J. Söding

发表

Sequence context-specific profiles for homology searching

A. Biegert, J. Söding, 2009, Proceedings of the National Academy of Sciences.

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

A. Biegert, J. Söding, M. Remmert, 2011, Nature Methods.

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

D. Higgins, T. Gibson, K. Karplus, 2011, Molecular systems biology.

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

J. Söding, Martin Steinegger, M. Mirdita, 2018, bioRxiv.

Prediction of protein functional residues from sequence by probability density estimation

Johannes Söding, Christian E. Mayer, J. D. Fischer, 2008, Bioinform..

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

J. Söding, Holger Hartmann, E. Guthöhrlein, 2013, Genome research.

HHsenser: exhaustive transitive profile search using HMM–HMM comparison

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2006, Nucleic Acids Res..

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

Daniel N. Wilson, M. Habeck, J. Söding, 2010, Proceedings of the National Academy of Sciences.

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

Johannes Söding, Michael Habeck, Eric Westhof, 2010, Proceedings of the National Academy of Sciences.

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

J. Söding, A. Lupas, 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

A vocabulary of ancient peptides at the origin of folded proteins

J. Söding, A. Lupas, V. Alva, 2015, eLife.

Big-data approaches to protein structure prediction

Johannes Söding, J. Söding, 2017, Science.

Evolution of Outer Membrane -Barrels from an Ancestral Hairpin

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2010 .

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

Johannes Söding, Milot Mirdita, Martin Steinegger, 2018, Nature Methods.

Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition.

Johannes Söding, Patrick Cramer, Phillipp Torkler, 2014, Molecular cell.

On the origin of the histone fold

Johannes Söding, Andrei N Lupas, Vikram Alva, 2007, BMC Structural Biology.

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

Johannes Söding, Michael Remmert, J. Söding, 2011, Current opinion in structural biology.

Evolution of Outer Membrane b-Barrels from an Ancestral bb Hairpin

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2010 .

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

J. Söding, A. Biegert, J. Söding, 2010, Molecular biology and evolution.

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

Johannes Söding, J. Söding, M. Siebert, 2016, bioRxiv.

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

J. Söding, M. Lucas, Christof Angermueller, 2011, Cell.

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

J. Söding, S. Roche, D. Niessing, 2010, PloS one.

Reverse regression increases power for detecting trans-eQTLs

Franco L. Simonetti, J. Söding, Saikat Banerjee, 2020, bioRxiv.

Evolution of the β‐propeller fold

Johannes Söding, Andrei N. Lupas, J. Söding, 2008, Proteins.

Three-body decay of a rubidium Bose–Einstein condensate

J. Söding, D. Guéry-Odelin, J. Dalibard, 1998, cond-mat/9811339.

MMseqs 2 : sensitive protein sequence searching for analysis of massive data sets

J. Söding, Martin Steinegger, 2017 .

Cln5 represents a new type of cysteine-based S-depalmitoylase linked to neurodegeneration

J. Söding, G. Sheldrick, K. Hofmann, 2022, Science advances.

Sequence analysis MMseqs 2 desktop and local web server app for fast , interactive sequence searches

J. Söding, Martin Steinegger, M. Mirdita, 2019 .

Title Fast , scalable generation of high-quality protein multiplesequence alignments using Clustal Omega

D. Higgins, T. Gibson, K. Karplus, 2017 .

CCMpred — Supplementary Information

J. Söding, Stefan Seemayer, M. Gruber, 2014 .

The immune activation model for targeted inhibitors of mutated oncogenic kinases

J. Söding, Max-Planck, 2021 .

IS BOSE-EINSTEIN CONDENSATION OF ATOMIC CESIUM POSSIBLE?

J. Söding, D. Guéry-Odelin, J. Dalibard, 1998 .

Sub-Doppler manifestation of the magneto-optical radiation force.

J. Söding, A. Sidorov, R. Grimm, 1993 .

Observation of the Magneto-Optical Radiation Force by Laser Spectroscopy

J. Söding, A. Sidorov, R. Grimm, 1992 .

Recruitment of TREX to the Transcription Machinery by Its Direct Binding to the Phospho-CTD of RNA Polymerase II

E. O'Duibhir, F. Holstege, J. Söding, 2013, PLoS genetics.

Genome-associated RNA Polymerase II Includes the Dissociable Rpb4/7 Subcomplex*

Johannes Söding, Holger Hartmann, Patrick Cramer, 2008, Journal of Biological Chemistry.

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

Johannes Söding, Felix Gabler, Seung-Zin Nam, 2020, Current protocols in bioinformatics.

The HHpred interactive server for protein homology detection and structure prediction

Johannes Söding, Andrei N. Lupas, Andreas Biegert, 2005, Nucleic Acids Res..

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

Johannes Söding, Andrei N. Lupas, Seung-Zin Nam, 2016, Nucleic Acids Res..

Protein homology detection by HMM?CHMM comparison

Johannes Söding, J. Söding, 2005, Bioinform..

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

Johannes Söding, Martin Steinegger, J. Söding, 2017, bioRxiv.

kClust: fast and sensitive clustering of large protein sequence databases

Johannes Söding, Christian E. Mayer, Maria Hauser, 2013, BMC Bioinformatics.

In Vivo Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells

Katharina M. Hembach, K. Conzelmann, J. Söding, 2014, PLoS pathogens.

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.

Lukas Zimmermann, Johannes Söding, Felix Gabler, 2017, Journal of molecular biology.

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

J. Söding, P. Cramer, T. Graf, 2021, eLife.

Tejaas: reverse regression increases power for detecting trans-eQTLs

Franco L. Simonetti, J. Söding, Saikat Banerjee, 2021, Genome Biology.

Bayesian multiple logistic regression for case-control GWAS

Johannes Söding, Heribert Schunkert, Saikat Banerjee, 2018, PLoS genetics.

Bayesian Markov models improve the prediction of binding motifs beyond first order

Wanwan Ge, Markus Meier, Christian Roth, 2020, bioRxiv.

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

Johannes Söding, Armin Meier, J. Söding, 2015, PLoS Comput. Biol..

Different Binding Properties and Function of CXXC Zinc Finger Domains in Dnmt1 and Tet1

Johannes Söding, Heinrich Leonhardt, Weihua Qin, 2011, PloS one.

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

Johannes Söding, Andrei N. Lupas, Manjunatha R. Karpenahalli, 2007, BMC Bioinformatics.

Mechanisms for Active Regulation of Biomolecular Condensates.

J. Söding, David Zwicker, Salma Sohrabi-Jahromi, 2019, Trends in cell biology.

Discriminative modelling of context-specific amino acid substitution probabilities

Johannes Söding, Andreas Biegert, Christof Angermüller, 2012, Bioinform..

A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning.

William Stafford Noble, Jacob M. Schreiber, J. Söding, 2020, Molecular cell.

Uniform transitions of the general RNA polymerase II transcription complex

Johannes Söding, Patrick Cramer, Michael Lidschreiber, 2010, Nature Structural &Molecular Biology.

The BaMM web server for de-novo motif discovery and regulatory sequence analysis

Wanwan Ge, Johannes Söding, Christian Roth, 2018, Nucleic Acids Res..

DescribePROT: database of amino acid-level protein structure and function predictions

A Keith Dunker, Zoran Obradovic, Lukasz Kurgan, 2020, Nucleic Acids Res..

Lysine/RNA-interactions drive and regulate biomolecular condensation

J. Söding, E. Mandelkow, N. Rezaei-Ghaleh, 2019, Nature Communications.

Going to extremes - a metagenomic journey into the dark matter of life.

Sigmar K. Stefánsson, J. Söding, E. Karlsson, 2021, FEMS microbiology letters.

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

J. Söding, Mark Heron, A. Stewart, 2014, Cell.

Fast and sensitive taxonomic assignment to metagenomic contigs

M. Mirdita, M. Steinegger, F. Breitwieser, 2020, bioRxiv.

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

J. Söding, Martin Steinegger, M. Mirdita, 2018, bioRxiv.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

Johannes Söding, Milot Mirdita, J. Söding, 2020, Microbiome.

MMseqs2 desktop and local web server app for fast, interactive sequence searches

M Mirdita, M Steinegger, J Söding, 2018, bioRxiv.

Clustering huge protein sequence sets in linear time

Johannes Söding, Martin Steinegger, J. Söding, 2017, Nature Communications.

Uniclust databases of clustered and deeply annotated protein sequences and alignments

Maria Jesus Martin, Johannes Söding, Clovis Galiez, 2016, Nucleic Acids Res..

The MPI Bioinformatics Toolkit for protein sequence analysis

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2006, Nucleic Acids Res..

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

J. Söding, Holger Hartmann, T. Straub, 2011, Nucleic acids research.

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

J. Söding, D. Schwarzer, R. Sprangers, 2016, Molecular cell.

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

Jonathan Vincent, Johannes Söding, Clovis Galiez, 2017, Bioinform..

RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton

Eli Levy Karin, G. Eichele, J. Söding, 2023, NAR genomics and bioinformatics.

Fast and accurate automatic structure prediction with HHpred

Johannes Söding, Michael Remmert, Andrea Hildebrand, 2009, Proteins.

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

J. Söding, M. Mirdita, E. Levy Karin, 2020, bioRxiv.

Clustering huge protein sequence sets in linear time

J. Söding, Martin Steinegger, 2018, bioRxiv.

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

Markus Gruber, Johannes Söding, Stefan Seemayer, 2014, Bioinform..

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

Johannes Söding, Martin Steinegger, Maria Hauser, 2016, Bioinform..

Lysine/RNA-interactions drive and regulate biomolecular condensation

J. Söding, E. Mandelkow, N. Rezaei-Ghaleh, 2019, Nature Communications.

De novo identification of highly diverged protein repeats by probabilistic consistency

Johannes Söding, Andreas Biegert, A. Biegert, 2008, Bioinform..

HHomp—prediction and classification of outer membrane proteins

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2009, Nucleic Acids Res..

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

Johannes Söding, Michael Remmert, Andreas Biegert, 2006, Nucleic Acids Res..

REPPER—repeats and their periodicities in fibrous proteins

Markus Gruber, Johannes Söding, Andrei N. Lupas, 2005, Nucleic Acids Res..

In Vivo Ligands of MDA 5 and RIGI in Measles Virus-Infected Cells

Katharina M. Hembach, K. Conzelmann, J. Söding, 2014 .

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes.

J. Söding, P. Cramer, J. Andreani, 2017, Molecular cell.

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes Graphical

J. Söding, P. Cramer, J. Andreani, 2017 .

DBIRD integrates alternative mRNA splicing with RNA polymerase II transcript elongation

J. Söding, Mark Heron, Holger Hartmann, 2012, Nature.

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

C. Nüsslein-Volhard, J. Söding, H. Schwarz, 2005, Developmental dynamics : an official publication of the American Association of Anatomists.

A high-throughput screen for transcription activation domains reveals their sequence characteristics and permits reliable prediction by deep learning

William Stafford Noble, J. Söding, S. Hahn, 2019, bioRxiv.

A Conserved GA Element in TATA-Less RNA Polymerase II Promoters

J. Söding, P. Cramer, Holger Hartmann, 2011, PloS one.

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

J. Söding, Salma Sohrabi-Jahromi, 2021, bioRxiv.

Do inhibitors targeted against mutant oncogenic kinases act via kinase degradation-induced immune activation?

J. Söding, Max-Planck, 2021 .

A galaxy of folds

Johannes Söding, Michael Remmert, Andreas Biegert, 2009, Protein science : a publication of the Protein Society.

Giant spin relaxation of an ultracold cesium gas.

J. Söding, D. Guéry-Odelin, J. Dalibard, 1998 .

Gravitational laser trap for atoms with evanescent-wave cooling.

J. Söding, R. Grimm, Y. Ovchinnikov, 1995 .

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

J. Söding, R. Grimm, Y. Ovchinnikov, 1994, Optics letters.

Bbcontacts: Prediction of Β-strand Pairing from Direct Coupling Patterns

Johannes Söding, Jessica Andreani, J. Söding, 2015, Bioinform..

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

J. Söding, D. Linke, E. Takano, 2007, Microbiology.

Proposed mechanism for thrombotic thrombocytopenia induced by adenovirus-based COVID-19 vaccines

J. Söding, 2021 .

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

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

Comparative analysis of coiled-coil prediction methods.

Johannes Söding, Andrei N Lupas, Markus Gruber, 2006, Journal of structural biology.

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

J. Söding, A. Böttger, B. Pauly, 2010, Cell Research.

Fast and accurate protein structure search with Foldseek

J. Söding, Martin Steinegger, M. Mirdita, 2023, bioRxiv.

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

J. Söding, D. Linke, K. Zeth, 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

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

Robert D. Finn, Alex Bateman, Johannes Söding, 2008, Bioinform..

Short-distance atomic beam deceleration with a stimulated light force.

J. Söding, P. Bouyer, C. Salomon, 1997 .

Transcriptome- and genome-targeted cancer immunotherapy

J. Söding, Max-Planck, 2021 .

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

J. Söding, A. Böttger, Sandra Münder, 2013, The International journal of developmental biology.

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes

Johannes Söding, Nikolaos Papadopoulos, R Gonzalo Parra, 2018, bioRxiv.

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

Johannes Söding, Sergej Djuranovic, Vincent Truffault, 2005, Structure.

Universality of core promoter elements?

Johannes Söding, Matthias Siebert, J. Söding, 2014, Nature.

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes

J. Söding, R. G. Parra, Nikolaos Papadopoulos, 2018, bioRxiv.

Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains

J. Söding, Salma Sohrabi-Jahromi, Simon H. Stitzinger, 2021, bioRxiv.

Fast and accurate protein structure search with Foldseek

J. Söding, Martin Steinegger, M. Mirdita, 2022, bioRxiv.

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

Johannes Söding, Holger Hartmann, Sebastian Luehr, 2012, Nucleic Acids Res..

DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

J. Söding, Martin Steinegger, M. Mirdita, 2023, Nucleic acids research.

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

J. Söding, A. Lupas, 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs

J. Söding, Martin Steinegger, F. A. Jochheim, 2024, bioRxiv.

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

Johannes Söding, Stefan Seemayer, Susann Vorberg, 2018, bioRxiv.

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

J. Söding, Matthias Siebert, 2016 .