Publications

Selected recent publications of JCB members

2017

Brandes, S., Dietrich, S., Hünniger, K., Kurzai, O., Figge, M.T. (2017) Migration and Interaction Tracking for Quantitative Analysis of Phagocyte-Pathogen Confrontation Assays. Medical Image Analysis, 36, 172-183.

Hoffmann, B., Svensson, C.M., Straßburger, M., Gebser, B., Irmler, I.M., Kamradt, T., Saluz, H.P., Figge, M.T. (2017) Automated quantification of early bone alterations and pathological bone turnover in experimental arthritis by in vivo PET/CT imaging. Sci Rep, 7, 2217.

Klingberg, A., Hasenberg, A., Ludwig-Portugall, I., Medyukhina, A., Männ, L., Brenzel, A., Engel, D.R., Figge, M.T., Kurts, C., Gunzer, M. (2017) Fully automated evaluation of total glomerular number and capillary tuft size in murine nephritic kidneys using lightsheet microscopy. Journal of the American Society of Nephrology28, 452-459.

Meinel, C., Spartà, G., Dahse, H.-M., Hörhold, F., König, R., Westermann, M., Cseresnyes, Z., Figge, M.T., Hammerschmidt, S., Skerka, C., Zipfel, P.F. (2017) S. pneumoniae from HUS patients bind human plasminogen via the surface protein PspC and use plasmin to damage human endothelial cells. The Journal of Infectious Diseases [Accepted]

Svensson, C.-M., Bondoc, K. G., Pohnert, G., Figge, M.T. (2017) Segmentation of clusters by template rotation expectation maximization. Computer Vision and Image Understanding, 152, 64-72.

Svensson, C.M., Hoffmann, B., Irmler, I., Straßburger, M., Figge, M., Saluz, H.P., *authors contributed equally (2017) Quantification of arthritic bone degradation by analysis of 3D micro-computed tomography data. Sci Rep, 7, 44434.

Ewald, J., Bartl, M., Dandekar, T., Kaleta, C. (2017) Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. PLOS Computational Biology, 13, e1005371.

Schuster, S., Fichtner, M., Sasso, S. (2017) Use of Fibonacci numbers in lipidomics – Enumerating various classes offatty acids. Scientific Reports, 7, 39821.

Fichtner, M., Voigt, K., Schuster, S. (2017) The tip and hidden part of the iceberg: Proteinogenic and non-proteinogenicaliphatic amino acids. Biochimica and Biophysica Acta – General Subjects, 1861, 3258-3269.

Böcker, S. (2017) Searching molecular structure databases using tandem MS data: are we there yet?. Curr Opin Chem Biol, 36,1-6.

Bartels, B., Kulkarni, P., Danz, N., Böcker, S., Saluz, H. P., Svatoš, A. (2017) Mapping metabolites from rough terrain: laser ablation electrospray ionization on non-flat samples. RSC Adv, 7, 9045-9050.

Engler, M. S., Scheubert, K., Schubert, U. S., Böcker, S. (2017) Exploring the Limits of the Geometric Copolymerization Model. Polymers, 9,101.

Schymanski, E. L., Ruttkies, C., Krauss, M., Brouard, C., Kind, T., Dührkop, K., Allen, F. R., Vaniya, A., Verdegem, D., Böcker, S., Rousu, J., Shen, H., Tsugawa, H., Sajed, T., Fiehn, O., Ghesquière, B., Neumann, S. (2017) Critical Assessment of Small Molecule Identification 2016: Automated Methods. J Cheminf, 9, 22.

Fleischauer, M., Böcker, S. (2017) Bad Clade Deletion supertrees: A fast and accurate supertree algorithm. Mol Biol Evol, 2017. Accepted for publication. 

Fuchs, J., Hölzer, M., Schilling, M., Patzina, C., Schoen, A., Hoenen, T., Zimmer, G., Marz, M., Weber, F., Müller, M., Kochs, G. (2017) Evolution and antiviral specificity of interferon-induced Mx proteins of bats against Ebola-, Influenza-, and other RNA viruses. Journal of Virology,  pp. JVI.00361-17.

Möbius, P., Liebler-Tenorio, E., Hölzer, M., Köhler, H. (2017) Evaluation of associations between genotypes of Mycobacterium avium subsp. paratuberculosis and presence of intestinal lesions characteristic of paratuberculosis. Veterinary Microbiology201, 188-194.

Riege, K., Hölzer, M., Klassert, T. E., Barth, E., Bräuer, J., Collatz, M., Hufsky, F., Mostajo, N., Stock, M., Vogel, B., Slevogt, H., Marz, M. (2017) Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D. Scientific Reports (Nature PG), 7, 40598.

Klassert, T. E., Bräuer, J., Hölzer, M., Stock, M., Riege, K., Zubiria-Barrera, C., Müller, M. M., Rummler, S., Skerka, C., Marz, M., Slevogt, H. (2017) Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection. Scientific Reports (Nature PG), 7, 40599.

2016

Melzer, R., Theißen, G. (2016) The significance of developmental robustness for species diversity. Ann. Bot. [Epub ahead of print]

Dix, A., Vlaic, S., Guthke, R., Linde, J. (2016) Use of systems biology to decipher host microbial interactions and predict pathological consequences. Clin. Microbiol. Infect. [Epub ahead of print]

Schulze, S., Schleicher, J., Guthke, R., Linde, J. (2016) How to Predict Molecular Interactions between Species? Front. Microbiol., 7, 442.

Müller, P., Jahn, N., Ring, C., Maiwald, C., Neubert, R., Meißner, C., Brantl, S. (2016) A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the B. subtilis chromosome. RNA Biol. [Epub ahead of print]

Boecker, S., Duehrkop, K. (2016) Fragmentation trees reloaded. J. Cheminf., 8, 5.

Hufsky, F., Boecker, S. (2016) Mining molecular structure databases: Identification of small molecules based on fragmentation mass spectrometry data. Mass Spectrom. Rev. [Epub ahead of print]

Barth, E., Huebler, R., Baniahmad, A., Marz, M. (2016) The Evolution of COP9 signalosome in unicellular and multicellular organisms. Genome Biol. Evol. [Epub ahead of print]

Prauße, M.T.E., Schaeuble, S., Guthke, R., Schuster, S. (2016) Computing the various pathways of penicillin synthesis and their molar yields. Biotechnol. Bioeng., 113,  173-181.

Hennig. A., Markwart. R., Wolff. K., Schubert. K., Cui. Y., Prior. I.A., Esparza-Franco, M.A., Ladds, G., Rubio I. (2016) Feedback activation of neurofibromin terminates growth factor-induced Ras activation. Cell. Commun. Signal., 14, 5.

Ruffo, E., Malacarne, V., Larsen, S.E., Das, R., Patruss,i L., Wülfing ,C., Biskup, C., Kapnick, S.M., Verbist, K., Tedrick, P., Schwartzberg, P.L., Baldari, C.T., Rubio, I., Nichols, K.E., Snow, A.L., Baldanzi, G., Graziani, A. (2016) Inhibition of diacylglycerol kinase α restores restimulation-induced cell death and reduces immunopathology in XLP-1. Sci. Transl. Med., 8, 321ra7.

Richter, F., Leuchtweis, J., Bauer, R., Lehmenkühler , A., Schaible, H.G. (2016) Effects of interleukin-1ß on cortical spreading depolarization and cerebral vasculature.  J. Cereb. Blood Flow Metab. [Epub ahead of print]

Bens, M., Sahm, A., Groth M., Jahn N., Morhart M., Holtze S., Hildebrandt T.B., Platzer M., Szafranski K. (2016) FRAMA: from RNA-seq data to annotated mRNA assemblies. BMC Genomics, 17, 54.

Sponholz, C., Kramer, M., Schöneweck, F., Menzel, U., Inanloo Rahatloo, K., Giamarellos-Bourboulis, E.J., Papavassileiou, V., Lymberopoulou, K., Pavlaki, M., Koutelidakis, I., Perdios, I., Scherag, A., Bauer, M., Platzer, M., Huse, K. (2016) Polymorphisms of cystathionine beta-synthase gene are associated with susceptibility to sepsis. Eur. J. Hum. Genet. [Epub ahead of print]

Brewitz H.H., Goradia, N., Schubert, E., Galler, K., Kühl, T., Syllwasschy, B., Popp, J., Neugebauer, U. Hageluken G., Schiemann, O., Ohlenschläger O., Imhof, D. (2016) Heme interacts with histidine- and tyrosine-based protein motifs and inhibits enzymatic activity of chloramphenicol acetyltransferase from Escherichia coli.
Biochim. Biophys. Acta-Gen. Subj., 1860, 1343-1353.

Wiedemann, C., Bellstedt, P., Häfner, S., Herbst, C., Bordusa, F., Görlach, M., Ohlenschläger, O., Ramachandran, R.A. (2016) Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins. ChemPhysChem. [Epub ahead of print]

Kumar, S.T., Leppert, J., Bellstedt P., Wiedemann, C., Fändrich, M., Görlach, M. (2016) Solvent Removal Induces a Reversible β-to-α Switch in Oligomeric Aβ Peptide. J. Mol. Biol., 428, 268-273.

Duchardt-Ferner, E., Gottstein-Schmidtke, S.R, Weigand, J.E., Ohlenschläger, O., Wurm, J.-P., Hammann, C., Suess, B., Wöhnert, J. (2016) What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew. Chem.-Int. Edit., 55, 1527-1530.

Dix, A., Czakai, K., Springer, J., Fliesser, M., Bonin, M., Guthke, R., Schmitt, A.L., Einsele, H., Linde, J., Löffler J. (2016) Genome-wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. Front. Microbiol., 7, 320.

Durmus, S, Cakir, T., Guthke, R. (2016) Computational systems biology of pathogen-host interactions. Front. Microbiol., 7, 21.

Guthke, R., Gerber, S., Conrad, T., Vlaic, S., Durmus, S., Cakir, T., Sevilgen, E., Shelest, E., Linde, J. (2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front. Microbiol. [In press]

Marthandan, S., Baumgart, M., Priebe, S., Groth, M., Schaer, J., Kaether, C., Guthke, R., Cellerino, A., Platzer M., Diekmann, S., Hemmerich, P. (2016) Conserved senescence associated genes and pathways in primary human fibroblasts detected by RNA-seq. PLoS ONE [Accepted]

Matz-Soja, M., Rennert, C., Schönefeld, K., Aleithe, S., Boettger, J., Schmidt-Heck, W., Weiss, T.S., Hovhannisyan, A., Zellme,r S., Klöting, N., Schulz, A., Kratzsch, J., Guthke, R., Gebhardt, R. (2016) Hedgehog signaling is a potent regulator of liver lipid metabolism and reveals a GLI-code associated with steatosis. eLife [Accepted]

Teutschbein, J., Simon, S., Lother, J., Springer, J., Hortschansky, P., Morton, C.O., Löffler, J., Einsele, H., Conneally, E., Rogers, T.R., Guthke, R., Brakhage, A.A., Kniemeyer, O. (2016) Proteomic profiling of serological responses to Aspergillus fumigatus antigens in patients with invasive aspergillosis. J. Proteome Res. [Epub ahead of print]

Benoit, J.B., et al. (2016) Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat. Commun., 7, 10165. doi:10.1038/ncomms10165

Beran, F., Rahfeld, P., Luck, K., Nagel, R., Vogel, H., Wielsch, N., Irmisch, S., Ramasamy, S., Gershenzon, J., Heckel, D. G., Köllner, T. G. (2016) Novel family of terpene synthases evolved from trans-isoprenyl diphosphate synthases in a flea beetle. Proc. Natl. Acad. Sci. U. S. A., 113, 2922-2927 doi:10.1073/pnas.1523468113

Berasategui, A., Shukla, S., Salem, H., Kaltenpoth, M. (2016) Potential applications of insect symbionts in biotechnology. Appl. Microbiol. Biotechnol., 100, 1567-1577. doi:10.1007/s00253-015-7186-9

Bretschneider, A., Heckel, D.G., Vogel, H. (2016) Know your ABCs: Characterization and gene expression dynamics of ABC transporters in the polyphagous herbivore Helicoverpa armigera. Insect Biochem. Mol. Biol., 72, 1-9. doi:10.1016/j.ibmb.2016.03.001

Engel, K.C., Stökl, J., Schweizer, R., Vogel, H., Ayasse, M., Ruther, J., Steiger, S. (2016) A hormone-related female anti-aphrodisiac signals temporary infertility and causes sexual abstinence to synchronize parental care. Nat. Commun., 7, 11035. doi:10.1038/ncomms11035.

Groot, A.T., Dekker, T., Heckel, D.G. (2016) Genetic basis of pheromone evolution in moths. Annu. Rev. Entomol., 61, 99-117. doi:10.1146/annurev-ento-010715-023638

Huber, M., Epping, J., Gronover, C.S., Fricke, J., Aziz, Z., Brillatz, T., Swyers, M., Köllner, T.G., Vogel, H., Hammerbacher, A., Triebwasser-Freese, D., Robert, C., Verhoeven, K., Preite, V., Gershenzon, J., Erb, M. (2016) A latex metabolite benefits plant fitness under root herbivore attack. PLoS Biol., 14, e1002332. doi:10.1371/journal.pbio.1002332

Jacobs, C.G., Steiger, S., Heckel, D.G., Wielsch, N., Vilcinskas, A., Vogel, H. (2016) Sex, offspring and carcass determine antimicrobial peptide expression in the burying beetle. Sci Rep., 6, 25409, doi:10.1038/srep25409

Kirsch, R., Heckel, D.G., Pauchet, Y. (2016) How the rice weevil breaks down the pectin network: Enzymatic synergism and sub-functionalization. Insect Biochem. Mol. Biol., 71, 72-82. doi:10.1016/j.ibmb.2016.02.007

Krempl, C., Sporer, T., Reichelt, M., Ahn, S.-J., Heidel-Fischer, H., Vogel, H., Heckel, D.G., Joußen, N. (2016) Potential detoxification of gossypol by UDP-glycosyltransferases in the two Heliothine moth species Helicoverpa armigera and Heliothis virescens. Insect Biochem. Mol. Biol., 71, 49-57. doi:10.1016/j.ibmb.2016.02.005

Roy, A., Walker, W.B., Vogel, H., Chattington, S., Larsson, M.C., Anderson, P., Heckel, D.G., Schlyter, F. (2016) Diet dependent metabolic responses in three generalist insect herbivores Spodoptera spp. Insect Biochem. Mol. Biol., 71, 91-105. doi:10.1016/j.ibmb.2016.02.006

Shelomi, M., Heckel, D.G., Pauchet, Y. (2016) Ancestral gene duplication enabled the evolution of multifunctional cellulases in stick insects (Phasmatodea Insect Biochem. Mol. Biol., 71, 1-11. doi:10.1016/j.ibmb.2016.02.003

Staudacher, H., Kaltenpoth, M., Breeuwer, J.A.J., Menken, S.B.J., Heckel, D.G., Groot, A.T. (2016) Variability of bacterial communities in the moth Heliothis virescens indicates transient association with the host. PLoS One, 11, e0154514. doi:10.1371/journal.pone.0154514

Holmqvist, E., Wright, P.R., Li, L., Bischler, T., Barquist L., Reinhardt, R., Backofen, R., Vogel, J. (2016) Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. Embo J., 9, 991–1011.

 

2015

Lehnert, T., Timme, S., Pollmächer, J., Hünniger, K., Kurzai, O., Figge, M.T. (2015) Bottom-up modeling approach for the quantitative estimation of parameters in pathogen-host interactions. Front Microbiol., 6, 608.

Kraibooj, K., Schoeler, H., Svensson, C.M., Brakhage, A.A., Figge, M.T. (2015) Automated quantification of the phagocytosis of Aspergillus fumigatus conidia by a novel image analysis algorithm. Front Microbiol., 6, 549.

Pollmächer, J., Figge, M.T. (2015) Deciphering chemokine properties by a hybrid agent-based model of Aspergillus fumigatus infection in human alveoli. Front Microbiol., 6, 503.

Dühring, S., Germerodt, S., Skerka, C., Zipfel, P.F., Dandekar, T., Schuster, S. (2015) Host-pathogen interactions between the human innate immune system and Candida albicans – Understanding and modeling defense and evasion strategies. Front. Microbiol., 6, 625.

Ewald, J., Kötzing, M., Bartl, M., Kaleta, C. (2015) Footprints of Optimal Protein Assembly Strategies in the Operonic Structure of Prokaryotes. Metabolites, 5, 252-269.

D’Souza, G., Waschina, S., Kaleta, C., Kost, C. (2015) Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes. Evolution69, 1244-1254.

Schmidt, R., Waschina, S., Boettger-Schmidt, D., Kost, C., Kaleta C. (2015) Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions. Bioinformatics31, 373-381.

Horn, F., Linde, J., Mattern, D.J., Walther, G., Guthke, R., Brakhage, A.A., Valiante, V. (2015) Draft Genome Sequence of the Fungus* Penicillium brasilianum* MG11. Genome Announc.3, 5.

Schmidt-Heck, W., Matz-Soja, M., Aleithe, S., Marbach, E., Guthke, R., Gebhardt, R. (2015) Fuzzy modeling reveals a dynamic self-sustaining network of the GLI transcription factors controlling important metabolic regulators in adult mouse hepatocytes. Mol Biosyst.11, 2190-2197.

Dix, A., Hünniger, K., Weber, M., Guthke, R., Kurzai, O., Linde, J. (2015) Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol.6, 171.

Linde, J., Duggan, S., Weber, M., Horn, F., Sieber, P., Hellwig, D., Riege, K., Marz, M., Martin, R., Guthke, R., Kurzai, O. (2015) Defining the transcriptomic landscape of *Candida glabrata* by RNA-Seq. Nucleic Acids Res., 43, 1392-1406.

Priebe, S., Kreisel, C., Horn, F., Guthke, R., Linde, J. (2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics, 31, 445-446.

2014

Hünniger, K., Lehnert, T., Bieber, K., Martin, R., Figge, M.T., Kurzai, O. (2014) A virtual infection model quantifies innate effector mechanisms and Candida albicans immune escape in human blood. PLoS Comput Biol., 10, e1003479.

Schacht, T., Oswald, M., Eils, R., Eichmüller, S.B., König, R. (2014) Estimating the activity of transcription factors by the effect on their target genes. Bioinformatics, 30, i401-i407.

Boesger, J., Wagner, V., Weisheit, W., Mittag, M. (2014) Comparative phosphoproteomics to identify targets of the clock-relevant casein kinase 1 in C. reinhardtii Flagella. Methods Mol Biol.1158, 187-202.

Schmidt, C., Schneble, N., Wetzker, R. (2014) The fifth dimension of innate immunity. J Cell Commun Signal., 8, 363-367.

Schwartze, V.U., Winter, S., Shelest, E., Marcet-Houben, M., Horn, F., Wehner, S., Linde, J., Valiante, V., Sammeth, M., Riege, K., Nowrousian, M., Kaerger, K., Jacobsen, I.D., Marz, M., Brakhage, A.A., Gabaldón, T., Böcker, S., Voigt, K. (2014) Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet., 10, e1004496.

Baumgart, M., Groth, M., Priebe, S., Savino, A., Testa, G., Dix, A., Ripa, R., Spallotta, F., Gaetano, C., Ori, M., Terzibasi Tozzini, E., Guthke, R., Platzer, M., Cellerino, A. (2014) RNA-seq of the aging brain in the short-lived fish N. furzeri – conserved pathways and novel genes associated with neurogenesis. Aging Cell., 13, 965-974.

Bohl, K., Hummert, S., Werner, S., Basanta, D., Deutsch, A., Schuster, S., Theißen, G., Schroeter, A. (2014) Evolutionary game theory: molecules as players. Mol. Biosyst., 10,  3066-3074.

Hummert, S., Bohl, K., Basanta, D., Deutsch, A., Werner, S., Theißen, G., Schroeter, A., Schuster, S. (2014) Evolutionary game theory: cells as players. Mol. Biosyst., 10, 3044-3065.

Jetha, K., Theißen, G., Melzer, R. (2014) Arabidopsis SEPALLATA proteins differ in cooperative DNA-binding during the formation of floral quartet-like complexes. Nucl. Acids Res., 42, 10927-10942.

Kirsch, R., Gramzow, L., Theißen, G., Siegfried, B.D., Ffrench-Constant, R.H., Heckel, D.G., Pauchet, Y. (2014) Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: Key events in the evolution of herbivory in beetles. Insect Biochem Mol Biol., 52, 33-50.

Pande, S., Merker, H., Bohl, K., Reichelt, M., Schuster, S., de Figueiredo, L.F., Kaleta, C., Kost, C. (2014) Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME Journal, 8, 953–962.

Grützmann, K., Szafranski, K., Pohl, M., Voigt, K., Petzold, A., Schuster, S. (2014) Fungal alternative splicing is associated with multicellular complexity and virulence – A genome-wide multi-species study. DNA Research, 21, 37-39.

Szafranski, K., Fritsch, C., Schumann, F., Siebel, L., Sinha, R., Hampe, J., Hiller, M., Englert, C., Huse, K., Platzer, M. (2014) Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons. Nucl. Acids Res. 42, 8895-8904.

Schleicher, J., Guthke, R., Dahmen, U., Dirsch, O., Holzhütter, H. G., Schuster, S. (2014) A theoretical study of lipid accumulation in the liver – Implications for nonalcoholic fatty liver disease, Biochim. Biophys. Acta – Mol. Cell Biol. Lipids, 1841, 62-69.

Glöckner, G., Hülsmann, N., Schleicher, M., Noegel, A. A., Eichinger, L., Gallinger, C., Pawlowski, J., Sierra, R., Euteneuer, U., Pillet, L., Moustafa, A., Platzer, M., Groth, M., Szafranski, K., Schliwa, M. (2014) The Genome of the Foraminiferan Reticulomyxa filosa, Curr. Biol., 24, 11-18.

Ariyadasa, R., Mascher, M., Nussbaumer, T., Schulte, D., Frenkel, Z., Poursarebani, N., Zhou, R., Steuernagel, B., Gundlach, H., Taudien, S., Felder, M., Platzer, M., Himmelbach, A., Schmutzer, T., Hedley, P. E., Muehlbauer, G. J., Scholz, U., Korol, A., Mayer, K. F., Waugh, R., Langridge, P., Graner, A., Stein, N. (2014) A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms, Plant Physiol. 164, 412-423.

Heinemann, S. H., Hoshi, T., Westerhausen, M., Schiller, A. (2014) Carbon monoxide – physiology, detection and controlled release, Chem Commun (Camb). 50, 3644-3360.

Brantl, S., Brückner, R. (2014) Small regulatory RNAs from low-GC Gram-positive bacteria. RNA Biol., 11, 443-456.

2013

Schmeisser, K., Mansfeld, J., Kuhlow, D., Weimer, S., Zarse, K., Priebe, S., Heiland, I., Birringer, M., Groth, M., Segref, A., Werner, C., Schmeisser, S., Schuster, S., Pfeiffer, A., Guthke, R., Platzer, M., Hoppe, T., Cohen, H., Sinclair, D., Ristow, M. (2013) Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide, Nature Chemical Biology, 9, 693-700.

Priebe, S., Menzel, U., Zarse, K., Groth, M., Platzer, M., Ristow, M., Guthke, R. (2013) Extension of Life Span by Impaired Glucose Metabolism in Caenorhabditis elegans Is Accompanied by Structural Rearrangements of the Transcriptomic Network, PLoS One, 8, e77776.

Sahoo, N., Goradia, N., Ohlenschläger, O., Schönherr, R., Friedrich, M., Plass, W., Kappl, R., Hoshi, T., Heinemann, S.H. (2013) Heme impairs the ball-and-chain inactivation of potassium channels, Proc Natl Acad Sci U S A., 110, E4036-44.

Pauchet, Y., Heckel, D. G. (2013) The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer, Proc Biol Sci., 280, 20131021.

Wiedemann, C., Bellstedt, P., Görlach, M. (2013) CAPITO–a web server-based analysis and plotting tool for circular dichroism data, Bioinformatics, 29 (14), 1750-1757. [DOI: 10.1093/bioinformatics/btt278]

Mischo, A., Ohlenschläger, O., Hortschansky, P., Ramachandran, R., Görlach, M. (2013) Structural Insights into a Wildtype Domain of the Oncoprotein E6 and Its Interaction with a PDZ Domain, PLoS ONE, (4), e62584, 1-13.

Bartl, M., Kötzing, M., Schuster, S., Li, P., Kaleta, C. (2013) Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes, Nature Commun., 27, 2243.

Figge, M. T., Osiewacz, H. D., Reichert,  A. S. (2013) Quality control of mitochondria during aging: is there a good and a bad side of mitochondrial dynamics? Bioessays, 35 (4), 314-322.

Kaleta, C., Schäuble, S., Rinas, U., Schuster, S. (2013) Metabolic costs of amino acid and protein production in Escherichia coli, Biotechnol J., 8, 1105-1114.

Dahms, S.O., Kuester, M., Streb, C., Roth, C., Sträter, N. and Than, M.E. (2013) Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement, Acta Crystallographica Section D, 69, 284-297.

Ellenberger, S., Schuster, S. and Wöstemeyer, J. (2013) Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete Mucor mucedo, Journal of Theoretical Biology, 320, 66-75.

Lange, M., Orashakova, S., Lange, S., Melzer, R., Theißen, G., Smyth, D.R. and Becker, A. (2013) The seirena B class floral homeotic mutant of california poppy (Eschscholzia californica) reveals a function of the enigmatic PI motif in the formation of specific multimeric MADS domain protein complexes, Plant Cell, 25, 438-453.

Petzold, A., Reichwald, K., Groth, M., Taudien, S., Hartmann, N., Priebe, S., Shagin, D., Englert, C. and Platzer, M. (2013) The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels, BMC Genomics, 14, 185.

Scheubert, K., Hufsky, F. and Böcker, S. (2013) Computational mass spectrometry for small molecules, Journal of Cheminformatics, 5, 12.

Schmeisser, S., Schmeisser, K., Weimer, S., Groth, M., Priebe, S., Fazius, E., Kuhlow, D., Pick, D., Einax, J.W., Guthke, R., Platzer, M., Zarse, K. and Ristow, M. (2013) Mitochondrial hormesis links low-dose arsenite exposure to lifespan extension, Aging Cell, 12, 508-517.

Weber, M., Henkel, S., Vlaic, S., Guthke, R., van Zoelen, E. and Driesch, D. (2013) Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0, BMC Systems Biology, 7, 1.

2012

Guthke, R., Linde, J., Mech, F., Figge, M.T. (2012) Systems biology of microbial infection, Front Microbiol. 3, 328.

Figge, M. T., Reichert, A.S., Meyer-Hermann, M., Osiewacz, H. D. (2012) Deceleration of fusion-fission cycles improves mitochondrial quality control during aging, PLoS Comput Biol. 8, e1002576.

Altwasser, R., Linde, J., Buyko, E., Hahn, U. and Guthke, R. (2012) Genome-wide scale-free network inference for Candida albicans, Frontiers in Microbiology, 3, 51.

Bodenstein, C., Gosak, M., Schuster, S., Marhl, M. and Perc, M. (2012) Modeling the seasonal adaptation of circadian clocks by changes in the network structure of the suprachiasmatic nucleus, PLoS Computational Biology, 8, e1002697.

Caydasi, A.K., Lohel, M., Grünert, G., Dittrich, P., Pereira, G. and Ibrahim, B. (2012) A dynamical model of the spindle position checkpoint, Molecular Systems Biology, 8, 582.

Creemers, J.W.M., Choquet, H., Stijnen, P., Vatin, V., Pigeyre, M., Beckers, S., Meulemans, S., Than, M.E., Yengo, L., Tauber, M., Balkau, B., Elliott, P., Jarvelin, M.-R., Van Hul, W., Van Gaal, L., Horber, F., Pattou, F., Froguel, P. and Meyre, D. (2012) Heterozygous mutations causing partial prohormone convertase 1 deficiency contribute to human obesity, Diabetes, 61, 383-390.

Dahms, S.O., Könnig, I., Roeser, D., Gührs, K.-H., Mayer, M.C., Kaden, D., Multhaup, G. and Than, M.E. (2012) Metal binding dictates conformation and function of the Amyloid Precursor Protein (APP) E2 domain, Journal of Molecular Biology, 416, 438-452.

Fritsch, C., Herrmann, A., Nothnagel, M., Szafranski, K., Huse, K., Schumann, F., Schreiber, S., Platzer, M., Krawczak, M., Hampe, J. and Brosch, M. (2012) Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting, Genome Research, 22, 2208-2218.

Galimba, K.D., Tolkin, T.R., Sullivan, A.M., Melzer, R., Theißen, G. and Di Stilio, V.S. (2012) Loss of deeply conserved C-class floral homeotic gene function and C- and E-class protein interaction in a double-flowered ranunculid mutant, Proceedings of the National Academy of Sciences of the United States of America, 109, E2267–E2275.

Gessner, G., Cui, Y.-M., Otani, Y., Ohwada, T., Soom, M., Hoshi, T. and Heinemann, S.H. (2012) Molecular mechanism of pharmacological activation of BK channels, Proceedings of the National Academy of Sciences of the United States of America, 109, 3552-3557.

Godfrey, R., Arora, D., Bauer, R., Stopp, S., Müller, J.P., Heinrich, T., Böhmer, S.A., Dagnell, M., Schnetzke, U., Scholl, S., Östman, A. and Böhmer, F.D. (2012) Cell transformation by FLT3 ITD in acute myeloid leukemia involves oxidative inactivation of the tumor suppressor protein-tyrosine phosphatase DEP-1/ PTPRJ, Blood, 119, 4499-4511.

Gossmann, T.I., Ziegler, M., Puntervoll, P., de Figueiredo, L.F., Schuster, S. and Heiland, I. (2012) NAD(+) biosynthesis and salvage – a phylogenetic perspective, The FEBS Journal, 279, 3355-3363.

Gramzow, L., Barker, E., Schulz, C., Ambrose, B., Ashton, N., Theissen, G. and Litt, A. (2012) Selaginella genome analysis – entering the ‘homoplasy heaven’ of the MADS world, Frontiers in Plant Science, 3, 214.

Grünert, G., Escuela, G. and Dittrich, P. (2012) Symbol representations in evolving droplet computers. In Durand-Lose, J. and Jonoska, N. (eds), Unconventional Computation and Natural Computation. Lecture Notes in Computer Science 7445, Springer Berlin Heidelberg, pp. 130-140.

Haupt, C., Leppert, J., Rönicke, R., Meinhardt, J., Yadav, J.K., Ramachandran, R., Ohlenschläger, O., Reymann, K.G., Görlach, M. and Fändrich, M. (2012) Structural basis of beta-amyloid-dependent synaptic dysfunctions, Angewandte Chemie International Edition, 51, 1576-1579.

Hufsky, F., Dührkop, K., Rasche, F., Chimani, M. and Böcker, S. (2012) Fast alignment of fragmentation trees. Bioinformatics (ISMB 2012 Proceedings), accepted.

Kreyssig, P., Escuela, G., Reynaert, B., Veloz, T., Ibrahim, B. and Dittrich, P. (2012) Cycles and the qualitative evolution of chemical systems, PLoS ONE, 7, e45772.

Leipold, E., Borges, A. and Heinemann, S.H. (2012) Scorpion beta-toxin interference with NaV channel voltage sensor gives rise to excitatory and depressant modes, Journal of General Physiology, 139, 305-319.

Linde, J., Hortschansky, P., Fazius, E., Brakhage, A.A., Guthke, R. and Haas, H. (2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach, BMC Systems Biology, 6, 6.

Mischo, A., Ohlenschläger, O., Gührs, K.-H. and Görlach, M. (2012) Recombinant production of isotope labeled peptides and spontaneous cyclization of amino-terminal glutamine into pyroglutamic acid, ChemBioChem, 13, 1421-1423.

Ohlenschläger, O., Kuhnert, A., Schneider, A., Haumann, S., Bellstedt, P., Keller, H., Saluz, H.-P., Hortschansky, P., Hänel, F., Grosse, F., Görlach, M. and Pospiech, H. (2012) The N-terminus of the human RecQL4 helicase is a homeodomain-like DNA interaction motif, Nucleic Acids Research, 40, 8309-8324.

Rasche, F., Scheubert, K., Hufsky, F., Zichner, T., Kai, M., Svatoš, A. and Böcker, S. (2012) Identifying the unknowns by aligning fragmentation trees, Analytical Chemistry, 84, 3417-3426.

Rauf, I., Rasche, F., Nicolas, F. and Böcker, S. (2012) Finding maximum colorful subtrees in practice. In Lecture Notes in Computer Science (RECOMB 2012), 7262, 213-223. Springer-Verlag Berlin Heidelberg.

Recknagel, P., Gonnert, F.A., Westermann, M., Lambeck, S., Lupp, A., Rudiger, A., Dyson, A., Carré, J.E., Kortgen, A., Krafft, C., Popp, J., Sponholz, C., Fuhrmann, V., Hilger, I., Claus, R.A., Riedemann, N.C., Wetzker, R., Singer, M., Trauner, M. and Bauer, M. (2012) Liver dysfunction and phosphatidylinositol-3-kinase signalling in early sepsis: Experimental studies in rodent models of peritonitis, PLoS Medicine, 9, e1001338.

Reulecke, S., Schulz, S. and Voss, A. (2012) Autonomic regulation during quiet and active sleep states in very preterm neonates, Frontiers in Physiology, 3, 61.

Rubio, I. and Wetzker, R. (2012) Hormetic Signaling Patterns, Dose-Response, 10, 83-90.

Sahoo, N., Schönherr, R., Hoshi, T. and Heinemann, S.H. (2012) Cysteines control the N- and C-linker-dependent gating of KCNH1 potassium channels, Biochimica et Biophysica Acta (BBA) – Biomembranes, 1818, 1187-1195.

Schäuble, S., Klement, K., Marthandan, S., Münch, S., Heiland, I., Schuster, S., Hemmerich, P. and Diekmann, S. (2012) Quantitative model of cell cycle arrest and cellular senescence in primary human fibroblasts, PLoS ONE, 7, e42150.

Schmidt, C., Schneble, N., Müller, J.P., Bauer, R., Perino, A., Marone, R., Rybalkin, S.D., Wymann, M.P., Hirsch, E. and Wetzker, R. (2012) Phosphoinositide 3-kinase γ mediates microglial phagocytosis via lipid kinase-independent control of cAMP, Neuroscience, doi: 10.1016/j.neuroscience.2012.12.036.

Schnetzke, U., Fischer, M., Kuhn, A.-K., Spies-Weisshart, B., Zirm, E., Hochhaus, A., Müller, J.P. and Scholl, S. (2012) The E3 ubiquitin ligase TRAF6 inhibits LPS-induced AKT activation in FLT3-ITD-positive MV4-11 AML cells, Journal of Cancer Research and Clinical Oncology, doi: 10.1007/s00432-012-1362-4, 1-11.

Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W., Bolchacova, E., Voigt, K. and the Fungal Barcoding Consortium (2012) From the Cover: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, Proceedings of the National Academy of Sciences of the United States of America, 109, 6241-6246.

Schrödl, W., Heydel, T., Schwartze, V.U., Hoffmann, K., Grosse-Herrenthey, A., Walther, G., Alastruey-Izquierdo, A., Rodriguez-Tudela, J.L., Olias, P., Jacobsen, I.D., de Hoog, G.S. and Voigt, K. (2012) Direct analysis and identification of pathogenic Lichtheimia species by matrix-assisted laser desorption ionization-time of flight analyzer-mediated mass spectrometry, Journal of Clinical Microbiology, 50, 419-427.

Seeck, A., Rademacher, W., Fischer, C., Haueisen, J., Surber, R. and Voss, A. (2012) Prediction of atrial fibrillation recurrence after cardioversion—Interaction analysis of cardiac autonomic regulation, Medical Engineering & Physics, doi: 10.1016/j.medengphy.2012.06.002.

Sponholz, C., Huse, K., Kramer, M., Giamarellos-Bourboulis, E.J., Claus, R.A., Kern, A., Engel, C., Kuhnt, E., Kiehntopf, M., Routsi, C., Mylona, V., Tsangaris, I., Heinemann, S.H., Reinhart, K., Platzer, M. and Bauer, M. (2012) Gene polymorphisms in the heme degradation pathway and outcome of severe human sepsis, Shock, 38, 459-465.

Taudien, S., Gabel, G., Kuss, O., Groth, M., Grutzmann, R., Huse, K., Kluttig, A., Wolf, A., Nothnagel, M., Rosenstiel, P., Greiser, K.H., Werdan, K., Krawczak, M., Pilarsky, C. and Platzer, M. (2012) Association studies of the copy-number variable β-defensin cluster on 8p23.1 in adenocarcinoma and chronic pancreatitis, BMC Research Notes, 5, 629.

Tietze, A.A., Tietze, D., Ohlenschläger, O., Leipold, E., Ullrich, F., Kühl, T., Mischo, A., Buntkowsky, G., Görlach, M., Heinemann, S.H. and Imhof, D. (2012) Structurally diverse μ-conotoxin PIIIA isomers block sodium channel NaV 1.4, Angewandte Chemie International Edition, 51, 4058-4061.

The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome, Nature, 491, 711-716.

Vitale, R.G., de Hoog, G.S., Schwarz, P., Dannaoui, E., Deng, S., Machouart, M., Voigt, K., van de Sande, W.W.J., Dolatabadi, S., Meis, J.F. and Walther, G. (2012) Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales, Journal of Clinical Microbiology, 50, 66-75.

Vlaic, S., Schmidt-Heck, W., Matz-Soja, M., Marbach, E., Linde, J., Meyer-Baese, A., Zellmer, S., Guthke, R. and Gebhardt, R. (2012) The Extended TILAR Approach: A novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes, BMC Systems Biology, 6, 147.

Voss, A., Fischer, C., Schroeder, R., Figulla, H. and Goernig, M. (2012) Lagged segmented Poincaré plot analysis for risk stratification in patients with dilated cardiomyopathy, Medical and Biological Engineering and Computing, 50, 727-736.

Voss, A., Goernig, M., Schroeder, R., Truebner, S., Schirdewan, A. and Figulla, H.R. (2012) Blood Pressure Variability as Sign of Autonomic Imbalance in Patients with Idiopathic Dilated Cardiomyopathy, Pacing and Clinical Electrophysiology, 35, 471-479.

Wingen, L.U., Münster, T., Faigl, W., Deleu, W., Sommer, H., Saedler, H. and Theißen, G. (2012) Molecular genetic basis of pod corn (Tunicate maize), Proceedings of the National Academy of Sciences of the United States of America, 109, 7115-7120.

Zarse, K., Schmeisser, S., Groth, M., Priebe, S., Beuster, G., Kuhlow, D., Guthke, R., Platzer, M., Kahn, C.R. and Ristow, M. (2012) Impaired Insulin/IGF1 signaling extends life span by promoting mitochondrial L-proline catabolism to induce a transient ROS signal, Cell Metabolism, 15, 451-465.

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.

Bartsch, C., Bekhite, M.M., Wolheim, A., Richter, M., Ruhe, C., Wissuwa, B., Marciniak, A., Müller, J., Heller, R., Figulla, H.-R., Sauer, H. and Wartenberg, M. (2011) NADPH oxidase and eNOS control cardiomyogenesis in mouse embryonic stem cells on ascorbic acid treatment, Free Radical Biology and Medicine, 51, 432-443.

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, 21, 1882-1891.

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.

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, 12, 134-146.

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 NAv1.8 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.

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 RNnν 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.

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