Selected recent publications of JCB members

2011

Arora, D., Stopp, S., Böhmer, S.-A., Schons, J., Godfrey, R., Masson, K., Razumovskaya, E., Rönnstrand, L., Tänzer, S., Bauer, R., Böhmer, F.-D. and Müller, J.P. (2011) Protein-tyrosine phosphatase DEP-1 controls receptor tyrosine kinase FLT3 signaling, Journal of Biological Chemistry, 286, 10918-10929.

Banks, J.A., Nishiyama, T., Hasebe, M., Bowman, J.L., Gribskov, M., dePamphilis, C., Albert, V.A., Aono, N., Aoyama, T., Ambrose, B.A., Ashton, N.W., Axtell, M.J., Barker, E., Barker, M.S., Bennetzen, J.L., Bonawitz, N.D., Chapple, C., Cheng, C., Correa, L.G.G., Dacre, M., DeBarry, J., Dreyer, I., Elias, M., Engstrom, E.M., Estelle, M., Feng, L., Finet, C., Floyd, S.K., Frommer, W.B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K.G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T.P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-Roeber, B., Nelson, D.R., Obara, M., Oguri, Y., Olmstead, R.G., Onodera, N., Petersen, B.L., Pils, B., Prigge, M., Rensing, S.A., Riano-Pachón, D.M., Roberts, A.W., Sato, Y., Scheller, H.V., Schulz, B., Schulz, C., Shakirov, E.V., Shibagaki, N., Shinohara, N., Shippen, D.E., Sorensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theißen, G., Ulvskov, P., Wakazuki, S., Weng, J., Willats, W.W.G.T., Wipf, D., Wolf, P.G., Yang, L., Zimmer, A.D., Zhu, Q., Mitros, T., Hellsten, U., Loqué, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E., Lucas, S., Rokhsar, D. and Grigoriev, I.V. (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants, Science, 332, 960-963.

Bartl, M., Li, P. and Biegler, L.T. (2011) Improvement of state profile accuracy in nonlinear dynamic optimization with the quasi-sequential approach, AIChE Journal, 57, 2185-2197.

Bekhite, M.M., Finkensieper, A., Binas, S., Möller, J., Wetzker, R., Figulla, H.-R., Sauer, H. and Wartenberg, M. (2011) VEGF-mediated PI3K class IA and PKC signaling in cardiomyogenesis and vasculogenesis of mouse embryonic stem cells, Journal of Cell Science, 124, 1819-1830.

Beuster, G., Zarse, K., Kaleta, C., Thierbach, R., Kiehntopf, M., Steinberg, P., Schuster, S. and Ristow, M. (2011) Inhibition of alaninie aminotransferase (ALAT) in silico and in vivo promotes mitochondrial metabolism to impair malignant growth, Journal of Biological Chemistry, 286, 22323-22330.

Böcker, S., Briesemeister, S. and Klau, G.W. (2011) Exact algorithms for cluster editing: Evaluation and experiments, Algorithmica, 60, 316-334.

Burmester, A., Shelest, E., Glöckner, G., Heddergott, C., Schindler, S., Staib, P., Heidel, A., Felder, M., Petzold, A., Szafranski, K., Feuermann, M., Pedruzzi, I., Priebe, S., Groth, M., Winkler, R., Li, W., Kniemeyer, O., Schroeckh, V., Hertweck, C., Hube, B., White, T., Platzer, M., Guthke, R., Heitman, J., Wöstemeyer, J., Zipfel, P., Monod, M. and Brakhage, A. (2011) Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi, Genome Biology, 12, R7.

Carella, M., Becher, J., Ohlenschläger, O., Ramachandran, R., Gührs, K.-H., Wellenreuther, G., Meyer-Klaucke, W., Heinemann, S.H. and Görlach, M. (2011) Structure–function relationship in an archaebacterial methionine sulphoxide reductase B, Molecular Microbiology, 79, 342-358.

Fazius, E., Shelest, V. and Shelest, E. (2011) SiTar: a novel tool for transcription factor binding site prediction, Bioinformatics, 27, 2806-2811.

Geletu, A., Hoffmann, A., Klöppel, M. and Li, P. (2011) Monotony analysis and sparse-grid integration for nonlinear chance constrained process optimization, Engineering Optimization, 43, 1019-1041.

Geurts, J., Vermeij, E.A., Pohlers, D., Arntz, O.J., Kinne, R.W., van den Berg, W.B. and van de Loo, F.A.J. (2011) A novel Saa3-promoter reporter distinguishes inflammatory subtypes in experimental arthritis and human synovial fibroblasts, Annals of the Rheumatic Diseases, 70, 1311-1319.

Heidel, A.J., Lawal, H.M., Felder, M., Schilde, C., Helps, N.R., Tunggal, B., Rivero, F., John, U., Schleicher, M., Eichinger, L., Platzer, M., Noegel, A.A., Schaap, P. and Glöckner, G. (2011) Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication, Genome Research, doi: 10.1101/gr.121137.111.

Herbst, C., Herbst, J., Leppert, J., Ohlenschläger, O., Görlach, M. and Ramachandran, R. (2011) Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes, Journal of Biomolecular NMR, 50, 277-284.
Hoffmann, K. and Voigt, K. (2011) Lichtheimia (Absidia-like fungi). In Liu, D. (ed), Molecular detection of human fungal pathogens. Taylor & Francis CRC Press Inc, 735-748.

Hou, S., Xu, R., Clark, J.F., Wurster, W.L., Heinemann, S.H. and Hoshi, T. (2011) Bilirubin oxidation end products directly alter K⁺ channels important in the regulation of vascular tone, Journal of Cerebral Blood Flow & Metabolism, 31, 102-112.

Kaleta, C., de Figueiredo, L.F., Guthke, R., Ristow, M. and Schuster, S. (2011) In silico evidence for gluconeogenesis from fatty acids in humans, PLoS Computational Biology, 7, e1002116.

Kuester, M., Becker, G.L., Hardes, K., Lindberg, I., Steinmetzer, T. and Than, M.E. (2011) Purification of the proprotein convertase furin by affinity chromatography based on PC-specific inhibitors, Biological Chemistry, 392, 973-981.

Kuester, M., Kemmerzehl, S., Dahms, S.O., Roeser, D. and Than, M.E. (2011) The crystal structure of Death Receptor 6 (DR6): A potential receptor of the Amyloid Precursor Protein (APP), Journal of Molecular Biology, 409, 189-201.

Leipold, E., Markgraf, R., Miloslavina, A., Kijas, M., Schirmeyer, J., Imhof, D. and Heinemann, S.H. (2011) Molecular determinants of the subtype specificity of µ-conotoxin SIIIA targeting neuronal voltage-gated sodium channels, Neuropharmacology, 61, 105-111.

Mech, F., Thywissen, A., Guthke, R., Brakhage, A. and Figge, M.T. (2011) Automated image analysis of the host-pathogen interaction between phagocytes and Aspergillus fumigatus, PLoS ONE, 6, e19591.

Mika, J., Clanton, T.O., Pretzel, D., Schneider, G., Ambrose, C.G. and Kinne, R.W. (2011) Surgical preparation for articular cartilage regeneration without penetration of the subchondral bone plate: in vitro and in vivo studies in humans and sheep, The American Journal of Sports Medicine, 39, 624-631.

Mondragón-Palomino, M. and Theißen, G. (2011) Conserved differential expression of paralogous DEFICIENS- and GLOBOSA-like MADS-box genes in the flowers of Orchidaceae: refining the ‘orchid code’, Plant Journal, 66, 1008-1019.

Müller, S., Fleck, C.B., Wilson, D., Hummert, C., Hube, B. and Brock, M. (2011) Gene acquisition, duplication and metabolic specification: The evolution of fungal methylisocitrate lyases, Environmental Microbiology, 13, 1534-1548.

Papp, T., Hoffmann, K., Nyilasi, I., Petkovits, T., Wagner, L., Vágvölgyi, C. and Voigt, K. (2011) Mortierella. In Liu, D. (ed), Molecular detection of human fungal pathogens. Taylor & Francis CRC Press Inc, 749-758.

Pretzel, D., Linss, S., Rochler, S., Endres, M., Kaps, C., Alsalameh, S. and Kinne, R.W. (2011) Relative percentage and zonal distribution of mesenchymal progenitor cells in human osteoarthritic and normal cartilage, Arthritis Research & Therapy, 13, R64.

Rasche, F., Svatos, A., Maddula, R.K., Böttcher, C. and Böcker, S. (2011) Computing fragmentation trees from tandem mass spectrometry data, Analytical Chemistry, 83, 1243-1251.

Scheubert, K., Hufsky, F., Rasche, F. and Böcker, S. (2011) Computing fragmentation trees from metabolite multiple mass spectrometry data. In Proceedings of Research in Computational Molecular Biology (RECOMB 2011). Springer, 377-391.

Schwartze, V., Rothhardt, J. and Voigt, K. (2011) Entomophthorales. In Liu, D. (ed), Molecular detection of human fungal pathogens. Taylor & Francis CRC Press, 723-734.

Sielaff, F., Than, M.E., Bevec, D., Lindberg, I. and Steinmetzer, T. (2011) New furin inhibitors based on weakly basic amidinohydrazones, Bioorganic & Medicinal Chemistry Letters, 21, 836-840.

Taudien, S., Szafranski, K., Felder, M., Groth, M., Huse, K., Raffaelli, F., Petzold, A., Zhang, X., Rosenstiel, P., Hampe, J., Schreiber, S. and Platzer, M. (2011) Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing, BMC Genomics, 12, 243.

Thieme, C.J., Gramzow, L., Lobbes, D. and Theißen, G. (2011) SplamiR – prediction of spliced miRNAs in plants, Bioinformatics, 27, 1215-1223.

Tietze, D., Voigt, S., Mollenhauer, D., Tischler, M., Imhof, D., Gutmann, T., González, L., Ohlenschläger, O., Breitzke, H., Görlach, M. and Buntkowsky, G. (2011) Revealing the position of the substrate in NiSOD: a model study, Angewandte Chemie International Edition, 50, 2946-2950.

Wessely, F., Bartl, M., Guthke, R., Schuster, S. and Kaleta, C. (2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs, Molecular Systems Biology, 7, 515.

2010

Alastruey-Izquierdo, A., Hoffmann, K., de Hoog, G.S., Rodriguez-Tudela, J.L., Voigt, K., Bibashi, E. and Walther, G. (2010) Species recognition and clinical relevance of the zygomycetous genus Lichtheimia (syn. Absidia Pro Parte, Mycocladus), Journal of Clinical Microbiology, 48, 2154-2170.

Albrecht, D., Kniemeyer, O., Brakhage, A.A. and Guthke, R. (2010) Missing values in gel-based proteomics, Proteomics, 10, 1202-1211.

Anderson, R., Franch, A., Castell, M., Perez-Cano, F.J., Bräuer, R., Pohlers, D., Gajda, M., Siskos, A.P., Katsila, T., Tamvakopoulos, C., Rauchhaus, U., Panzner, S. and Kinne, R.W. (2010) Liposomal encapsulation enhances and prolongs the anti-inflammatory effects of water-soluble dexamethasone phosphate in experimental adjuvant arthritis, Arthritis Research & Therapy, 12, R147.

Aumann, F., Sühnel, J., Langowski, J. and Diekmann, S. (2010) Rigid assembly and Monte Carlo models of stable and unstable chromatin structures: the effect of nucleosomal spacing, Theoretical Chemistry Accounts, 125, 217-231.

Bär, K.-J., Schuhmacher, A., Höfels, S., Schulz, S., Voss, A., Yeragani, V.K., Maier, W. and Zobel, A. (2010) Reduced cardio-respiratory coupling after treatment with nortriptyline in contrast to S-citalopram, Journal of Affective Disorders, 127, 266-273.

Bartl, M., Li, P. and Schuster, S. (2010) Modelling the optimal timing in metabolic pathway activation – Use of Pontryagin’s Maximum Principle and role of the Golden section, BioSystems, 101, 67-77.

Baumert, M., Seeck, A., Faber, R., Nalivaiko, E. and Voss, A. (2010) Longitudinal changes in QT interval variability and rate adaptation in pregnancies with normal and abnormal uterine perfusion, Hypertension Research, 33, 555-560.

Becker, G.L., Sielaff, F., Than, M.E., Lindberg, I., Routhier, S., Day, R., Lu, Y., Garten, W. and Steinmetzer, T. (2010) Potent inhibitors of furin and furin-like proprotein convertases containing decarboxylated P1 arginine mimetics, Journal of Medicinal Chemistry, 53, 1067-1075.

Bodenstein, C., Knoke, B., Marhl, M., Perc, M. and Schuster, S. (2010) Using Jensen’s inequality to explain the role of regular calcium oscillations in protein activation, Physical Biology, 7, 036009.

Brantl, S. and Licht, A. (2010) Characterisation of Bacillus subtilis transcriptional regulators involved in metabolic processes, Current Protein and Peptide Science, 11, 274-291.

Buchwald, M., Pietschmann, K., Müller, J.P., Böhmer, F.D., Heinzel, T. and Krämer, O.H. (2010) Ubiquitin conjugase UBCH8 targets active FMS-like tyrosine kinase 3 for proteasomal degradation, Leukemia, 24, 1412-1421.

Dahms, S.O., Hoefgen, S., Roeser, D., Schlott, B., Gührs, K.-H. and Than, M.E. (2010) Structure and biochemical analysis of the heparin-induced E1 dimer of the amyloid precursor protein, Proceedings of the National Academy of Sciences of the United States of America, 107, 5381-5386.

Dormann, D., Rodde, R., Edbauer, D., Bentmann, E., Fischer, I., Hruscha, A., Than, M.E., Mackenzie, I.R.A., Capell, A., Schmid, B., Neumann, M. and Haass, C. (2010) ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import, EMBO Journal, 29, 2841-2857.

Ebert, A., Jochum, T., Ritter, J., Boettger, M.K., Schulz, S., Voss, A. and Bär, K.-J. (2010) Does parasympathetic modulation prior to ECT treatment influence therapeutic outcome?, Progress in Neuro-Psychopharmacology and Biological Psychiatry, 34, 1174-1180.

Fliegerová, K., Mrázek, J., Hoffmann, K., Zábranská, J. and Voigt, K. (2010) Diversity of anaerobic fungi within cow manure determined by ITS1 analysis, Folia Microbiologica, 55, 319-325.

Gimpel, M., Heidrich, N., Mäder, U., Krügel, H. and Brantl, S. (2010) A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon, Molecular Microbiology, 76, 990-1009.

Govind, G., Mittapalli, O., Griebel, T., Allmann, S., Böcker, S. and Baldwin, I.T. (2010) Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants, PLoS ONE, 5, e8735.

Gramzow, L., Ritz, M.S. and Theißen, G. (2010) On the origin of MADS-domain transcription factors, Trends in Genetics, 26, 149-153.

Gramzow, L. and Theissen, G. (2010) A hitchhiker’s guide to the MADS world of plants, Genome Biology, 11, 214.

Griffith, G.W., Baker, S., Fliegerova, K., Liggenstoffer, A., van der Giezen, M., Voigt, K. and Beakes, G. (2010) Anaerobic fungi: Neocallimastigomycota, IMA Fungus, 1, 181-185.

Guillemot, S. and Mnich, M. (2010) Kernel and fast algorithm for dense triplet inconsistency. In Kratochvíl J. et al. (ed), Theory and Applications of Models of Computation. Lecture Notes in Computer Science, 6108, 247-257.

Hecker, M., Goertsches, R.H., Fatum, C., Koczan, D., Thiesen, H.J., Guthke, R. and Zettl, U.K. (2010) Network analysis of transcriptional regulation in response to intramuscular interferon-beta-1a multiple sclerosis treatment, Pharmacogenomics Journal, doi: 10.1038/tpj.2010.77.

Herbst, C., Herbst, J., Carella, M., Leppert, J., Ohlenschläger, O., Görlach, M. and Ramachandran, R. (2010) Broadband ¹⁵N–¹³C dipolar recoupling via symmetry-based RF pulse schemes at high MAS frequencies, Journal of Biomolecular NMR, 47, 7-17.

Hou, S., Vigeland, L.E., Zhang, G., Xu, R., Li, M., Heinemann, S.H. and Hoshi, T. (2010) Zn²⁺ activates large-conductance Ca²⁺-activated K⁺ channel via an intracellular domain, Journal of Biological Chemistry, 285, 6434-6442.

Hüffner, F., Betzler, N. and Niedermeier, R. (2010) Separator-based data reduction for signed graph, Journal of Combinatorial Optimization, 20, 335-360.

Hufsky, F., Kuchenbecker, L., Jahn, K., Stoye, J. and Böcker, S. (2010) Swiftly computing center strings. In Moulton, V. and Singh, M. (eds), Algorithms in Bioinformatics. Lecture Notes in Computer Science, 6293, 325-336.

Kaleta, C., Göhler, A., Schuster, S., Jahreis, K., Guthke, R. and Nikolajewa, S. (2010) Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis, BMC Systems Biology, 4, 116.

Kinne, R.W., Emmrich, F. and M., F. (2010) Clinical impact of radiolabeled anti-CD4 antibodies in the diagnosis of rheumatoid arthritis, Quarterly Journal of Nuclear Medicine and Molecular Imaging, 54, 629-638.

Krügel, H., Licht, A., Biedermann, G., Petzold, A., Lassak, J., Hupfer, Y., Schlott, B., Hertweck, C., Platzer, M., Brantl, S. and Saluz, H.-P. (2010) Cervimycin C resistance in Bacillus subtilis is due to a promoter up-mutation and increased mRNA stability of the constitutive ABC-transporter gene bmrA, FEMS Microbiology Letters, 313, 155-163.

Linde, J., Wilson, D., Hube, B. and Guthke, R. (2010) Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells, BMC Systems Biology, 4, 148.

Rebholz-Schuhmann, D., Yepes, A.J.J., van Mulligen, E.M., Kang, N., Kors, J., Milward, D., Corbett, P., Buyko, E., Beisswanger, E. and Hahn, U. (2010) The CALBC Silver Standard Corpus: Harmonizing Multiple Semantic Annotations in a Large Biomedical Corpus, Journal of Bioinformatics and Computational Biology, 8, 1-15.

Ruppin, E., Papin, J.A., de Figueiredo, L.F. and Schuster, S. (2010) Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks, Current Opinion in Biotechnology, 21, 502-510.

Schirmeyer, J., Szafranski, K., Leipold, E., Mawrin, C., Platzer, M. and Heinemann, S.H. (2010) A subtle alternative splicing event of the NA_v1.8 voltage-gated sodium channel is conserved in human, rat, and mouse, Journal of Molecular Neuroscience, 41, 310-314.

Shelest, V., Albrecht, D. and Shelest, E. (2010) DistanceScan: a tool for promoter modeling, Bioinformatics, 26, 1460-1462.

Sinha, R., Lenser, T., Jahn, N., Gausmann, U., Friedel, S., Szafranski, K., Huse, K., Rosenstiel, P., Hampe, J., Schuster, S., Hiller, M., Backofen, R. and Platzer, M. (2010) TassDB2 – A comprehensive database of subtle alternative splicing events, BMC Bioinformatics, 11, 216.

Spitzenberg, V., König, C., Ulm, S., Marone, R., Röpke, L., Müller, J., Grün, M., Bauer, R., Rubio, I., Wymann, M., Voigt, A. and Wetzker, R. (2010) Targeting PI3K in neuroblastoma, Journal of Cancer Research and Clinical Oncology, 136, 1881-1890.

Stuhlmüller, B., Häupl, T., Hernandez, M.M., Grützkau, A., Kuban, R.J., Tandon, N., Voss, J.W., Salfeld, J., Kinne, R.W. and Burmester, G.R. (2010) CD11c as a transcriptional biomarker to predict response to anti-TNF monotherapy with adalimumab in patients with rheumatoid arthritis, Clinical Pharmacology & Therapeutics, 87, 311-321.

Tamimi, J. and Li, P. (2010) A combined approach to nonlinear model predictive control of fast systems, Journal of Process Control, 20, 1092-1102.

Taudien, S., Groth, M., Huse, K., Petzold, A., Szafranski, K., Hampe, J., Rosenstiel, P., Schreiber, S. and Platzer, M. (2010) Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing, BMC Genomics, 11, 252.

Tietze, D., Tischler, M., Voigt, S., Imhof, D., Ohlenschläger, O., Görlach, M. and Buntkowsky, G. (2010) Development of a functional cis-prolyl bond biomimetic and mechanistic implications for Nickel Superoxide Dismutase, Chemistry, 16, 7572-7578.

Wang, Y.-Q., Melzer, R. and Theißen, G. (2010) Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of ‘floral quartets’, The Plant Journal, 64, 177-190.

Werner, S., Diekert, G. and Schuster, S. (2010) Revisiting the thermodynamic theory of optimal ATP stoichiometries by analysis of various ATP-producing metabolic pathways, Journal of Molecular Evolution, 71, 346-355.

2009

Bär, K.-J., Berger, S., Metzner, M., Böttger, M.K., Schulz, S., Ramachandraiah, C.T., Terhaar, J., Voss, A., Yeragani, V.K. and Sauer, H. (2009) Autonomic dysfunction in unaffected first-degree relatives of patients suffering from schizophrenia, Schizophrenia Bulletin, sbp024.

Baum, N., Schiene-Fischer, C., Frost, M., Schumann, M., Sabapathy, K., Ohlenschläger, O., Grosse, F. and Schlott, B. (2009) The prolyl cis/trans isomerase cyclophilin 18 interacts with the tumor suppressor p53 and modifies its functions in cell cycle regulation and apoptosis, Oncogene, 28, 3915-3925.

Böcker, S., Briesemeister, S., Bui, Q.B.A. and Truss, A. (2009) Going weighted: parameterized algorithms for cluster editing, Theoretical Computer Science, 410, 5467-5480.

Böcker, S., Bui, Q.B.A., Seeber, P. and Truss, A. (2009) Computing bond types in molecule graphs. In, Computing and Combinatorics. COCOON 2009 Proceedings. Springer, Berlin, Heidelberg, 297-306.

Böcker, S., Letzel, M.C., Lipták, Z. and Pervukhin, A. (2009) SIRIUS: decomposing isotope patterns for metabolite identification, Bioinformatics, 25, 218-224.

Brantl, S. (2009) RNAs, Small etc. In Schaechter, M. (ed), Encyclopedia of Microbiology. Academic Press, Oxford, 409-437.

Brantl, S. (2009) Bacterial chromosome-encoded small regulatory RNAs, Future Microbiology, 4, 85-103.

Cerutti, S., Hoyer, D. and Voss, A. (2009) Multiscale, multiorgan and multivariate complexity analyses of cardiovascular regulation, Philosophical Transactions of the Royal Society A, 367, 1337-1358.

de Figueiredo, L.F., Schuster, S., Kaleta, C. and Fell, D.A. (2009) Can sugars be produced from fatty acids? A test case for pathway analysis tools, Bioinformatics, 25, 152-158.

DeLuca, D., Beisswanger, E., Wermter, J., Horn, P., Hahn U. and Blasczyk, R. (2009) MaHCO: An Ontology of the Major Histocompatibility Complex for Immunoinformatic Applications and Text Mining, Bioinformatics, 25, 2009, 2064-2070.

Eckart, R.A., Brantl, S. and Licht, A. (2009) Search for additional targets of the transcriptional regulator CcpN from Bacillus subtilis, FEMS Microbiology Letters, 299, 223-231.

Friedel, M., Nikolajewa, S., Sühnel, J. and Wilhelm, T. (2009) DiProGB: The dinucleotide properties genome browser, Bioinformatics, 25, 2603-2604.

Friedel, M., Nikolajewa, S., Sühnel, J. and Wilhelm, T. (2009) DiProDB: A database for dinucleotide properties, Nucleic Acids Research, 37, D37-40.

Hecker, M., Görtsches, R., Engelmann, R., Thiesen, H.-J. and Guthke, R. (2009) Integrative modeling of transcriptional regulation in response to antirheumatic therapy, BMC Bioinformatics, 10, 262.

Hecker, M., Lambeck, S., Töpfer, S., van Someren, E. and Guthke, R. (2009) Gene regulatory network inference: data integration in dynamic models – A review, Biosystems, 96, 86-103.

Herbst, C., Herbst, J., Kirschstein, A., Leppert, J., Ohlenschläger, O., Görlach, M. and Ramachandran, R. (2009) Design of high-power, broadband 180° pulses and mixing sequences for fast MAS solid state chemical shift correlation NMR spectroscopy, Journal of Biomolecular NMR, 43, 51-61.

Herbst, C., Herbst, J., Leppert, J., Ohlenschläger, O., Görlach, M. and Ramachandran, R. (2009) Numerical design of RN_n^ν symmetry-based RF pulse schemes for recoupling and decoupling of nuclear spin interactions at high MAS frequencies, Journal of Biomolecular NMR, 44, 235-244.

Kaleta, C., de Figueiredo, L.F. and Schuster, S. (2009) Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns, Genome Research, 19, 1872-1883.

Kaleta, C., Richter, S. and Dittrich, P. (2009) Using chemical organization theory for model checking, Bioinformatics, 25, 1915-1922.

Knoke, B., Textor, S., Gershenzon, J. and Schuster, S. (2009) Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves, Phytochemistry Reviews, 8, 39-51.

Komusiewicz, C., Niedermeier, R. and Uhlmann, J. (2009) Deconstructing intractability: A case study for interval constrained coloring. In Kucherov, G. and Ukkonen, E. (eds), Combinatorial Pattern Matching, CPM 2009, Proceedings. Springer, Berlin, Heidelberg, 207-220.

Kunisch, E. Jansen, A., Kojima, F. Löffler, I., Kapoor, M., Kawai, S., Rubio, I., Crofford, L.J. and Kinne, R.W. (2009) Prostaglandin E₂ differentially modulates proinflammatory/prodestructive effects of TNF-α on synovial fibroblasts via specific E prostanoid receptors/cAMP, Journal of Immunology, 183, 1328-1336.

Lehmann, K., Müller, J.P., Schlott, B., Skroblin, P., Barz, D., Norgauer, J. and Wetzker, R. (2009) PI3Kγ controls oxidative bursts in neutrophils via interactions with PKCα and p47phox, Biochemical Journal, 419, 603-610.

Lenser, T., Theißen, G. and Dittrich, P. (2009) Developmental robustness by obligate interaction of class B floral homeotic genes and proteins, PLoS Computational Biology, 5, e1000264.

Lohel, M., Ibrahim, B., Diekmann, S. and Dittrich, P. (2009) The role of localization in the operation of the mitotic spindle assembly checkpoint, Cell Cycle, 8, 2650-2660.

Melzer, R., Verelst, W. and Theißen, G. (2009) The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro, Nucleic Acids Research, 37, 144-157.

Melzer, R. and Theißen, G. (2009) Reconstitution of ‘floral quartets’ in vitro involving class B and class E floral homeotic proteins, Nucleic Acids Research, 37, 2723-2736.

Mondragón-Palomino, M., Hiese, L., Härter, A., Koch, M. and Theißen, G. (2009) Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses, BMC Evolutionary Biology, 9, 81.

Preis, H., Eckart, R.A., Gudipati, R.K., Heidrich, N. and Brantl, S. (2009) CodY activates transcription of a small RNA in Bacillus subtilis, Journal of Bacteriology, 191, 5446-5457.

Pudimat, R., Backofen, R. and Schukat-Talamazzini, E.G. (2009) Fast feature subset selection in biological sequence analysis, International Journal of Pattern Recognition and Artificial Intelligence, 23, 191-207.

Reichwald, K., Lauber, C., Nanda, I., Kirschner, J., Hartmann, N., Schories, S., Gausmann, U., Taudien, S., Schilhabel, M. Szafranski, K., Glöckner, G., Schmid, M., Cellerino, A., Schartl, M., Englert, C. and Platzer, M. (2009) High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: A new vertebrate model for aging research, Genome Biology, 10, R16.

Richter, J.F., Gitter, A.H., Günzel, D., Weiss, S., Mohamed, W., Chakraborty, T., Fromm, M. and Schulzke, J.-D. (2009) Listeriolysin O affects barrier function and induces chloride secretion in HT-29/B6 colon epithelial cells, American Journal of Physiology – Gastrointestinal and Liver Physiology, 296, G1350-G1359.

Schmidt-Arras, D., Böhmer, S.-A., Koch, S., Müller, J.P., Blei, L., Cornils, H., Bauer, R., Korasikha, S., Thiede, C. and Böhmer, F.-D. (2009) Anchoring of FLT3 in the endoplasmic reticulum alters signaling quality, Blood, 113, 3568-3576.

Sinha, R., Nikolajewa, S., Szafranski, K., Hiller, M., Jahn, N., Huse, K., Platzer, M. and Backofen, R. (2009) Accurate prediction of NAGNAG alternative splicing, Nucleic Acids Research, 37, 3569-3579.

Voss, A., Schulz, S., Schröder, R., Baumert, M. and Caminal, P. (2009) Methods derived from nonlinear dynamics for analysing heart rate variability, Philosophical Transactions of the Royal Society A, 367, 277-296.

Weller, M., Komusiewicz, C., Niedermeier, R. and Uhlmann, J. (2009) On making directed graphs transitive. In Dehne, F., Gavrilova, M., Sack, J.-R. and Toth, C.D. (eds), Algorithms and Data Structures, WADS 2009, Proceedings. Springer, Berlin, Heidelberg, 542-553.

Wermter, J., Tomanek, K. and Hahn, U. (2009) High-Performance Gene Name Normalization with GeNo, Bioinformatics, 25, 815-821.

Wicker, T., Taudien, S., Houben, A., Keller, B., Graner, A., Platzer, M. and Stein, N. (2009) A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley, The Plant Journal, 59, 712-722.

Wollbold, J., Huber, R., Pohlers, D., Koczan, D., Guthke, R., Kinne, R. and Gausmann, U. (2009) Adapted Boolean network models for extracellular matrix formation, BMC Systems Biology, 3, 77.

2008

Albrecht, D., Guthke, R., Kniemeyer, O. and Brakhage, A.A. (2008) Systems biology of human-pathogenic fungi. In Daskalaki, A. (ed), Handbook of Research on Systems Biology Applications in Medicine. IGI Global, 400-418.

Altman, R., Bergman, C., Blake, J., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, L.J., Krallinger, M., Mons, B., O’Donoghue, S.I., Peitsch, M., Rebholz-Schumann, D., Shatkay, H. and Valencia, A. (2008) Text Mining for Biology: The Way Forward. Opinions from Leading Scientists, Genome Biology, 9, S7.

Bär, K.-J., Böttger, M.K., Schulz, S., Neubauer, R., Jochum, T., Voss, A. and Yeragani, V.K. (2008) Reduced cardio-respiratory coupling in acute alcohol withdrawal, Drug and Alcohol Dependence, 98, 210-217.

Bär, K.-J., Koschke, M., Berger, S., Schulz, S., Tancer, M., Voss, A. and Yeragani, V.K. (2008) Influence of olanzapine on QT variability and complexity measures of heart rate in patients with schizophrenia, Journal of Clinical Psychopharmacology, 28, 694-698.

Bartholmes, C., Nutt, P. and Theißen, G. (2008) Germline transformation of Shepherd’s purse (Capsella bursa-pastoris) by the ‘floral dip’ method as a tool for evolutionary and developmental biology, Gene, 409, 11-19.

Behre, J., Wilhelm, T., von Kamp, A., Ruppin, E. and Schuster, S. (2008) Structural robustness of metabolic networks with respect to multiple knockouts, Journal of Theoretical Biology, 252, 433-441.

Beisswanger, E., Schulz, S., Stenzhorn H. and Hahn, U., (2008) BioTop: An Upper Domain Ontology for the Life Sciences – A Description of Its Current Structure, Contents, and Interfaces to OBO Ontologies, Applied Ontology, 3, 205-212.

Betzler, N., Fellows, M.R., Komusiewicz, C. and Niedermeier, R. (2008) Parameterized algorithms and hardness results for some graph motif problems. In Ferragina, P. and Landau, G.M. (eds), Combinatorial Pattern Matching, CPM 2008, Proceedings. Springer, Berlin, Heidelberg, 31-43.

Böcker, S., Briesemeister, S. and Klau, G.W. (2008) Exact algorithms for cluster editing: evaluation and experiments. In, Experimental Algorithms. WEA 2008 proceedings. Springer, Berlin, Heidelberg, 289-302.

Böcker, S., Jahn, K., Mixtacki, J. and Stoye, J. (2008) Computation of median gene clusters. In, Research in Computational Molecular Biology. RECOMB 2008 Proceedings. Springer, Berlin, Heidelberg.

Böcker, S. and Rasche, F. (2008) Towards de novo identification of metabolites by analyzing tandem mass spectra, Bioinformatics, 24, i49-i55.

Bortfeldt, R., Schindler, S., Szafranski, K., Schuster, S. and Holste, D. (2008) Comparative analysis of sequence features involved in the recognition of tandem splice sites, BMC Genomics, 9, 202.

Centler, F., Kaleta, C., di Fenizio, P.S. and Dittrich, P. (2008) Computing chemical organizations in biological networks, Bioinformatics, 24, 1611-1618.

Eichardt, R., Haueisen, J., Knösche, T.R. and Schukat-Talamazzini, E.G. (2008) Reconstruction of multiple neuromagnetic sources using augmented evolution strategies – a comparative study, IEEE Transactions on Biomedical Engineering, 55, 703-712.

Friedel, M., Nikolajewa, S. and Wilhelm, T. (2008) The decomposition tree for analyses of boolean functions, Mathematical Structures in Computer Science, 18, 411-426.

Geist, C. and Brantl, S. (2008) TraM protein of plasmid R1: In vitro selection of the target region reveals two consensus 7 bp binding motifs spaced by a 4 bp linker of defined sequence, Plasmid, 59, 20-35.

Görnig, M., Schröder, R., Roth, T., Truebner, S., Palutke, I., Figulla, H.R., Leder, U. and Voss, A. (2008) Peripheral arterial disease alters heart rate variability in cardiovascular patients, Pacing and Clinical Electrophysiology, 31, 858-862.

Gramm, J., Nickelsen, A. and Tantau, T. (2008) Fixed-parameter algorithms in phylogenetics. In Keith, J.M. (ed), Bioinformatics: Data, Sequence Analysis and Evolution. Humana Press, 507-535.

Heller, F., Fromm, A., Gitter, A.H., Mankertz, J. and Schulzke, J.-D. (2008) Epithelial apoptosis is a prominent feature of the epithelial barrier disturbance in intestinal inflammation: effect of pro-inflammatory interleukin-13 on epithelial cell function, Mucosal Immunology, 1 (Suppl 1), S58-S61.

Herbst, C., Riedel, K., Ihle, Y., Leppert, J., Ohlenschläger, O., Görlach, M. and Ramachandran, R. (2008) MAS solid state NMR of RNAs with multiple receivers, Journal of Biomolecular NMR, 41, 121-125.

Hiller, M. and Platzer, M. (2008) Widespread and subtle: Alternative splicing at short-distance tandem sites, Trends in Genetics, 24, 246-255.

Hiller, M., Szafranski, K., Huse, K., Backofen, R. and Platzer, M. (2008) Selection against tandem splice sites affecting structured protein regions, BMC Evolutionary Biology, 8, 89.

Hiller, M., Szafranski, K., Sinha, R., Huse, K., Nikolajewa, S., Rosenstiel, P., Schreiber, S., Backofen, R. and Platzer, M. (2008) Assessing the fraction of short-distance tandem splice sites under purifying selection, RNA, 14, 616-629.

Hou, S., Xu, R., Heinemann, S.H. and Hoshi, T. (2008) Reciprocal regulation of the Ca²⁺ and H⁺ sensitivity in the SLO1 BK channel conferred by the RCK1 domain, Nature Structural and Molecular Biology, 15, 403-410.

Huber, R., Hummert, C., Gausmann, U., Pohlers, D., Koczan, D., Guthke, R. and Kinne, R. (2008) Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane, Arthritis Research & Therapy, 10, R98.

Hüffner, F., Niedermeier, R. and Wernicke, S. (2008) Developing fixed-parameter algorithms to solve combinatorially explosive biological problems. In Keith, J.M. (ed), Bioinformatics: Structure, Function and Applications. Humana Press, 395-421.

Ibrahim, B., Diekmann, S., Schmitt, E. and Dittrich, P. (2008) In-silico modeling of the mitotic spindle assembly checkpoint, PLoS ONE, 3, e1555.

Kaleta, C., Centler, F., di Fenizio, P. and Dittrich, P. (2008) Phenotype prediction in regulated metabolic networks, BMC Systems Biology, 2, 37.

Kassmann, M., Hansel, A., Leipold, E., Birkenbeil, J., Lu, S.-Q., Hoshi, T. and Heinemann, S.H. (2008) Oxidation of multiple methionine residues impairs rapid sodium channel inactivation, Pflügers Archiv: European Journal of Physiology, 456, 1085-1095.

Licht, A., Golbik, R. and Brantl, S. (2008) Identification of ligands affecting the activity of the transcriptional repressor CcpN from Bacillus subtilis, Journal of Molecular Biology, 380, 17-30.

Meyer, M. and Sühnel, J. (2008) Density functional study of adenine tetrads with N6-H6…N3 hydrogen bonds, Journal of Physical Chemistry A, 112, 4336-4341.

Mondragón-Palomino, M. and Theißen, G. (2008) MADS about the evolution of orchid flowers, Trends in Plant Science, 13, 51-59.

Müller, J.P., Schönherr, C., Markova, B., Bauer, R., Stocking, C. and Böhmer, F.D. (2008) Role of SHP2 for FLT3-dependent proliferation and transformation in 32D cells, Leukemia, 22, 1945-1948.

Ohlenschäger, O., Haumann, S., Ramachandran, R. and Görlach, M. (2008) Conformational signatures of ¹³C chemical shifts in RNA ribose, Journal of Biomolecular NMR, 42, 139-142.

Schindler, S., Szafranski, K., Hiller, M., Ali, G.S., Palusa, S.G., Backofen, R., Platzer, M. and Reddy, A.S.N. (2008) Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes, BMC Genomics, 9, 159.

Schuster, S., Pfeiffer, T. and Fell, D.A. (2008) Is maximization of molar yield in metabolic networks favoured by evolution?, Journal of Theoretical Biology, 252, 497-504.

Schwalbe, M., Ohlenschläger, O., Marchanka, A., Ramachandran, R., Häfner, S., Heise, T. and Görlach, M. (2008) Solution structure of stem-loop α of the hepatitis B virus post-transcriptional regulatory element, Nucleic Acids Research, 36, 1681-1689.

Soom, M., Gessner, G., Heuer, H., Hoshi, T. and Heinemann, S.H. (2008) A mutually exclusive alternative exon of slo 1 codes for a neuronal BK channel with altered function, Channels, 2, 278-282.

Su, K., Zhao, S., Shan, H., Kong, H., Lu, W., Theissen, G., Chen, Z. and Meng, Z. (2008) The MIK region rather than the C-terminal domain of AP3-like class B floral homeotic proteins determines functional specificity in the development and evolution of petals, New Phytologist, 178, 544-558.

Weidtkamp-Peters, S., Lenser, T., Negorev, D., Gerstner, N., Hofmann, T.G., Schwanitz, G., Hoischen, C., Maul, G., Dittrich, P. and Hemmerich, P. (2008) Dynamics of component exchange at PML nuclear bodies, Journal of Cell Science, 121, 2731-2743.

Wicher, D., Schäfer, R., Bauernfeind, R., Stensmyr, M.C., Heller, R., Heinemann, S.H. and Hansson, B.S. (2008) Drosophila odorant receptors are both ligand-gated and cyclic-nucleotide-activated cation channels, Nature, 452, 1007-1011.

Wollbold, J., Guthke, R. and Ganter, B. (2008) Constructing a knowledge base for gene regulatory dynamics by formal concept analysis methods. In, Algebraic Biology. AB 2008 Proceedings. Springer, Berlin, Heidelberg, 230-244.

2007

Albrecht, D., Kniemeyer, O., Brakhage, A.A., Berth, M. and Guthke, R. (2007) Integration of transcriptome and proteome data from human-pathogenic fungi by using a data warehouse, Journal of Integrative Bioinformatics, 4, 52.

Bahrmann, P., Werner, G.S., Heusch, G., Ferrari, M., Pörner, T.C., Voss, A. and Figulla, H.R. (2007) Detection of coronary microembolization by Doppler ultrasound in patients with stable angina pectoris undergoing elective percutaneous coronary interventions, Circulation, 115, 600-608.

Bär, K.-J., Böttger, M.K., Berger, S., Baier, V., Sauer, H., Yeragani, V.K. and Voss, A. (2007) Decreased baroreflex sensitivity in acute schizophrenia, Journal of Applied Physiology, 102, 1051-1056.

Böcker, S. and Kaltenbach, H.-M. (2007) Mass spectra alignments and their significance, Journal of Discrete Algorithms, 5, 714-728.

Böcker, S. and Lipták, Z. (2007) A fast and simple algorithm for the money changing problem, Algorithmica, 48, 413-432.

Brantl, S. (2007) Regulatory mechanisms employed by cis-encoded antisense RNAs, Current Opinion in Microbiology, 10, 102-109.

Centler, F. and Dittrich, P. (2007) Chemical organizations in atmospheric photochemistries – a new method to analyze chemical reaction networks, Planetary and Space Science, 55, 413-428.

Dittrich, P. and di Fenizio, P.S. (2007) Chemical organisation theory, Bulletin of Mathematical Biology, 69, 1199-1231.

Guthke, R., Kniemeyer, O., Albrecht, D., Brakhage, A.A. and Möller, U. (2007) Discovery of gene regulatory networks in Aspergillus fumigatus. In, Knowledge Discovery and Emergent Complexity in Bioinformatics. KDECB 2006 Revised Selected Papers. Springer, Berlin, Heidelberg, 22-41.

Hahn, U., Wermter, J., Blasczyk R. and Horn, P. (2007) Text Mining: Powering the Database Revolution, Nature, 448, 130.

Heidrich, N. and Brantl, S. (2007) Antisense RNA-mediated transcriptional attenuation in plasmid pIP501: the simultaneous interaction between two complementary loop pairs is required for efficient inhibition by the antisense RNA, Microbiology, 153, 420-427.

Heidrich, N., Moll, I. and Brantl, S. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA, Nucleic Acids Research, 35, 4331-4346.

Hiller, M., Nikolajewa, S., Huse, K., Szafranski, K., Rosenstiel, P., Schuster, S., Backofen, R. and Platzer, M. (2007) TassDB: a database of alternative tandem splice sites, Nucleic Acids Research, 35, D188-192.

Hüffner, F., Wernicke, S. and Zichner, T. (2007) FASPAD: Fast signaling pathway detection, Bioinformatics, 23, 1708-1709.

Hühne, R., Koch, F.-T. and Sühnel, J. (2007) A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules, Briefings in Functional Genomics and Proteomics, 6, 220-239.

Kanno, A., Hirai, M., Ochiai, T., Simon, H. and Theissen, G. (2007) Reduced expression of DEFICIENS-like genes in the sepaloid tepals of viridiflora tulips. Proceedings of the International Horticulture Congress, Acta Horticulturae, 763, 43-48.

Kinne, R.W., Stuhlmüller, B. and Burmester, G.-R. (2007) Cells of the synovium in rheumatoid arthritis. Macrophages, Arthritis Research & Therapy, 9, 224.

Kunisch, E., Gandesiri, M., Fuhrmann, R., Roth, A., Winter, R. and Kinne, R.W. (2007) Predominant activation of MAP kinases and pro-destructive/pro-inflammatory features by TNF α in early-passage synovial fibroblasts via TNF receptor-1: Failure of p38 inhibition to suppress matrix metalloproteinase-1 in rheumatoid arthritis, Annals of the Rheumatic Diseases, 66, 1043-1051.

Leipold, E., DeBie, H., Zorn, S., Adolfo, B., Olivera, B.M., Terlau, H. and Heinemann, S.H. (2007) µO-Conotoxins Inhibit Na_v Channels by Interfering with their Voltage Sensors in Domain-2, Channels, 1, 253-262.

Nikolajewa, S., Pudimat, R., Hiller, M., Platzer, M. and Backofen, R. (2007) BioBayesNet: A web server for feature extraction and Bayesian network modeling of biological sequence data, Nucleic Acids Research, 35, W688-693.

Pachkov, M., Dandekar, T., Korbel, J., Bork, P. and Schuster, S. (2007) Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism, Gene, 396, 215-225.

Pohlers, D., Beyer, A., Koczan, D., Wilhelm, T., Thiesen, H.-J. and Kinne, R.W. (2007) Constitutive upregulation of the transforming growth factor-β pathway in rheumatoid arthritis synovial fibroblasts, Arthritis Research & Therapy, 9, R59.

Romualdi, A., Felder, M., Rose, D., Gausmann, U., Schilhabel, M., Glöckner, G., Platzer, M. and Sühnel, J. (2007) GenColors: Annotation and comparative genomics of prokaryotes made easy, Methods in Molecular Biology, 395, 75-96.

Schuster, S. and Fell, D.A. (2007) Modeling and simulating metabolic networks. In Lengauer, T. (ed), Bioinformatics – From Genomes to Therapies. Wiley-VCH, Weinheim, 755-805.

Schulz, S. and Hahn, U. (2007) Towards the Ontological Foundations of Symbolic Biological Theories, Artificial Inteligence in Medicine, 39, 237-250.

Schulz, S., Marko, K. and Hahn, U. (2007), Spatial Location and its Relevance for Terminological Inferences in Bio-Ontologies, BMC Bioinformatics, 8, 134.

Scutt, C.P., Theissen, G. and Ferrandiz, C. (2007) The evolution of plant development: past, present and future, Annals of Botany, 100, 599-601.

Skerka, C., Lauer, N., Weinberger, A.A.W.A., Keilhauer, C.N., Sühnel, J., Smith, R., Schlötzer-Schrehardt, U., Fritsche, L., Heinen, S., Hartmann, A., Weber, B.H.F. and Zipfel, P.F. (2007) Defective complement control of factor H (Y402H) and FHL-1 in age-related macular degeneration, Molecular Immunology, 44, 3398-3406.

Szafranski, K., Schindler, S., Taudien, S., Hiller, M., Huse, K., Jahn, N., Schreiber, S., Backofen, R. and Platzer, M. (2007) Violating the splicing rules: TG dinucleotides function als alternative 3′ splice sites in U2-dependent introns, Genome Biology, 8, R154.

Theissen, G. and Melzer, R. (2007) Molecular mechanisms underlying origin and diversification of the angiosperm flower, Annals of Botany, 100, 603-619.

Töpfer, S., Guthke, R., Driesch, D., Wötzel, D. and Pfaff, M. (2007) The Net Gene rator algorithm: reconstruction of gene regulatory networks. In, Knowledge Discovery and Emergent Complexity in Bioinformatics. KDECB 2006 Revised Selected Papers. Springer, Berlin, Heidelberg, 119-130.

Tröger, H., Richter, J.F., Beutin, L., Günzel, D., Dobrindt, U., Epple, H.-J., Gitter, A.H., Zeitz, M., Fromm, M. and Schulzke, J.-D. (2007) Escherichia coliα-haemolysin induces focal leaks in colonic epithelium: a novel mechanism of bacterial translocation, Cellular Microbiology, 9, 2530-2540.

Voss, A., Schröder, R., Trübner, S., Görnig, M., Figulla, H.R. and Schirdewan, A. (2007) Comparison of nonlinear methods symbolic dynamics, detrended fluctuation, and Poincaré plot analysis in risk stratification in patients with dilated cardiomyopathy, Chaos, 17, 015120.

Wernicke, S. and Rasche, F. (2007) Simple and fast alignment of metabolic pathways by exploiting local diversity, Bioinformatics, 23, 1978-1985.