Rainer Merkl

Summary

Affiliation: University of Regensburg
Country: Germany

Publications

  1. pmc Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes
    Torsten Hain
    Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, Giessen, D 35392, Germany
    BMC Genomics 13:144. 2012
  2. pmc CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure
    Jan Oliver Janda
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
    BMC Bioinformatics 13:55. 2012
  3. pmc Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions
    Conrad von Mandach
    University of Hagen, Germany
    BMC Genomics 11:617. 2010
  4. pmc Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
    Stephan Waack
    Institut fur Informatik, Universitat Gottingen, Lotzestr, 16 18, 37083 Göttingen, Germany
    BMC Bioinformatics 7:142. 2006
  5. pmc Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
    Peter Meinicke
    Abteilung Bioinformatik, Institut fur Mikrobiologie und Genetik, Georg August Universitat Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 5:169. 2004
  6. ncbi request reprint AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise conserved gene arrangements
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    In Silico Biol 6:281-306. 2006
  7. pmc Modelling the evolution of the archeal tryptophan synthase
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Regensburg, Germany
    BMC Evol Biol 7:59. 2007
  8. pmc H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, D 93040 Regensburg, Germany
    BMC Bioinformatics 9:151. 2008
  9. pmc GO4genome: a prokaryotic phylogeny based on genome organization
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, 93040, Regensburg, Germany
    J Mol Evol 68:550-62. 2009
  10. ncbi request reprint A comparative categorization of protein function encoded in bacterial or archeal genomic islands
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, D 93040 Regensburg, Germany
    J Mol Evol 62:1-14. 2006

Collaborators

Detail Information

Publications35

  1. pmc Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes
    Torsten Hain
    Institute of Medical Microbiology, Justus Liebig University, Schubertstrasse 81, Giessen, D 35392, Germany
    BMC Genomics 13:144. 2012
    ..monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans...
  2. pmc CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure
    Jan Oliver Janda
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
    BMC Bioinformatics 13:55. 2012
    ..This is why we were interested to design a new classifier that differentiates between functionally and structurally important sites and to assess its performance on representative datasets...
  3. pmc Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions
    Conrad von Mandach
    University of Hagen, Germany
    BMC Genomics 11:617. 2010
    ..Whereas CUB and the overrepresentation of individual proteins have been studied in detail, it is still unclear which high-level metabolic categories are subject to translational optimization in different habitats...
  4. pmc Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
    Stephan Waack
    Institut fur Informatik, Universitat Gottingen, Lotzestr, 16 18, 37083 Göttingen, Germany
    BMC Bioinformatics 7:142. 2006
    ..Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands...
  5. pmc Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
    Peter Meinicke
    Abteilung Bioinformatik, Institut fur Mikrobiologie und Genetik, Georg August Universitat Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 5:169. 2004
    ..Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations in terms of positional and compositional variability of the underlying biological signals...
  6. ncbi request reprint AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise conserved gene arrangements
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    In Silico Biol 6:281-306. 2006
    ..In addition, cons(CL) values provide a sound basis for non-homologous gene annotation. Based on cons(CL) values, examples of conserved clusters containing annotated genes and single ones with unknown function are given...
  7. pmc Modelling the evolution of the archeal tryptophan synthase
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Regensburg, Germany
    BMC Evol Biol 7:59. 2007
    ..In several prokaryotic genomes, two variants of trpB (named trpB1 or trpB2) occur in different combinations. The evolutionary history of these trpB genes is under debate...
  8. pmc H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, D 93040 Regensburg, Germany
    BMC Bioinformatics 9:151. 2008
    ..In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues...
  9. pmc GO4genome: a prokaryotic phylogeny based on genome organization
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, 93040, Regensburg, Germany
    J Mol Evol 68:550-62. 2009
    ..Genomes of strains belonging to Escherichia coli, Shigella, Streptococcus, Methanosarcina, and Yersinia were analyzed. Differences from the findings of classical methods are discussed...
  10. ncbi request reprint A comparative categorization of protein function encoded in bacterial or archeal genomic islands
    Rainer Merkl
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, D 93040 Regensburg, Germany
    J Mol Evol 62:1-14. 2006
    ..However, only specific subsets of operational genes were enriched in GIs. Modification of the cell envelope, cell motility, secretion, and protection of cellular DNA are major issues in HGT...
  11. ncbi request reprint Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple-sequence alignments
    Susanne Dietrich
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    Biochemistry 51:5633-41. 2012
    ..Our findings demonstrate that positions with high conn(k) values have an increased probability of being important for enzyme function or stability...
  12. ncbi request reprint CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data
    Jan Oliver Janda
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, D 93040 Regensburg, Germany and Faculty of Mathematics and Computer Science, University of Hagen, D 58084 Hagen, Germany
    Bioinformatics 29:3029-35. 2013
    ..The precise identification of functionally and structurally important residues of a protein is still an open problem, and state-of-the-art classifiers predict only one or at most two different categories...
  13. doi request reprint A fast and precise approach for computational saturation mutagenesis and its experimental validation by using an artificial (βα)8-barrel protein
    Andre Fischer
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Regensburg, Germany
    Chembiochem 12:1544-50. 2011
    ..90, which is statistically significant. This degree of coherence is stronger than the ones we obtained for established computational methods of mutational analysis...
  14. doi request reprint PresCont: predicting protein-protein interfaces utilizing four residue properties
    Hermann Zellner
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
    Proteins 80:154-68. 2012
    ..Moreover, we show that for permanent complexes a segmentation of PPIs into core and rim residues has only a moderate influence on prediction quality. PresCont is available as a web service at http://www-bioinf.uni-regensburg.de/...
  15. doi request reprint Turning catalytically inactive human Argonaute proteins into active slicer enzymes
    Judith Hauptmann
    Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
    Nat Struct Mol Biol 20:814-7. 2013
    ..In addition, PIWI-domain mutations in Ago1 may misarrange the catalytic center. Our work helps in understanding of the structural requirements that make an Argonaute protein an active endonucleolytic enzyme. ..
  16. pmc The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation
    Inga Loedige
    Biochemistry Center Regensburg BZR, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
    Genes Dev 28:749-64. 2014
    ..Using structural homology modeling, we predict that the NHL domains of all TRIM-NHL proteins have the potential to bind RNA, indicating that Brat is part of a conserved family of RNA-binding proteins. ..
  17. doi request reprint Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era
    Bernd Reisinger
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D 93053 Regensburg, Germany
    J Am Chem Soc 136:122-9. 2014
    ..5 billion years ago. ..
  18. pmc TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis
    Andre Fischer
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Regensburg, Germany
    BMC Bioinformatics 10:54. 2009
    ..Computational enzyme design is far from being applicable for the general case. Due to computational complexity and limited knowledge of the structure-function interplay, heuristic methods have to be used...
  19. doi request reprint Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds
    Markus Richter
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    J Mol Biol 398:763-73. 2010
    ..Most likely, the (beta alpha)(2) quarter-barrel and (beta alpha)(4) half-barrel intermediates on this pathway were stabilised by disulfide bonds that became dispensable upon consolidation of the (beta alpha)(8)-barrel...
  20. doi request reprint PROCOS: computational analysis of protein-protein complexes
    Florian Fink
    Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
    J Comput Chem 32:2575-86. 2011
    ..In conclusion, a novel fully automated method is presented that allows the reliable evaluation of protein-protein complexes...
  21. pmc H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments
    Jan Oliver Janda
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, D 93040 Regensburg, Germany
    BMC Bioinformatics 15:118. 2014
    ..One typical algorithm is H2r, which characterizes each individual residue position k by the conn(k)-value, which is the number of significantly correlated pairs it belongs to...
  22. ncbi request reprint Exploiting protein symmetry to design light-controllable enzyme inhibitors
    Bernd Reisinger
    Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, 93040 Regensburg Germany
    Angew Chem Int Ed Engl 53:595-8. 2014
    ..Switching from the flexible, ring-open to the rigid, ring-closed isomer reduces inhibition activity by one order of magnitude. ..
  23. doi request reprint Dimerization determines substrate specificity of a bacterial prenyltransferase
    David Peterhoff
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitatsstrasse 31, 93053 Regensburg, Germany
    Chembiochem 13:1297-303. 2012
    ..We provide a plausible hypothesis as to how dimerization determines substrate specificity of PcrB...
  24. doi request reprint Computational design of enzymes
    Reinhard Sterner
    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
    Chem Biol 15:421-3. 2008
    ..Sophisticated computational methods have recently led to impressive progress in this exciting and rapidly evolving field (Röthlisberger et al., 2008; Jiang et al., 2008)...
  25. pmc Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone
    Karen D Larbig
    Klinische Forschergruppe, Medizinische Hochschule Hannover, Hannover, Germany
    J Bacteriol 184:6665-80. 2002
    ....
  26. ncbi request reprint Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine
    Kerstin Helmstaedt
    Abteilung Molekulare Mikrobiologie und Genetik, Institut fur Mikrobiologie und Genetik, Grisebachstrasse 8, 37077 Gottingen, Germany
    Arch Microbiol 181:195-203. 2004
    ..The kinetic data show Michaelis-Menten substrate saturation with a Km of 290 microM, and a kcat/ Km value of 180 s(-1) mM(-1). TtCM was inhibited by tyrosine with a Ki =34 microM, possibly in a competitive manner...
  27. ncbi request reprint YACOP: Enhanced gene prediction obtained by a combination of existing methods
    Maike Tech
    Göttingen Genomics Laboratory, Institut für Mikrobiologie and Genetik, Grisebachstrasse 8, D 37077 Gottingen, Germany
    In Silico Biol 3:441-51. 2003
    ..8% and up to 32.3% of the positions given in the annotations differed from the locus predicted by any of the programs tested. YACOP can be downloaded from http://www.g2l.bio.uni-goettingen.de...
  28. pmc SIGI: score-based identification of genomic islands
    Rainer Merkl
    Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut fur Mikrobiologie und Genetik, Georg August Universität Göttingen and Göttingen Genomics Laboratory, Grisebachstr, 8, 37077 Gottingen, Germany
    BMC Bioinformatics 5:22. 2004
    ..Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands...
  29. ncbi request reprint The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential
    Birgit Veith
    Göttingen Genomics Laboratory and Competence Centre for Genome Research on Bacteria, Institute of Microbiology and Genetics, University of Gottingen, Gottingen, Germany
    J Mol Microbiol Biotechnol 7:204-11. 2004
    ..Many new genes of potential interest for biotechnological applications were found in B. licheniformis; candidates include proteases, pectate lyases, lipases and various polysaccharide degrading enzymes...
  30. ncbi request reprint A comparative categorization of gene flux in diverse microbial species
    Arnim Wiezer
    Göttingen Genomics Laboratory, Grisebachstrasse 8, D 37077 Gottingen, Germany
    Genomics 86:462-75. 2005
    ..The analysis of related genomes showed that the composition of GIs cannot be explained with trends of gene content known to depend on genome size...
  31. ncbi request reprint The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea
    Uwe Deppenmeier
    Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University, Goettingen, Germany
    J Mol Microbiol Biotechnol 4:453-61. 2002
    ..These findings might indicate that lateral gene transfer has played an important evolutionary role in forging the physiology of this metabolically versatile methanogen...
  32. ncbi request reprint The genome sequence of the extreme thermophile Thermus thermophilus
    Anke Henne
    Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Gottingen, Germany
    Nat Biotechnol 22:547-53. 2004
    ..thermophilus HB27. Candidates include various proteases and key enzymes of other fundamental biological processes such as DNA replication, DNA repair and RNA maturation...
  33. ncbi request reprint A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency
    Rainer Merkl
    Abteilung Molekulare Genetik und Präparative Molekularbiologie, Institut fur Mikrobiologie und Genetik, Göttingen Genomics Laboratory, Georg August Universitat Gottingen, Grisebachstrasse 8, D 37077 G6ttingen, Germany
    J Mol Evol 57:453-66. 2003
    ..g21.bio.uni-goettingen.de. The method was applied to complete bacterial genomes. The relation of codon usage bias with amino acid composition and the choice of stop codons were determined and discussed...
  34. ncbi request reprint secureBLAST
    Arnim Wiezer
    Goettingen Genomics Laboratory, Institut fuer Mikrobiologie and Genetik, Grisebachstrasse 8, D 37077 Goettingen, Germany
    In Silico Biol 3:405-9. 2003
    ..Therefore, secureBLAST is valuable for institutions that have to restrict access to their datasets or just want to administer BLAST servers via a web interface...
  35. pmc The genome sequence of Clostridium tetani, the causative agent of tetanus disease
    Holger Bruggemann
    Göttingen Genomics Laboratory and Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University, Grisebachstrasse 8, D 37077 Gottingen, Germany
    Proc Natl Acad Sci U S A 100:1316-21. 2003
    ..tetani: The organism can rely on an extensive sodium ion bioenergetics. Additional candidate genes involved in the establishment and maintenance of a pathogenic lifestyle of C. tetani are presented...