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Clustering huge protein sequence sets in linear time

Nature communications, 2018-06, Vol.9 (1), p.2542-8, Article 2542

2018

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

Nature methods, 2019-07, Vol.16 (7), p.603-606

2019

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

PLoS computational biology, 2015-10, Vol.11 (10), p.e1004343-e1004343

2015

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

Nucleic acids research, 2016-07, Vol.44 (W1), p.W410-W415

2016

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

BMC bioinformatics, 2019-09, Vol.20 (1), p.473-473, Article 473

2019

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Uniclust databases of clustered and deeply annotated protein sequences and alignments

Nucleic acids research, 2017-01, Vol.45 (D1), p.D170-D176

2017

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

Nucleic acids research, 2016-07, Vol.44 (13), p.6055-6069

2016

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Mechanisms for Active Regulation of Biomolecular Condensates

Trends in cell biology, 2020-01, Vol.30 (1), p.4-14

2020

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Uniform transitions of the general RNA polymerase II transcription complex

Nature structural & molecular biology, 2010-10, Vol.17 (10), p.1272-1278

2010

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Big-data approaches to protein structure prediction

Science (American Association for the Advancement of Science), 2017-01, Vol.355 (6322), p.248-249

Soding, Johannes

2017

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A vocabulary of ancient peptides at the origin of folded proteins

eLife, 2015-12, Vol.4, p.e09410-e09410

2015

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

Microbiome, 2020-04, Vol.8 (1), p.48-48, Article 48

2020

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

eLife, 2021-03, Vol.10

2021

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Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

Current Protocols in Bioinformatics, 2020-12, Vol.72 (1), p.e108-n/a

2020

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

Nucleic acids research, 2021-01, Vol.49 (D1), p.D298-D308

2021

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

Molecular systems biology, 2011-10, Vol.7 (1), p.539-n/a

2011

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

PLoS computational biology, 2018-11, Vol.14 (11), p.e1006526-e1006526

2018

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

Molecular cell, 2016-01, Vol.61 (2), p.247-259

2016

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

Molecular cell, 2017-04, Vol.66 (1), p.38-49.e6

2017

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The HHpred interactive server for protein homology detection and structure prediction

Nucleic acids research, 2005-07, Vol.33 (Web Server issue), p.W244-W248

2005

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kClust: fast and sensitive clustering of large protein sequence databases

BMC bioinformatics, 2013-08, Vol.14 (1), p.248-248, Article 248

2013

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Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

Molecular cell, 2014-09, Vol.55 (5), p.745-757

2014

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

Current opinion in structural biology, 2011-06, Vol.21 (3), p.404-411

2011

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Bayesian multiple logistic regression for case-control GWAS

PLoS genetics, 2018-12, Vol.14 (12), p.e1007856-e1007856

2018

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

PLoS pathogens, 2014-04, Vol.10 (4), p.e1004081-e1004081

2014

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Clustering huge protein sequence sets in linear time

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

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

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

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

Uniclust databases of clustered and deeply annotated protein sequences and alignments

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

Mechanisms for Active Regulation of Biomolecular Condensates

Uniform transitions of the general RNA polymerase II transcription complex

Big-data approaches to protein structure prediction

A vocabulary of ancient peptides at the origin of folded proteins

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

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

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

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

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

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

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

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

The HHpred interactive server for protein homology detection and structure prediction

kClust: fast and sensitive clustering of large protein sequence databases

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

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

Bayesian multiple logistic regression for case-control GWAS

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

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