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Number of items at this level: 61.


Merkl, Rainer and Plach, Maximilian G. and 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 and Žváček, Clemens and 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 and Popal, Ajmal and Bauer, Jochen and Busch, Markus and Klocke, Michael and Spitzer, Wolfgang and 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 and Borst, Nadine and Schlee, Sandra and Schneider, Daniel and Janda, Jan-Oliver and 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.

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

Janda, Jan-Oliver and Busch, Markus and Kuck, Fabian and 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 and Ghai, Rohit and Billion, Andre and Kuenne, Carsten Tobias and Steinweg, Christiane and Izar, Benjamin and Mohamed, Walid and Mraheil, Mobarak and Domann, Eugen and Schaffrath, Silke and Kärst, Uwe and Goesmann, Alexander and Oehm, Sebastian and Pühler, Alfred and Merkl, Rainer and Vorwerk, Sonja and Glaser, Philippe and Garrido, Patricia and Rusniok, Christophe and Buchrieser, Carmen and 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 and Zellner, Hermann and Guldan, Harald and Merkl, Rainer and 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.


Zellner, H. and Staudigel, M. and Trenner, T. and Bittkowski, M. and Wolowski, V. and Icking, C. and Merkl, Rainer (2011) Prescont: Predicting protein-protein interfaces utilizing four residue properties. Proteins.

Ohlmann, Andreas and Merkl, Rainer and Tamm, Ernst R. (2011) Focus on Molecules: Norrin. Experimental eye research.

Fink, Florian and Hochrein, Jochen and Wolowski, Vincent and Merkl, Rainer and Gronwald, Wolfram (2011) PROCOS: Computational analysis of protein–protein complexes. Journal of Computational Chemistry 32 (12), pp. 2575-2586.

Fischer, André and Seitz, Tobias and Lochner, Adriane and Sterner, Reinhard and 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.

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

Pürzer, Andreas and Grassmann, Felix and 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).


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 and Exler, Josef H. and Merkl, Rainer and Dachauer, Karoline and Brehm, Alexander and Grummt, Ingrid and Längst, Gernot (2010) DNA sequence encoded repression of rRNA gene transcription in chromatin. Nucleic acids research 38 (16), pp. 5304-5314.

Richter, Markus and Bosnali, Manal and Carstensen, Linn and Seitz, Tobias and Durchschlag, Helmut and Blanquart, Samuel and 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.

Wiedemann, Sonja M. and Mildner, Silke N. and Bönisch, Clemens and Israel, Lars and Maiser, Andreas and Matheisl, Sarah and Straub, Tobias and Merkl, Rainer and Leonhardt, Heinrich and Kremmer, Elisabeth and 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.


Merkl, Rainer and Waack, Stephan (2009) Bioinformatik Interaktiv
Algorithmen und Praxis
2. erweiterte und neubearbeitete Auflage.
Wiley-VCH, Weinheim.

Merkl, Rainer and Wiezer, Arnim (2009) GO4genome: A prokaryotic phylogeny based on genome organisation. Journal of Molecular Evolution 68 (5), pp. 550-562.

Fischer, André and Enkler, Nils and Neudert, Gerd and Bocola, Marco and 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 and Merkl, Rainer and Raushel, Frank M. (2008) Computational design of enzymes. Chemistry & Biology 15 (5), pp. 421-423.


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, F. and Merkl, Rainer and Gronwald, W. (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). NIC Series, 36. NIC Series, p. 127.


Merkl, Rainer (2006) A comparative categorization of protein function encoded in bacterial or archeal genomic islands. J Mol Evol 62 (1), pp. 1-14.

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.

Waack, Stephan and Keller, Oliver and Asper, Roman and Brodag, Thomas and Damm, Carsten and Fricke, Wolfgang Florian and Surovcik, Katharina and 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.


Helmstaedt, Kerstin and Heinrich, Gabriele and 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.

Meinicke, Peter and Tech, Maike and 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 and Herzberg, Christina and Steckel, Silke and Feesche, Jörg and Maurer, Karl Heinz and Ehrenreich, Petra and Bäumer, Sebastian and Henne, Anke and Liesegang, Heiko and Merkl, Rainer and 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.

Henne, Anke and Brüggemann, Holger and Raasch, Carsten and Wiezer, Arnim and Hartsch, Thomas and Liesegang, Heiko and Johann, Andre and Lienard, Tanja and Gohl, Olivia and Martinez-Arias, Rosa and Jacobi, Carsten and Starkuviene, Vytaute and Schlenczeck, Silke and Dencker, Silke and Huber, Robert and Klenk, Hans Peter and Kramer, Wilfried and Merkl, Rainer and Gottschalk, Gerhard and Fritz, Hans Joachim (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nature Biotechnology 22 (5), pp. 547-553.


Brüggemann, Holger and Baumer, Sebastian and Fricke, Wolfgang Florian and Wiezer, Arnim and Liesegang, Heiko and Decker, Ivona and Herzberg, Christina and Martinez-Arias, Rosa and Merkl, Rainer and 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.

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.

Wiezer, Arnim and Merkl, Rainer (2003) secureBLAST. In Silico Biology 3 (4), 0033.


Merkl, Rainer and Waack, Stephan (2002) Bioinformatik Interaktiv. Wiley-VCH, Weinheim. ISBN 78-3-527-30662-6.

Larbig, Karen D. and Christmann, Andreas and Johann, André and Klockgether, Jens and Hartsch, Thomas and Merkl, Rainer and Wiehlmann, Lotz and 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 and Johann, André and Hartsch, Thomas and Merkl, Rainer and Schmitz, Ruth A: and Martinez-Arias, Rosa and Henne, Anke and Wiezer, Arnim and Bäumer, Sebastian and Jacobi, Carsten and Brüggemann, Holger and Lienard, Tanja and Christmann, Andreas and Bömeke, Mechthild and Steckel, Silke and Bhattacharyya, Anamitra and Lykidis, Athanasios and Overbeek, Ross and Klenk, Hans Peter and Gunsalus, Robert P. and 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.


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. and Merkl, Rainer and 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.


Gläsner, W. and Merkl, Rainer and Schmidt, Sebastian and 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.

Sander, Chris and Vriend, Gerrit and Bazan, Fernando and Horovitz, Amnon and Nakamura, Haruki and Ribas, Luis and Finkelstein, Alexei V. and Lockhart, Andrew and Merkl, Rainer and Perry, L. Jeanne and Emery, Stephen C. and Gaboriaud, Christine and Marks, Cara and Moult, John and Verlinde, Christophe and Eberhard, Marc and Elofsson, Arne and Hubbard, Tim J. P. and Regan, Lynne and Banks, Jay and Jappelli, Roberto and 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.

Merkl, Rainer and Kröger, Manfred and 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. and Weber, K. and Merkl, Rainer (1991) Versatile controlling system for cryopreparation techniques in electron microscopy. J Electron Microsc Tech 17 (4), pp. 450-455.


Fisher, P. R. and 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. and Maubach, P. and Merkl, Rainer and Senner, H. and Hellwig, H. and Wirtzfeld, A. (1989) [Ultra-high dose thrombolytic therapy with streptokinase in peripheral venous thrombosis]. Medizinische Klinik 84 (4), 183-7, 226.


Bozzaro, Salvatore and 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.

Hohmann, H. P. and Bozzaro, S. and Yoshida, M. and 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.


Francis, D. and Toda, K. and Merkl, Rainer and 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. and Harloff, C. and Hirth, P. and Merkl, Rainer and Modersitzki, M. and Stadler, J. and Weinhart, U. and 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 and Bozzaro, Salvatore and Lottspeich, Friedrich and 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.

Heumann, R. and Schwab, M. and 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.


Häder, D. P. and Claviez, M. and 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.


Ochiai, H. and Stadler, J. and Westphal, M. and Wagle, G. and 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. and Schwarz, H. and Merkl, Rainer and 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.

This list was generated on Fri Apr 29 23:44:01 2016 CEST.
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