengjel, S. Duman, S. Stevanovic, R. Klein: Detection of novel non-M2-related antimitochondrial antibodies in patients with anti-M2 negative primary biliary cirrhosis. Gut, 2009; 58 (7): 983-989.
  24. E. Kastenhuber, U. Kern, J. Bonkovsky, C.B. Chien, W. Driever, J. Schweitzer: Netrin-DCC, Robo-Slit, and Heparan Sulfate Proteoglycans Coordinate Lateral Positioning of Longitudinal Dopaminergic Diencephalospinal Axons. J Neurosci, 2009; 29 (28): 8914-8926.
  25. H.L. Bader, D.R. Keene, B. Charvet, G. Veit, W. Driever, M. Koch, F. Ruggiero: Zebrafish collagen XII is present in embryonic connective tissue sheaths (fascia) and basement membranes. Matrix Biology, 2009; 28 (1): 32-43.
  26. H. Löhr, S. Ryu, W. Driever: Zebrafish diencephalic A11-related dopaminergic neurons share a conserved transcriptional network with neuroendocrine cell lineages. Development, 2009; 136 (6): 1007-1017.
  27. J. Schweitzer, W. Driever: Development of the Dopamine Systems in Zebrafish. Development and Engineering of Dopamine Neurons, 2009; 651: 1-14.
  28. M. Emmenlauer, O. Ronnenberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, H. Burkhardt: XuvTools: free, fast and reliable stitching of large 3D datasets. Journal of Microscopy-Oxford, 2009; 233 (1): 42-60.
  29. N. Tiso, A. Fillipi, F. Benato, E. Negrisolo, N. Modena, E. Vaccari, W. Driever, F. Argenton: Differential Expression and Regulation of olig Genes in Zebrafish. The Journal of Comparative Neurology, 2009; 515 (3): 378-396.
  30. J. Schwenk, N. Harmel, G. Zolles, W. Bildl, A. Kulik, B. Heimrich, O. Chisaka, P. Jonas, U. Schulte, B. Fakler, N. Klöcker: Functional proteomics identify Cornichon proteins as auxiliary subunits of AMPA receptors. Science, 2009; 323: 1313-1319.
  31. A.C. Mallory, A. Hinze, M.R. Tucker, N. Bouché, V. Gasciolli, V. Elmayan, D. Laressergues, V. Jauvion, H. Vaucheret, T. Laux: Redundant and specific roles of the ARGONAUTE (AGO) proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLOS Genetics, 2009; 5 (9): e1000646.
  32. E. van der Graaff, T. Laux, S.A. Rensing: The WUS homeobox-containing (WOX) protein family. Genome Biology, 2009; 10 (12): 248.
  33. I. Rieu, T. Laux: Signaling pathways maintaining stem cells at the plant shoot apex. Seminars in Cell & Developmental Biology, 2009; 20 (9): 1083-1088.
  34. C. Jackson, R.F. Murphy, J. Kovacevic: Intelligent Acquisition and Learning of Fluorescence Microscope Data Models. IEEE TRANSACTIONS ON IMAGE PROCESSING, 2009; 18 (9): 2071-2084.
  35. J.H. Boysen, S. Fanning, J. Newberg, R.F. Murphy, A.P. Mitchell: Detection of Protein-Protein Interactions Through Vesicle Targeting. Genetics, 2009; 182 (1): 33-39.
  36. L.P. Coelho, A. Shariff, R. Murphy: Nuclei Segmentation In Microscope Cell Images: A Hand-Segmented Dataset And Comparison Of Algorithms. Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging, 2009; 518-521.
  37. S. Hugh, D. Lee, R. Murphy: Efficient framework for automated classification of subcellular patterns in budding yeast. CYTOMETRY PART A, 2009; 75A (11): 934-940.
  38. A. Pfeiffer, T. Kunkel, A. Hiltbrunner, G. Neuhaus, I. Wolf, V. Speth, E. Adam, F. Nagy, E. Schäfer: A cell-free system for light-dependent nuclear import of Phytochrome. Plant J, 2009; 57 (4): 680-689.
  39. J.J. Favory, A. Stec, H. Gruber, L. Rizzini, A. Oravecz, M. Funk, A. Albert, C. Cloix, G. Jenkins, E. Oakeley, H. Seidlitz, F. Nagy, R. Ulm: Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. The EMBO Journal, 2009; 28 (5): 591-601.
  40. A. Kugler, B. Kohler, K. Palme, P. Wolff, P. Dietrich: Salt-dependent regulation of a CNG channel subfamily in Arabidopsis. Bmc Plant Biology, 2009; 9: 140.
  41. D. Geiger, D. Becker, D. Vosloh, F. Gambale, K. Palme, M. Rehers, U. Anschuetz, I. Dreyer, J. Kudla, R. Hedrich: Heteromeric AtKC1/AKT1 channels in Arabidopsis roots facilitate growth under K+ limiting conditions. Journal of Biological Chemistry, 2009; 284 (32): 21288-21295.
  42. I.A. Paponov, W. Teale, D. Lang, M. Paponov, R. Reski, S.A. Rensing, K. Palme: The evolution of nuclear auxin signalling. Bmc Evolutionary Biology, 2009; 9: 126.
  43. J. Hejátko, H. Ryu, S.M. Choi, P. Porkovcová, G.-T. Kim, P. Soucek, M. Pernisová, K. Palme, B. Brzobohatý, I. Hwang: The Histidine Kinases CYTOKININ-INDEPENDENT1 and ARABIDOPSIS HISTIDINE KINASE2 and 3 Regulate Vascular Tissue Development in Arabidopsis Shoots. Plant Cell, 2009; 21 (7): 2008-2021.
  44. J. Sun, Y. Xu, S. Ye, Q. Chen, W. Zhou, R. Chen, F. Liu, X. Xugang Li, X. Wu, H. Jiang, J. Cohen, K. Palme, C. Li: Arabidopsis ASA1 Is Important for Jasmonate-Mediated Regulation of Auxin Biosynthesis and Transport during Lateral Root Formation. Plant Cell, 2009; 21: 1495-1511.
  45. R. Tsugeki, F.A. Ditengou, Y. Sumi, K. Palme, K. Okada: The Novel Nuclear Factor NO VEIN Mediates Auxin-Dependent Specification and Patterning in the Embryo, Shoot and Root. Plant Cell, 2009; 21 (10): 3133-3151.
  46. A. Raue, C. Kreutz, T. Maiwald, J. Bachmann, M. Schilling, U. Klingmüller, J. Timmer: Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics, 2009; 25 (15): 1923-1929.
  47. B. Buchner, S. Fuchs, G. Prinz, D. Pfeifer, K. Bartholome, M. Burger, N. Chevalier, L. Vallat, J. Timmer, J.G. Gribben, H. Jumaa, H. Veelken, C. Dierks, K. Zirlik: Spleen Tyrosine Kinase Is Overexpressed and Represents a Potential Therapeutic Target in Chronic Lymphocytic Leukemia. Cancer Research, 2009; 69 (13): 5424-5432.
  48. B. Hellwig, P. Mund, B. Schelter, B. Guschlbauer, J. Timmer, C.H. Lücking: A longitudinal study of tremor frequencies in Parkinson´s disease and essential tremor. Clinical Neurophysiology, 2009; 120 (2): 431-435.
  49. B. Rumberger, C. Kreutz, C. Nickel, M. Klein, S. Lagoutte, S. Teschner, J. Timmer, P. Gerke, G. Walz, J. Donauer: Combination of immunosuppressive drugs leaves specific \"fingerprint\" on gene expression in vitro. Immunopharmacology and Immunotoxicology, 2009; 31 (2): 283-292.
  50. B. Schelter, J. Timmer, M. Eichler: Assessing the strength of directed influences among neural signals using renormalized partial directed coherence. Journal of Neuroscience Methods, 2009; 179 (1): 121-130.
  51. C. Kreutz, J. Timmer: Systems biology: experimental design. Febs Journal, 2009; 276 (4): 923-942.
  52. E. Mammen, S. Nandi, T. Maiwald, J. Timmer: Effect of jump discontinuity for phase-randomized surrogate data testing. International Journal of Bifurcation and Chaos, 2009; 19 (1): 402-408.
  53. F. Amtage, K. Henschel, B. Schelter, J. Vesper, J. Timmer, C.H. Luecking, B. Hellwig: High functional connectivityof tremor related subthalamic neurons in Parkinson´s disease. Clinical Neurophysics, 2009; 120 (9): 1755-1761.
  54. H. Drentrup, B. Schelter, M. Jachan, J. Nawrath, R. Sandner, A. Brandt, J. Timmer, A. Schulze-Bonhage: Predicting Epileptic Seizures: An Assessment of Two Different Kinds to Combine Prediction Methods. Epilepsia, 2009; 50: 22-23.
  55. J. Rausenberger, C. Fleck, J. Timmer, M. Kollmann: Signature of gene expression noise in cellular systems. Progress Biophysics Molecular Biology, 2009; 100: 57-66.
  56. K. Bartholome, C. Kreutz, J. Timmer: Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets. Journal of Computational Biology, 2009; 16 (7): 959-967.
  57. K. Wester, S. Digiuni, F. Geier, J. Timmer, C. Fleck, M. Huelskamp: Functional diversity of R3 single-repeat genes in trichome development. Development, 2009; 136: 1487-1496.
  58. L. Sommerhalde, K. Henschel, J. Wohlmuth, F. Jachan, F. Amtage, B. Hellwig, C.H. Luecking, J. Timmer, B. Schelter: Time-variant estimation of directed influence during Parkinsonian tremor. Journal of Physiology, 2009; 103 (6): 348-352.
  59. M. Gerstung, J. Timmer, C. Fleck: Noisy signaling through promoter logic gates. Physical Review E, 2009; 79 (1): 011923.
  60. M. Jachan, K. Henschel, J. Nawrath, A. Schad, J. Timmer, B. Schelter: Inferring direct directed-information flow from multivariate non-linear time series. Physical Review E, 2009; 80 (1): 011138.
  61. M. Jachan, M. Reinhard, L. Spindeler, A. Hetzel, B. Schelter, J. Timmer: Parametric Versus Nonparametric Transfer Function Estimation of Cerebral Autoregulation from Spontaneous Blood-Pressure Oscillations. Cardiovascular Engineering, 2009; 9 (7): 72-82.
  62. M. Joschko, R. Gebbers, D. Barkusky, J. Rogasik, W. Hohn, W. Hierold, C. Fox, J. Timmer: Location-dependency of earthworm response to reduced tillage on sandy soil. Soil & Tillage Research, 2009; 102 (1): 55-66.
  63. M. Schilling, T. Maiwald, S. Hengl, D. Winter, C. Kreutz, W. Kolch, W.D. Lehmann, J. Timmer, U. Klingmüller: Theoretical and experimental analysis links isoformspecific ERK signalling to cell fate decisions. Molecular Systems Biology, 2009; 5: 334.
  64. N. Borisov, E. Aksamitiene, A. Kiyatkin, S. Legewie, J. Berkhout, T. Maiwald, N.P. Kaimachnikov, J. Timmer, J.B. Hoek, B.N. Kholodenko: Systems-level interactions between insulin–EGF networks amplify mitogenic signaling. Molecular Systems Biology, 2009; 5: 256.
  65. S. Lassmann, C. Kreutz, A. Schoepflin, U. Hopt, J. Timmer, M. Werner: A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. Journal of Molecular Medicine, 2009; 87 (2): 211-224.
  66. T. Wiech, E. Nikolopoulos, R. Weis, R. Langer, K. Bartholome, J. Timmer, A. Walch, H. Höfler, M. Werner: Genome-wide analysis of genetic alterations in Barrett´s adenocarcinoma using single nucleotide polymorphism arrays. Laboratory Investigation, 2009; 89 (4): 385-397.
  67. H. Tsuboi, H. Yamashita, M. Wada: Chloroplasts do not have a polarity for light-induced accumulation movement. Journal of Plant Research, 2009; 122 (1): 131-140.
  68. N. Inoue, M. Watanabe, T. Nanba, M. Wada, T. Akamizu, Y. Iwatani: Involvement of functional polymorphisms in the TNFA gene in the pathogenesis of autoimmune thyroid diseases and production of anti-thyrotropin receptor antibody. Clinical and Experimental Immunology, 2009; 156 (2): 199-204.
  69. Y. Kodama, M. Wada: Simultaneous visualization of two protein complexes in a single plant cell using multicolor fluorescence complementation analysis. Plant Mol Biol, 2009; 70: 211-217.


Scientific Staff

  1. A.L. Angelova, M. Aprahamian, S.P. Grekova, A. Hajri, B. Leuchs, N.A. Giese, C. Dinsart, A. Herrmann, J. Rommelaere, Z. Raykov: Improvement of Gemcitabine-Based Therapy of Pancreatic Carcinoma by Means of Oncolytic Parvovirus H-1PV. Clin Cancer Res, 2009; 15: 511-519.
  2. S. Réjiba, C. Parmentier, C. Bignad, A. Hajri: Gemcitabin-based chemogene therapy of pancreatic cancer using Ad-dCK::UMK GDEPT and TS/RRM2 siRNAs strategies. Neoplasia, 2009; 11: 637-650.