Browse by Institutions of the University

Straub, Kristina (2019) Ancestral Sequence Reconstruction: Methods and Applications. PhD, Universität Regensburg.

Ziegler, Christian, Graf, Johannes, Faderl, Stefan, Schedlbauer, Jessica, Strieder, Nicholas, Förstl, Bianca, Spang, Rainer, Bruckmann, Astrid, Merkl, Rainer , Hombach, Sonja and Kretz, Markus (2019) The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis. EMBO Rep., e46612. Fulltext not available.

Kneuttinger, Andrea C., Winter, Martin, Simeth, Nadja Anita , Heyn, Kristina , Merkl, Rainer , König, Burkhard and Sterner, Reinhard (2018) Artificial Light Regulation of an Allosteric Bienzyme Complex by a Photosensitive Ligand. ChemBioChem. Fulltext not available.

Löffler, Patrick (2017) Computationally modeling interactions and dynamics to promote the understanding of protein function. PhD, Universität Regensburg.

Merkl, Rainer, Löffler, Patrick , Schmitz, Samuel, Hupfeld, Enrico and Sterner, Reinhard (2017) Rosetta:MSF: a modular framework for multi-state computational protein design. PLOS Computational Biology 13 (6), e1005600.

Kandlinger, Florian, Plach, Maximilian G. and Merkl, Rainer (2017) AGeNNT: annotation of enzyme families by means of refined neighborhood networks. BMC Bioinformatics 18 (1), pp. 1-13.

Merkl, Rainer, Verprinsky, Valery, Plach, Maximilian G. and Heizinger, Leonhard (2017) Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism. BMC Evolutionary Biology 17 (36), pp. 1-15.

Dueck, A., Evers, M., Henz, S. R., Unger, K., Eichner, N., Merkl, Rainer , Berezikov, E., Engelmann, Julia C., Weigel, D., Wenzl, S. and Meister, Gunter (2016) Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. BMC Genomics 17 (1), p. 853.

Merkl, Rainer, Plach, Maximilian G., Reisinger, Bernd and Sterner, Reinhard (2016) Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation. PLoS Genetics 12 (1), pp. 1-14.

Merkl, Rainer, Žváček, Clemens, Heizinger, Leonhard and Friedrichs, Gerald (2015) An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. BMC Bioinformatics 16 (359), pp. 1-8.

Janda, Jan-Oliver (2014) Data mining for important amino acid residues in multiple sequence alignments and protein structures. PhD, Universität Regensburg.

Janda, Jan-Oliver, Popal, Ajmal, Bauer, Jochen, Busch, Markus, Klocke, Michael, Spitzer, Wolfgang, Keller, Jörg and Merkl, Rainer (2014) H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments. BMC Bioinformatics 15 (118).

Birzer, Dietmar (2013) Entwicklung von Enzymdesignalgorithmen mit flexibler Ligandenpositionierung. PhD, Universität Regensburg.

Dietrich, Susanne, Borst, Nadine, Schlee, Sandra, Schneider, Daniel, Janda, Jan-Oliver, Sterner, Reinhard and Merkl, Rainer (2012) Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple sequence alignments. Biochemistry. Fulltext not available.

Zellner, Hermann Josef (2012) PresCont: Vorhersage von Protein-Protein Interaktionsflächen unter Verwendung struktureller und evolutionärer Eigenschaften. PhD, Universität Regensburg.

Janda, Jan-Oliver, Busch, Markus, Kuck, Fabian, Porfenenko, Mikhail and Merkl, Rainer (2012) CLIPS-1D: Analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure. BMC Bioinformatics 13, p. 55.

Hain, Torsten, Ghai, Rohit, Billion, Andre, Kuenne, Carsten Tobias, Steinweg, Christiane, Izar, Benjamin, Mohamed, Walid, Mraheil, Mobarak, Domann, Eugen, Schaffrath, Silke, Kärst, Uwe, Goesmann, Alexander, Oehm, Sebastian, Pühler, Alfred, Merkl, Rainer, Vorwerk, Sonja, Glaser, Philippe, Garrido, Patricia, Rusniok, Christophe, Buchrieser, Carmen, Goebel, Werner and Chakraborty, Trinad (2012) Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC genomics 13 (1), p. 144.

Peterhoff, David, Zellner, Hermann, Guldan, Harald, Merkl, Rainer, Sterner, Reinhard and Babinger, Patrick (2012) Dimerization determines substrate specificity of a bacterial prenyltransferase. Chembiochem : a European journal of chemical biology 13 (9), pp. 1297-1303. Fulltext not available.

Zellner, H., Staudigel, M., Trenner, T., Bittkowski, M., Wolowski, V., Icking, C. and Merkl, Rainer (2011) Prescont: Predicting protein-protein interfaces utilizing four residue properties. Proteins. Fulltext not available.

Ohlmann, Andreas, Merkl, Rainer and Tamm, Ernst R. (2011) Focus on Molecules: Norrin. Experimental eye research. Fulltext not available.

Fink, Florian, Hochrein, Jochen, Wolowski, Vincent, Merkl, Rainer and Gronwald, Wolfram (2011) PROCOS: Computational analysis of protein–protein complexes. Journal of Computational Chemistry 32 (12), pp. 2575-2586. Fulltext not available.

Fischer, André, Seitz, Tobias, Lochner, Adriane, Sterner, Reinhard, Merkl, Rainer and Bocola, Marco (2011) A Fast and Precise Approach for Computational Saturation Mutagenesis and its Experimental Validation by Using an Artificial (βα)8-Barrel Protein. ChemBioChem. Fulltext not available.

Dietrich, Susanne (2011) Mutationsanalyse und kinetische Untersuchungen zum Reaktionsmechanismus der Indolglycerinphosphat-Synthase aus Sulfolobus solfataricus. PhD, Universität Regensburg.

Pürzer, Andreas, Grassmann, Felix, Birzer, Dietmar and Merkl, Rainer (2011) Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation. Journal of integrative bioinformatics 8 (1). Fulltext not available.

von Mandach, Conrad and Merkl, Rainer (2010) Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions. BMC genomics 11 (1), p. 617.

Felle, Max, Exler, Josef H., Merkl, Rainer, Dachauer, Karoline, Brehm, Alexander, Grummt, Ingrid and Längst, Gernot (2010) DNA sequence encoded repression of rRNA gene transcription in chromatin. Nucleic acids research 38 (16), pp. 5304-5314. Fulltext not available.

Richter, Markus, Bosnali, Manal, Carstensen, Linn, Seitz, Tobias, Durchschlag, Helmut, Blanquart, Samuel, Merkl, Rainer and Sterner, Reinhard (2010) Computational and Experimental Evidence for the Evolution of a (betaalpha)(8)-Barrel Protein from an Ancestral Quarter-Barrel Stabilised by Disulfide Bonds. J Mol Biol 398, pp. 763-773. Fulltext not available.

Wiedemann, Sonja M., Mildner, Silke N., Bönisch, Clemens, Israel, Lars, Maiser, Andreas, Matheisl, Sarah, Straub, Tobias, Merkl, Rainer, Leonhardt, Heinrich, Kremmer, Elisabeth, Schermelleh, Lothar and Hake, Sandra B. (2010) Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. The Journal of cell biology 190 (5), pp. 777-791. Fulltext not available.

Merkl, Rainer and Waack, Stephan (2009) Bioinformatik Interaktiv
Algorithmen und Praxis
2. erweiterte und neubearbeitete Auflage. Wiley-VCH, Weinheim. Fulltext not available.

Merkl, Rainer and Wiezer, Arnim (2009) GO4genome: A prokaryotic phylogeny based on genome organisation. Journal of Molecular Evolution 68 (5), pp. 550-562. Fulltext not available.

Fischer, André, Enkler, Nils, Neudert, Gerd, Bocola, Marco, Sterner, Reinhard and Merkl, Rainer (2009) TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis. BMC Bioinformatics 10, p. 54.

Fischer, André (2008) TRANSCENT - ein Enzymdesignprogramm zum Transfer aktiver Zentren unter Wahrung Katalyse-relevanter Rahmenbedingungen. PhD, Universität Regensburg.

Sterner, Reinhard, Merkl, Rainer and Raushel, Frank M. (2008) Computational design of enzymes. Chemistry & Biology 15 (5), pp. 421-423. Fulltext not available.

Merkl, Rainer and Zwick, Matthias (2007) H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. BMC Bioinformatics 9, p. 151.

Merkl, Rainer (2007) Modelling the evolution of the archeal tryptophan synthase. BMC Evolutionary Biology 7, p. 59.

Fink, Florian, Merkl, Rainer and Gronwald, Wolfram (2007) Verification of protein-protein interactions by use of docking techniques. In: Hansmann, U. H. E. and Meinke, J. Mohanty S. and Zimmermann, O., (eds.) From computational biophysics to systems biology (CBSB07). Proceedings of the NIC Workshop 2007. NIC Series, 36. John von Neumann Institute for Computing, Jülich, pp. 125-127. ISBN 978-3-9810843-2-0.

Merkl, Rainer (2006) A comparative categorization of protein function encoded in bacterial or archeal genomic islands. J Mol Evol 62 (1), pp. 1-14. Fulltext not available.

Merkl, Rainer (2006) AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise and dissect conserved gene arrangements. In Silico Biology 6, 0027. Fulltext not available.

Waack, Stephan, Keller, Oliver, Asper, Roman, Brodag, Thomas, Damm, Carsten, Fricke, Wolfgang Florian, Surovcik, Katharina, Meinicke, Peter and Merkl, Rainer (2006) Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7, p. 142.

Wiezer, Arnim and Merkl, Rainer (2005) A comparative categorization of gene flux in diverse microbial species. Genomics 86 (4), pp. 462-475. Fulltext restricted.

Helmstaedt, Kerstin, Heinrich, Gabriele, Merkl, Rainer and Braus, Gerhard H. (2004) Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine. Archives of Microbiology 181 (3), pp. 195-203. Fulltext not available.

Meinicke, Peter, Tech, Maike, Morgenstern, Burkhard and Merkl, Rainer (2004) Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. BMC Bioinformatics 5 (1), p. 169.

Merkl, Rainer (2004) SIGI: score-based identification of genomic islands. BMC Bioinformatics 5, p. 22.

Veith, Birgit, Herzberg, Christina, Steckel, Silke, Feesche, Jörg, Maurer, Karl Heinz, Ehrenreich, Petra, Bäumer, Sebastian, Henne, Anke, Liesegang, Heiko, Merkl, Rainer, Ehrenreich, Armin and Gottschalk, Gerhard (2004) The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. Journal of Molecular Microbiology and Biotechnology 7 (4), pp. 204-211. Fulltext restricted.

Henne, Anke, Brüggemann, Holger, Raasch, Carsten, Wiezer, Arnim, Hartsch, Thomas, Liesegang, Heiko, Johann, Andre, Lienard, Tanja, Gohl, Olivia, Martinez-Arias, Rosa, Jacobi, Carsten, Starkuviene, Vytaute, Schlenczeck, Silke, Dencker, Silke, Huber, Robert, Klenk, Hans Peter, Kramer, Wilfried, Merkl, Rainer, Gottschalk, Gerhard and Fritz, Hans Joachim (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nature Biotechnology 22 (5), pp. 547-553. Fulltext not available.

Brüggemann, Holger, Baumer, Sebastian, Fricke, Wolfgang Florian, Wiezer, Arnim, Liesegang, Heiko, Decker, Ivona, Herzberg, Christina, Martinez-Arias, Rosa, Merkl, Rainer, Henne, Anke and Gottschalk, Gerhard (2003) The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proceedings of the National Academy of Sciences of the United States of America (PNAS) ISSN 1091-6490.

Merkl, Rainer (2003) A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. Journal of Molecular Evolution 57, pp. 453-466. Fulltext not available.

Tech, Maike and Merkl, Rainer (2003) YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biology 3 (4), pp. 441-451. Fulltext not available.

Wiezer, Arnim and Merkl, Rainer (2003) secureBLAST. In Silico Biology 3 (4), 0033. Fulltext not available.

Merkl, Rainer and Waack, Stephan (2002) Bioinformatik Interaktiv. Wiley-VCH, Weinheim. ISBN 78-3-527-30662-6. Fulltext not available.

Larbig, Karen D., Christmann, Andreas, Johann, André, Klockgether, Jens, Hartsch, Thomas, Merkl, Rainer, Wiehlmann, Lotz, Fritz, Hans Joachim and Tümmler, Burkhard (2002) Gene Islands Integrated into tRNA(Gly) Genes Confer Genome Diversity on a Pseudomonas aeruginosa Clone. Journal of Bacteriology 184 (23), pp. 6665-6680.

Deppenmeier, Uwe, Johann, André, Hartsch, Thomas, Merkl, Rainer, Schmitz, Ruth A:, Martinez-Arias, Rosa, Henne, Anke, Wiezer, Arnim, Bäumer, Sebastian, Jacobi, Carsten, Brüggemann, Holger, Lienard, Tanja, Christmann, Andreas, Bömeke, Mechthild, Steckel, Silke, Bhattacharyya, Anamitra, Lykidis, Athanasios, Overbeek, Ross, Klenk, Hans Peter, Gunsalus, Robert P., Fritz, Hans Joachim and Gottschalk, Gerhard (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. Journal of Molecular Microbiology and Biotechnology 4 (4), pp. 453-461. Fulltext not available.

Merkl, Rainer and Fritz, Hans Joachim (1996) Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in Haemophilus influenzae Rd. Nucleic Acids Research 24 (21), pp. 4146-4151.

Gläsner, W., Merkl, Rainer, Schellenberger, V. and Fritz, Hans Joachim (1995) Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome. Journal of Molecular Biology 245 (1), pp. 1-7. Fulltext not available.

Gläsner, W., Merkl, Rainer, Schmidt, Sebastian, Cech, D. and Fritz, Hans Joachim (1992) Fast quantitative assay of sequence-specific endonuclease activity based on DNA sequencer technology. Biological chemistry Hoppe-Seyler 373 (12), pp. 1223-1225. Fulltext not available.

Sander, Chris, Vriend, Gerrit, Bazan, Fernando, Horovitz, Amnon, Nakamura, Haruki, Ribas, Luis, Finkelstein, Alexei V., Lockhart, Andrew, Merkl, Rainer, Perry, L. Jeanne, Emery, Stephen C., Gaboriaud, Christine, Marks, Cara, Moult, John, Verlinde, Christophe, Eberhard, Marc, Elofsson, Arne, Hubbard, Tim J. P., Regan, Lynne, Banks, Jay, Jappelli, Roberto, Lesk, Arthur M. and Tramontano, Anna (1992) Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins 12 (2), pp. 105-110. Fulltext not available.

Merkl, Rainer, Kröger, Manfred, Rice, Peter and Fritz, Hans Joachim (1992) Statistical evaluation and biological interpretation of non-random abundance in the E. coli K-12 genome of tetra- and pentanucleotide sequences related to VSP DNA mismatch repair. Nucleic Acids Research 20 (7), pp. 1657-1662.

Humbel, B. M., Weber, K. and Merkl, Rainer (1991) Versatile controlling system for cryopreparation techniques in electron microscopy. J Electron Microsc Tech 17 (4), pp. 450-455. Fulltext not available.

Fisher, P. R., Merkl, Rainer and Gerisch, G. (1989) Quantitative Analysis of Cell Motility and Chemotaxis in Dictyostelium discoideum by Using an Image Processing System and a Novel Chemotaxis Chamber Providing Stationary Chemical Gradients. The Journal of Cell Biology (JCB) 108 (3), pp. 973-984.

Fahn, H., Maubach, P., Merkl, Rainer, Senner, H., Hellwig, H. and Wirtzfeld, A. (1989) [Ultra-high dose thrombolytic therapy with streptokinase in peripheral venous thrombosis]. Medizinische Klinik 84 (4), 183-7, 226. Fulltext not available.

Bozzaro, Salvatore, Merkl, Rainer and Gerisch, Günther (1987) Cell adhesion: its quantification, assay of the molecules involved, and selection of defective mutants in Dictyostelium and Polysphondylium. Methods in Cell Biology 28, pp. 359-385. Fulltext not available.

Hohmann, H. P., Bozzaro, S., Yoshida, M., Merkl, Rainer and Gerisch, G. (1987) Two-step Glycosylation of the Contact Site A Protein of Dictyostelium discoideum and Transport of an Incompletely Glycosylated Form to the Cell Surface. The Journal of Biological Chemistry 262 (34), pp. 16618-16624. Fulltext not available.

Francis, D., Toda, K., Merkl, Rainer, Hatfield, T. and Gerisch, G. (1985) Mutants of Polysphondylium pallidum altered in cell aggregation and in the expression of a carbohydrate epitope on cell surface glycoproteins. EMBO Journal 4 (10), pp. 2525-2532.

Noegel, A., Harloff, C., Hirth, P., Merkl, Rainer, Modersitzki, M., Stadler, J., Weinhart, U., Westphal, M. and Gerisch, G. (1985) Probing an adhesion mutant of Dictyostelium discoideum with cDNA clones and monoclonal antibodies indicates a specific defect in the contact site A glycoprotein. EMBO Journal 4 (13B), pp. 3805-3810.

Toda, Katsumi, Bozzaro, Salvatore, Lottspeich, Friedrich, Merkl, Rainer and Gerisch, Günther (1984) Monoclonal anti-glycoprotein antibody that blocks cell adhesion in Polysphondylium pallidum. European Journal Of Biochemistry 140 (1), pp. 73-81. Fulltext not available.

Heumann, R., Schwab, M., Merkl, Rainer and Thoenen, H. (1984) Nerve growth factor-mediated induction of choline acetyltransferase in PC12 cells: evaluation of the site of action of nerve growth factor and the involvement of lysosomal degradation products of nerve growth factor. European Journal Of Neuroscience 4 (12), pp. 3039-3050. Fulltext not available.

Häder, D. P., Claviez, M., Merkl, Rainer and Gerisch, G. (1983) Responses of Dictyostelium discoideum amoebae to local stimulation by light. Cell Biology International Reports 7 (8), pp. 611-616. Fulltext not available.

Ochiai, H., Stadler, J., Westphal, M., Wagle, G., Merkl, Rainer and Gerisch, G. (1982) Monoclonal antibodies against contact sites A of Dictyostelium discoideum: detection of modifications of the glycoprotein in tunicamycin-treated cells. EMBO Journal 1 (8), pp. 1011-1016.

Ochiai, H., Schwarz, H., Merkl, Rainer, Wagle, G. and Gerisch, G. (1982) Stage-specific antigens reacting with monoclonal antibodies against contact site A, a cell-surface glycoprotein of Dictyostelium discoideum. Cell Differentiation 11 (1), pp. 1-13. Fulltext restricted.