Johannes Söding

50.5k total citations · 13 hit papers
107 papers, 32.2k citations indexed

About

Johannes Söding is a scholar working on Molecular Biology, Ecology and Atomic and Molecular Physics, and Optics. According to data from OpenAlex, Johannes Söding has authored 107 papers receiving a total of 32.2k indexed citations (citations by other indexed papers that have themselves been cited), including 88 papers in Molecular Biology, 15 papers in Ecology and 12 papers in Atomic and Molecular Physics, and Optics. Recurrent topics in Johannes Söding's work include Genomics and Phylogenetic Studies (45 papers), RNA and protein synthesis mechanisms (43 papers) and Protein Structure and Dynamics (27 papers). Johannes Söding is often cited by papers focused on Genomics and Phylogenetic Studies (45 papers), RNA and protein synthesis mechanisms (43 papers) and Protein Structure and Dynamics (27 papers). Johannes Söding collaborates with scholars based in Germany, United States and South Korea. Johannes Söding's co-authors include Martin Steinegger, A. Biegert, Andrei N. Lupas, Michael Remmert, Toby J. Gibson, Desmond G. Higgins, Kevin Karplus, Julie Thompson, Andreas Wilm and Hamish McWilliam and has published in prestigious journals such as Nature, Cell and Proceedings of the National Academy of Sciences.

In The Last Decade

Johannes Söding

104 papers receiving 31.9k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

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

2011 11.2k citations Michael Remmert, Johannes Söding et al. profile →
The HHpred interactive server for protein homology detection and structure prediction

2005 2.8k citations Johannes Söding, A. Biegert et al. Nucleic Acids Research profile →
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

2017 2.2k citations Martin Steinegger, Johannes Söding Nature Biotechnology profile →
Protein homology detection by HMM–HMM comparison

2004 1.9k citations Johannes Söding Bioinformatics profile →
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

2011 1.6k citations Michael Remmert, A. Biegert et al. profile →
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

2017 1.6k citations Johannes Söding, Andrei N. Lupas et al. profile →
Fast and accurate protein structure search with Foldseek

2023 956 citations Michel van Kempen, Stephanie Kim et al. Nature Biotechnology profile →
HH-suite3 for fast remote homology detection and deep protein annotation

2019 667 citations Martin Steinegger, Markus Meier et al. profile →
Clustering huge protein sequence sets in linear time

2018 489 citations Martin Steinegger, Johannes Söding Nature Communications profile →
Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

2020 466 citations Milot Mirdita, Martin Steinegger et al. profile →
Uniclust databases of clustered and deeply annotated protein sequences and alignments

2016 446 citations Milot Mirdita, Clovis Galiez et al. Nucleic Acids Research profile →
MMseqs2 desktop and local web server app for fast, interactive sequence searches

2019 341 citations Milot Mirdita, Martin Steinegger et al. Bioinformatics profile →
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

2019 264 citations Martin Steinegger, Milot Mirdita et al. profile →

Peers

Countries citing papers authored by Johannes Söding

Since Specialization

Citations

This map shows the geographic impact of Johannes Söding's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Johannes Söding with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Johannes Söding more than expected).

Fields of papers citing papers by Johannes Söding

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Johannes Söding. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Johannes Söding. The network helps show where Johannes Söding may publish in the future.

Co-authorship network of co-authors of Johannes Söding

This figure shows the co-authorship network connecting the top 25 collaborators of Johannes Söding. A scholar is included among the top collaborators of Johannes Söding based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Johannes Söding. Johannes Söding is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	Evaluation of metagenome binning: advances and challenges 2025 ·Briefings in Bioinformatics ·(unknown), (unknown), (unknown), (unknown), Johannes Söding	0
2	CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets 2025 ·Genome biology ·(unknown), Johannes Söding, (unknown), (unknown), Peter Wad Sackett, Antonio Fernàndez-Guerra, Gabriel Renaud	0
3	Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs 2024 ·Microbiome ·(unknown), (unknown), (unknown), (unknown), (unknown), Johannes Söding	1
4	DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options 2023 ·Nucleic Acids Research ·Sushmita Basu, Bi Zhao, (unknown), Eshel Faraggi, Jörg Gsponer, Gang Hu, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Johannes Söding, Martin Steinegger, Duolin Wang, (unknown), Dong Xu, Jian Zhang, Lukasz Kurgan	7
5	Fast and accurate protein structure search with Foldseek breakdown → 2023 ·Nature Biotechnology ·Michel van Kempen, Stephanie Kim, Charlotte Tumescheit, Milot Mirdita, Jeong-Jae Lee, Cameron L. M. Gilchrist, Johannes Söding, Martin Steinegger	956
6	Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains 2022 ·NAR Genomics and Bioinformatics ·(unknown), Salma Sohrabi-Jahromi, Johannes Söding	9
7	Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins 2021 ·Bioinformatics ·Salma Sohrabi-Jahromi, Johannes Söding	5
8	Bayesian Markov models improve the prediction of binding motifs beyond first order 2021 ·NAR Genomics and Bioinformatics ·(unknown), Markus Meier, (unknown), Johannes Söding	5
9	SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts 2021 ·Bioinformatics ·(unknown), Milot Mirdita, Eli Levy Karin, (unknown), Clovis Galiez, Johannes Söding	56
10	Fast and sensitive taxonomic assignment to metagenomic contigs 2021 ·Bioinformatics ·Milot Mirdita, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, Eli Levy Karin	150
11	MMseqs2 desktop and local web server app for fast, interactive sequence searches breakdown → 2019 ·Bioinformatics ·Milot Mirdita, Martin Steinegger, Johannes Söding	341
12	PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes 2019 ·Bioinformatics ·Νικόλαος Παπαδόπουλος, (unknown), Johannes Söding	32
13	Clustering huge protein sequence sets in linear time breakdown → 2018 ·Nature Communications ·Martin Steinegger, Johannes Söding	489
14	MMseqs software suite for fast and deep clustering and searching of large protein sequence sets 2016 ·Bioinformatics ·(unknown), Martin Steinegger, Johannes Söding	136
15	bbcontacts: prediction of β -strand pairing from direct coupling patterns 2015 ·Bioinformatics ·Jessica Andréani, Johannes Söding	27
16	Discriminative modelling of context-specific amino acid substitution probabilities 2012 ·Bioinformatics ·(unknown), A. Biegert, Johannes Söding	39
17	Sequence context-specific profiles for homology searching 2009 ·Proceedings of the National Academy of Sciences ·A. Biegert, Johannes Söding	135
18	A galaxy of folds 2009 ·Protein Science ·Vikram Alva, Michael Remmert, A. Biegert, Andrei N. Lupas, Johannes Söding	66
19	The MPI Bioinformatics Toolkit for protein sequence analysis 2006 ·Nucleic Acids Research ·A. Biegert, Claudine Mayer, Michael Remmert, Johannes Söding, Andrei N. Lupas	241
20	Protein homology detection by HMM–HMM comparison breakdown → 2004 ·Bioinformatics ·Johannes Söding	1883

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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