Johannes Söding

35 papers Journal 34Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Phylograd: fast column-specific calculation of substitution model gradients.
BMC Bioinform.
Benjamin Lieser, Georgy Belousov, Johannes Söding
2025 J jnl
Enhancing genome recovery across metagenomic samples using MAGmax.
Bioinform.
Arangasamy Yazhini, Johannes Söding
2025 J jnl
Evaluation of metagenome binning: advances and challenges.
Briefings Bioinform.
Arangasamy Yazhini, Étienne Morice, Annika Jochheim, Benjamin Lieser, Johannes Söding
2021 J jnl
DescribePROT: database of amino acid-level protein structure and function predictions.
Nucleic Acids Res.
Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan
2021 J jnl
Fast and sensitive taxonomic assignment to metagenomic contigs.
Bioinform.
Milot Mirdita, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, Eli Levy Karin
2021 J jnl
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts.
Bioinform.
Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, Johannes Söding
2021 J jnl
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins.
Bioinform.
Salma Sohrabi-Jahromi, Johannes Söding
2019 J jnl
HH-suite3 for fast remote homology detection and deep protein annotation.
BMC Bioinform.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
2019 J jnl
MMseqs2 desktop and local web server app for fast, interactive sequence searches.
Bioinform.
Milot Mirdita, Martin Steinegger, Johannes Söding
2019 J jnl
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.
Bioinform.
Nikolaos Papadopoulos, R. Gonzalo Parra, Johannes Söding
2018 J jnl
Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.
PLoS Comput. Biol.
Susann Vorberg, Stefan Seemayer, Johannes Söding
2018 J jnl
The BaMM web server for de-novo motif discovery and regulatory sequence analysis.
Nucleic Acids Res.
Anja Kiesel, Christian Roth, Wanwan Ge, Maximilian Weß, Markus Meier, Johannes Söding
2017 J jnl
Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Nucleic Acids Res.
Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria Jesus Martin, Johannes Söding, Martin Steinegger
2017 J jnl
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs.
Bioinform.
Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding
2016 J jnl
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets.
Bioinform.
Maria Hauser, Martin Steinegger, Johannes Söding
2016 J jnl
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.
Nucleic Acids Res.
Vikram Alva, Seung-Zin Nam, Johannes Söding, Andrei N. Lupas
2015 J jnl
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.
PLoS Comput. Biol.
Armin Meier, Johannes Söding
2015 J jnl
Context similarity scoring improves protein sequence alignments in the midnight zone.
Bioinform.
Armin Meier, Johannes Söding
2015 J jnl
bbcontacts: prediction of
Bioinform.
Jessica Andreani, Johannes Söding
2014 J jnl
CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations.
Bioinform.
Stefan Seemayer, Markus Gruber, Johannes Söding
2014 J jnl
Universality of core promoter elements?
Nat.
Matthias Siebert, Johannes Söding
2013 J jnl
kClust: fast and sensitive clustering of large protein sequence databases.
BMC Bioinform.
Maria Hauser, Christian E. Mayer, Johannes Söding
2012 J jnl
Discriminative modelling of context-specific amino acid substitution probabilities.
Bioinform.
Christof Angermüller, Andreas Biegert, Johannes Söding
2012 J jnl
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.
Nucleic Acids Res.
Sebastian Luehr, Holger Hartmann, Johannes Söding
2009 J jnl
HHomp - prediction and classification of outer membrane proteins.
Nucleic Acids Res.
Michael Remmert, Dirk Linke, Andrei N. Lupas, Johannes Söding
2009 J jnl
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors.
Bioinform.
Alex Bateman, Robert D. Finn, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding
2008 J jnl
Prediction of protein functional residues from sequence by probability density estimation.
Bioinform.
J. D. Fischer, Christian E. Mayer, Johannes Söding
2007 J jnl
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.
BMC Bioinform.
Manjunatha R. Karpenahalli, Andrei N. Lupas, Johannes Söding
2006 J jnl
HHrep:
Nucleic Acids Res.
Johannes Söding, Michael Remmert, Andreas Biegert
2006 J jnl
HHsenser: exhaustive transitive profile search using HMM-HMM comparison.
Nucleic Acids Res.
Johannes Söding, Michael Remmert, Andreas Biegert, Andrei N. Lupas
2006 J jnl
The MPI Bioinformatics Toolkit for protein sequence analysis.
Nucleic Acids Res.
Andreas Biegert, Christian E. Mayer, Michael Remmert, Johannes Söding, Andrei N. Lupas
2005 J jnl
Protein homology detection by HMM?CHMM comparison.
Bioinform.
Johannes Söding
2005 J jnl
REPPER - repeats and their periodicities in fibrous proteins.
Nucleic Acids Res.
Markus Gruber, Johannes Söding, Andrei N. Lupas
2005 J jnl
The HHpred interactive server for protein homology detection and structure prediction.
Nucleic Acids Res.
Johannes Söding, Andreas Biegert, Andrei N. Lupas
2003 — conf
0n the Evolution of Proteins from Peptides(Invited Talk).
German Conference on Bioinformatics
Johannes Söding, Andrei N. Lupas