List of works - Rainer Merkl

A comparative categorization of gene flux in diverse microbial species

scientific article published in October 2005

A comparative categorization of protein function encoded in bacterial or archeal genomic islands

scientific article published on 06 December 2005

A fast and precise approach for computational saturation mutagenesis and its experimental validation by using an artificial (βα)8-barrel protein

scientific article

A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency.

scientific article

AGeNNT: annotation of enzyme families by means of refined neighborhood networks.

scientific article

An assessment of catalytic residue 3D ensembles for the prediction of enzyme function

scientific article published on 4 November 2015

Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction

scientific article published on 23 December 2019

Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation

scientific article published on 01 January 2019

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes

scientific article published on 8 June 2016

Ancestral protein reconstruction: techniques and applications

scientific article published on September 2015

Artificial Light Regulation of an Allosteric Bienzyme Complex by a Photosensitive Ligand

scientific article published on 29 May 2018

Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism

scientific article (publication date: 26 January 2017)

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

scientific article

CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data

scientific article

Cell adhesion: its quantification, assay of the molecules involved, and selection of defective mutants in Dictyostelium and Polysphondylium

scientific article published on 01 January 1987

Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.

scientific article published in February 2019

Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine

scientific article

Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex

scientific article published on 9 December 2016

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

scientific article

Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds

article

Computational design of enzymes

scientific article

Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products

scientific article published on 03 January 2020

Conversion of anthranilate synthase into isochorismate synthase: implications for the evolution of chorismate-utilizing enzymes

scientific article published on September 2015

DNA sequence encoded repression of rRNA gene transcription in chromatin

scientific article published on 25 April 2010

Development of photoswitchable inhibitors for β-galactosidase

article

Dimerization determines substrate specificity of a bacterial prenyltransferase

scientific article published on 21 May 2012

Elucidation of the functional roles of the Q and I motifs in the human chromatin-remodeling enzyme BRG1

scientific article published on 15 January 2019

Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era

scientific article

Evolutionary diversification of protein-protein interactions by interface add-ons

scientific article published on 18 September 2017

Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple-sequence alignments

scientific article published on 6 July 2012

Exploiting protein symmetry to design light-controllable enzyme inhibitors

scientific article published on 25 November 2013

Fast quantitative assay of sequence-specific endonuclease activity based on DNA sequencer technology

scientific article published on December 1, 1992

Focus on molecules: Norrin

scientific article published on 30 June 2011

GO4genome: a prokaryotic phylogeny based on genome organization

scientific article

Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone

scientific article published on December 2002

Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

scientific article

Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage

scientific article

H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.

scientific article

H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments.

scientific article

Hexamerization of Geranylgeranylglyceryl Phosphate Synthase Ensures Structural Integrity and Catalytic Activity at High Temperatures

scientific article published on 11 April 2018

Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y.

scientific article

Identification of the retinoschisin-binding site on the retinal Na/K-ATPase

scientific article published on 02 May 2019

Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design

scientific article published on 12 February 2015

Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation

scientific article published on March 4, 2011

Light-Regulation of Tryptophan Synthase by Combining Protein Design and Enzymology

scientific article published on 15 October 2019

Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation

scientific article published on 29 January 2016

Maize EMBRYO SAC family peptides interact differentially with pollen tubes and fungal cells.

scientific article published on 12 June 2015

Modelling the evolution of the archeal tryptophan synthase

scientific article

Monoclonal anti-glycoprotein antibody that blocks cell adhesion in Polysphondylium pallidum

scientific article published on 01 April 1984

Monoclonal antibodies against Dictyostelium plasma membranes: their binding to simple sugars

scientific article published in August 1985

Monoclonal antibodies against contact sites A of Dictyostelium discoideum: detection of modifications of the glycoprotein in tunicamycin-treated cells

scientific article published on January 1982

Mutants of Polysphondylium pallidum altered in cell aggregation and in the expression of a carbohydrate epitope on cell surface glycoproteins.

scientific article published on October 1985

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.

scientific article

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites

scientific article

PROCOS: computational analysis of protein-protein complexes

scientific article published on 31 May 2011

Pathomechanism of mutated and secreted retinoschisin in X-linked juvenile retinoschisis

scientific article published on 21 July 2018

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

scientific article

Post-translational glycosylation of the contact site A protein of Dictyostelium discoideum is important for stability but not for its function in cell adhesion

scientific article published on December 1987

PresCont: predicting protein-protein interfaces utilizing four residue properties.

scientific article published on 31 October 2011

Probing an adhesion mutant of Dictyostelium discoideum with cDNA clones and monoclonal antibodies indicates a specific defect in the contact site A glycoprotein.

scientific article published in December 1985

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.

scientific article published on March 1989

Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase

scientific article published on 08 March 2018

Responses of Dictyostelium discoideum amoebae to local stimulation by light

scientific article published on 01 August 1983

Rosetta design with co-evolutionary information retains protein function

scientific article published on 19 January 2021

Rosetta:MSF: a modular framework for multi-state computational protein design

scientific article

SIGI: score-based identification of genomic islands

scientific article

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

scientific article published on 16 March 2006

Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase

scientific article published on 01 February 2019

Stage-specific antigens reacting with monoclonal antibodies against contact site A, a cell-surface glycoprotein of Dictyostelium discoideum

scientific article published on 01 January 1982

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

scientific article

Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in Haemophilus influenzae Rd.

scientific article published on November 1996

Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.

scientific article

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

scientific article

The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex.

scientific article published on 24 March 2018

The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events

scientific article published on 21 December 2016

The Complete Genome Sequence of Bacillus licheniformis DSM13, an Organism with Great Industrial Potential

scientific article

The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation

scientific article

The extended AT-hook is a novel RNA binding motif.

scientific article published on 9 July 2015

The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea

scientific article (publication date: July 2002)

The genome sequence of Clostridium tetani, the causative agent of tetanus disease

scientific article

The genome sequence of the extreme thermophile Thermus thermophilus

scientific article

The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis

scientific article published on 08 January 2019

TransCent: computational enzyme design by transferring active sites and considering constraints relevant for catalysis

scientific article

TrpB2 enzymes are O-phospho-l-serine dependent tryptophan synthases

scientific article

Turning catalytically inactive human Argonaute proteins into active slicer enzymes

scientific article published on 12 May 2013

Two-step glycosylation of the contact site A protein of Dictyostelium discoideum and transport of an incompletely glycosylated form to the cell surface

scientific article published in December 1987

Versatile controlling system for cryopreparation techniques in electron microscopy

scientific article published on 01 April 1991

YACOP: Enhanced gene prediction obtained by a combination of existing methods.

scientific article published in January 2003

secureBLAST.

scientific article published in January 2003

List of works by Rainer Merkl

A comparative categorization of gene flux in diverse microbial species

A comparative categorization of protein function encoded in bacterial or archeal genomic islands

A fast and precise approach for computational saturation mutagenesis and its experimental validation by using an artificial (βα)8-barrel protein

A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency.

AGeNNT: annotation of enzyme families by means of refined neighborhood networks.

An assessment of catalytic residue 3D ensembles for the prediction of enzyme function

Analysis of allosteric communication in a multienzyme complex by ancestral sequence reconstruction

Ancestral Sequence Reconstruction as a Tool for the Elucidation of a Stepwise Evolutionary Adaptation

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes

Ancestral protein reconstruction: techniques and applications

Artificial Light Regulation of an Allosteric Bienzyme Complex by a Photosensitive Ligand

Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data

Cell adhesion: its quantification, assay of the molecules involved, and selection of defective mutants in Dictyostelium and Polysphondylium

Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.

Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine

Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds

Computational design of enzymes

Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products

Conversion of anthranilate synthase into isochorismate synthase: implications for the evolution of chorismate-utilizing enzymes

DNA sequence encoded repression of rRNA gene transcription in chromatin

Development of photoswitchable inhibitors for β-galactosidase

Dimerization determines substrate specificity of a bacterial prenyltransferase

Elucidation of the functional roles of the Q and I motifs in the human chromatin-remodeling enzyme BRG1

Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era

Evolutionary diversification of protein-protein interactions by interface add-ons

Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple-sequence alignments

Exploiting protein symmetry to design light-controllable enzyme inhibitors

Fast quantitative assay of sequence-specific endonuclease activity based on DNA sequencer technology

Focus on molecules: Norrin

GO4genome: a prokaryotic phylogeny based on genome organization

Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone

Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

Generation of catalytic human Ago4 identifies structural elements important for RNA cleavage

H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.

H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments.

Hexamerization of Geranylgeranylglyceryl Phosphate Synthase Ensures Structural Integrity and Catalytic Activity at High Temperatures

Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y.

Identification of the retinoschisin-binding site on the retinal Na/K-ATPase

Improving thermal and detergent stability of Bacillus stearothermophilus neopullulanase by rational enzyme design

Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation

Light-Regulation of Tryptophan Synthase by Combining Protein Design and Enzymology

Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation

Maize EMBRYO SAC family peptides interact differentially with pollen tubes and fungal cells.

Modelling the evolution of the archeal tryptophan synthase

Monoclonal anti-glycoprotein antibody that blocks cell adhesion in Polysphondylium pallidum

Monoclonal antibodies against Dictyostelium plasma membranes: their binding to simple sugars

Monoclonal antibodies against contact sites A of Dictyostelium discoideum: detection of modifications of the glycoprotein in tunicamycin-treated cells

Mutants of Polysphondylium pallidum altered in cell aggregation and in the expression of a carbohydrate epitope on cell surface glycoproteins.

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.

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites

PROCOS: computational analysis of protein-protein complexes

Pathomechanism of mutated and secreted retinoschisin in X-linked juvenile retinoschisis

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

Post-translational glycosylation of the contact site A protein of Dictyostelium discoideum is important for stability but not for its function in cell adhesion

PresCont: predicting protein-protein interfaces utilizing four residue properties.

Probing an adhesion mutant of Dictyostelium discoideum with cDNA clones and monoclonal antibodies indicates a specific defect in the contact site A glycoprotein.

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.

Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase

Responses of Dictyostelium discoideum amoebae to local stimulation by light

Rosetta design with co-evolutionary information retains protein function

Rosetta:MSF: a modular framework for multi-state computational protein design

SIGI: score-based identification of genomic islands

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase

Stage-specific antigens reacting with monoclonal antibodies against contact site A, a cell-surface glycoprotein of Dictyostelium discoideum

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

Statistical evidence for a biochemical pathway of natural, sequence-targeted G/C to C/G transversion mutagenesis in Haemophilus influenzae Rd.

Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex.

The Arabidopsis THO/TREX component TEX1 functionally interacts with MOS11 and modulates mRNA export and alternative splicing events

The Complete Genome Sequence of Bacillus licheniformis DSM13, an Organism with Great Industrial Potential

The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation

The extended AT-hook is a novel RNA binding motif.

The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea