Söding, Johannes

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

Steinegger, M., & Söding, J. (2017) · Nature Biotechnology

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

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Fast and accurate protein structure search with Foldseek

van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2022) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Structure and Function

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Fast and accurate protein structure search with Foldseek

van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2024) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Structure and Function

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

Zimmermann, L., Stephens, A., Nam, S.-Z., Rau, D., Kübler, J., Lozajic, M., Gabler, F., Söding, J., Lupas, A. N., & Alva, V. (2018) · Journal of Molecular Biology

Genomics and Phylogenetic StudiesProtein Structure and Dynamics

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

Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2012) · Nature Methods

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

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

Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., & Söding, J. (2019) · BMC Bioinformatics

Genomics and Phylogenetic StudiesProtein Structure and Dynamics

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Clustering huge protein sequence sets in linear time

Steinegger, M., & Söding, J. (2018) · Nature Communications

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

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Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

Gabler, F., Nam, S., Till, S., Mirdita, M., Steinegger, M., Söding, J., Lupas, A. N., & Alva, V. (2020) · Current Protocols in Bioinformatics

Genomics and Phylogenetic StudiesProtein Structure and Dynamics

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

Mirdita, M., Steinegger, M., & Söding, J. (2019) · Bioinformatics

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

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

Steinegger, M., Mirdita, M., & Söding, J. (2019) · Nature Methods

Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

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

Levy Karin, E., Mirdita, M., & Söding, J. (2020) · Microbiome

Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

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

Söding, J., & Lupas, A. N. (2003) · BioEssays

Protein Structure and DynamicsOrigins and Evolution of Life

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

Saponaro, M., Kantidakis, T., Mitter, R., Kelly, G. P., Heron, M., Williams, H., Söding, J., Stewart, A., & Svejstrup, J. Q. (2014) · Cell

DNA Repair MechanismsGenomics and Chromatin Dynamics

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

Close, P., East, P., Dirac-Svejstrup, A. B., Hartmann, H., Heron, M., Maslen, S., Chariot, A., Söding, J., Skehel, M., & Svejstrup, J. Q. (2012) · Nature

RNA Research and SplicingGenomics and Chromatin Dynamics

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

Choi, J., Lysakovskaia, K., Stik, G., Demel, C., Söding, J., Tian, T. V., Graf, T., & Cramer, P. (2021) · eLife

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

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