List of works - Johannes Söding

A conserved GA element in TATA-less RNA polymerase II promoters

scientific article

A galaxy of folds

scientific article published on January 2010

A vocabulary of ancient peptides at the origin of folded proteins

scientific article

AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels

scientific article

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

scientific article

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

scientific article published on 23 October 2015

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

scientific article published on 9 June 2016

Bayesian multiple logistic regression for case-control GWAS

scientific article published on 31 December 2018

CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations

scientific article published on 26 July 2014

Clustering huge protein sequence sets in linear time.

scientific article

Coherent beam splitter for atoms based on a bichromatic standing light wave

scientific article published on 01 May 1994

Comparative analysis of coiled-coil prediction methods.

scientific article published on 31 March 2006

Context similarity scoring improves protein sequence alignments in the midnight zone.

scientific article

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

scientific article

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

scientific article

De novo identification of highly diverged protein repeats by probabilistic consistency

scientific article published in February 2008

Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1

scientific article

Discriminative modelling of context-specific amino acid substitution probabilities

scientific article

Eph receptors and ephrin class B ligands are expressed at tissue boundaries in Hydra vulgaris.

scientific article

Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin

scientific article

Evolution of the beta-propeller fold.

scientific article published in May 2008

Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli

scientific article

Fast and accurate automatic structure prediction with HHpred.

scientific article

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

scientific article (publication date: 11 October 2011)

Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex.

scientific article

Giant Spin Relaxation of an Ultracold Cesium Gas

scientific article published in Physical Review Letters

Gravitational laser trap for atoms with evanescent-wave cooling

HH-suite3 for fast remote homology detection and deep protein annotation

scientific article published on 14 September 2019

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

scientific article

HHomp--prediction and classification of outer membrane proteins

scientific article

HHrep: de novo protein repeat detection and the origin of TIM barrels

scientific article published on July 2006

HHsenser: exhaustive transitive profile search using HMM-HMM comparison

scientific article published on July 2006

Implementation of renal key performance indicators: promoting improved clinical practice

scientific article

In vivo ligands of MDA5 and RIG-I in measles virus-infected cells

scientific article

Is Bose-Einstein condensation of atomic cesium possible?

article by D Guéry-Odelin et al published 1 October 1998 in Europhysics Letters

Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome

scientific article

Lysine/RNA-interactions drive and regulate biomolecular condensation

scientific article published on 02 July 2019

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

scientific article

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

scientific article published on 16 October 2017

Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails

scientific article published on 12 January 2016

More than the sum of their parts: on the evolution of proteins from peptides

scientific article

Observation of the Magneto-Optical Radiation Force by Laser Spectroscopy

article

Of Bits and Bugs — On the Use of Bioinformatics and a Bacterial Crystal Structure to Solve a Eukaryotic Repeat-Protein Structure

scientific article

On the origin of the histone fold

scientific article

P-value-based regulatory motif discovery using positional weight matrices

scientific article published on 18 September 2012

PDBalert: automatic, recurrent remote homology tracking and protein structure prediction.

scientific article

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors

scientific article

Prediction of protein functional residues from sequence by probability density estimation

scientific article published on 2 January 2008

Protein homology detection by HMM-HMM comparison

scientific article

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

scientific article published on 31 March 2011

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

scientific article published on 24 June 2019

RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress

scientific article

REPPER--repeats and their periodicities in fibrous proteins

scientific article

RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton

scientific article published in 2023

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II

scientific article

Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster

scientific article

ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize -butyrolactones

scientific article published on 01 May 2007

Sequence context-specific profiles for homology searching

scientific article

Short-Distance Atomic Beam Deceleration with a Stimulated Light Force

scientific article published in Physical Review Letters

Stimulated magneto-optical force in the dressed-atom picture

scientific article published on 01 September 1994

Sub-Doppler manifestation of the magneto-optical radiation force

article published in 1993

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

scientific article published on 05 November 2018

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

scientific article

Tejaas: reverse regression increases power for detecting trans-eQTLs

scientific article published on 06 May 2021

The HHpred interactive server for protein homology detection and structure prediction

scientific article

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

scientific article published on 27 October 2011

The MPI Bioinformatics Toolkit for protein sequence analysis

scientific article published on July 2006

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

scientific article

The Mre11:Rad50 Structure Shows an ATP-Dependent Molecular Clamp in DNA Double-Strand Break Repair

scientific article

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

scientific article published on 12 June 2012

The molecular cell death machinery in the simple cnidarian Hydra includes an expanded caspase family and pro- and anti-apoptotic Bcl-2 proteins

scientific article published on 18 May 2010

Three-body decay of a rubidium Bose–Einstein condensate

article

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

scholarly article by Carlo Baejen published in September 2014

Uniform transitions of the general RNA polymerase II transcription complex

scientific article

bbcontacts: prediction of β-strand pairing from direct coupling patterns.

scientific article

kClust: fast and sensitive clustering of large protein sequence databases

scientific article

List of works by Johannes Söding

A conserved GA element in TATA-less RNA polymerase II promoters

A galaxy of folds

A vocabulary of ancient peptides at the origin of folded proteins

AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

Bayesian multiple logistic regression for case-control GWAS

CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations

Clustering huge protein sequence sets in linear time.

Coherent beam splitter for atoms based on a bichromatic standing light wave

Comparative analysis of coiled-coil prediction methods.

Context similarity scoring improves protein sequence alignments in the midnight zone.

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

De novo identification of highly diverged protein repeats by probabilistic consistency

Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1

Discriminative modelling of context-specific amino acid substitution probabilities

Eph receptors and ephrin class B ligands are expressed at tissue boundaries in Hydra vulgaris.

Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin

Evolution of the beta-propeller fold.

Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli

Fast and accurate automatic structure prediction with HHpred.

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex.

Giant Spin Relaxation of an Ultracold Cesium Gas

Gravitational laser trap for atoms with evanescent-wave cooling

HH-suite3 for fast remote homology detection and deep protein annotation

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

HHomp--prediction and classification of outer membrane proteins

HHrep: de novo protein repeat detection and the origin of TIM barrels

HHsenser: exhaustive transitive profile search using HMM-HMM comparison

Implementation of renal key performance indicators: promoting improved clinical practice

In vivo ligands of MDA5 and RIG-I in measles virus-infected cells

Is Bose-Einstein condensation of atomic cesium possible?

Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome

Lysine/RNA-interactions drive and regulate biomolecular condensation

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails

More than the sum of their parts: on the evolution of proteins from peptides

Observation of the Magneto-Optical Radiation Force by Laser Spectroscopy

Of Bits and Bugs — On the Use of Bioinformatics and a Bacterial Crystal Structure to Solve a Eukaryotic Repeat-Protein Structure

On the origin of the histone fold

P-value-based regulatory motif discovery using positional weight matrices

PDBalert: automatic, recurrent remote homology tracking and protein structure prediction.

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors

Prediction of protein functional residues from sequence by probability density estimation

Protein homology detection by HMM-HMM comparison

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress

REPPER--repeats and their periodicities in fibrous proteins

RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II

Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster

ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize -butyrolactones

Sequence context-specific profiles for homology searching

Short-Distance Atomic Beam Deceleration with a Stimulated Light Force

Stimulated magneto-optical force in the dressed-atom picture

Sub-Doppler manifestation of the magneto-optical radiation force

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

Tejaas: reverse regression increases power for detecting trans-eQTLs

The HHpred interactive server for protein homology detection and structure prediction

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

The MPI Bioinformatics Toolkit for protein sequence analysis

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

The Mre11:Rad50 Structure Shows an ATP-Dependent Molecular Clamp in DNA Double-Strand Break Repair

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

The molecular cell death machinery in the simple cnidarian Hydra includes an expanded caspase family and pro- and anti-apoptotic Bcl-2 proteins

Three-body decay of a rubidium Bose–Einstein condensate

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

Uniform transitions of the general RNA polymerase II transcription complex

bbcontacts: prediction of β-strand pairing from direct coupling patterns.

kClust: fast and sensitive clustering of large protein sequence databases