Johannes Söding

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• PMGen: from peptide-MHC structure prediction to peptide generation

  Bioinformatics · 2026-06-01

• Metagenomic assemblies from real environmental samples for binning benchmarking

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-12

• Metagenomic assemblies from real environmental samples for binning benchmarking

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-12

• Additional file 1 of Phylograd: fast column-specific calculation of substitution model gradients

  Figshare · 2026-01-01

• Additional file 1 of Phylograd: fast column-specific calculation of substitution model gradients

  Open MIND · 2026-01-01

• Phylograd: fast column-specific calculation of substitution model gradients

  Figshare · 2026-01-01

• Phylograd: fast column-specific calculation of substitution model gradients

  Figshare · 2026-01-01

• Phylograd: fast column-specific calculation of substitution model gradients

  BMC Bioinformatics · 2025-12-23 · 1 citations

• PMGen: From Peptide-MHC Structure Prediction to Peptide GenerationPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-14

• Evaluation of metagenome binning: advances and challenges

  Briefings in Bioinformatics · 2025-11-01 · 2 citations

• CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets

  Genome biology · 2025-10-27 · 1 citations

• Enhancing genome recovery across metagenomic samples using MAGmax

  Bioinformatics · 2025-09-26 · 1 citations

• De novo discovery of conserved gene clusters in microbial genomes with Spacedust

  Nature Methods · 2025-09-15 · 4 citations

• Enhancing genome recovery across metagenomic samples using MAGmaxPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-01

• SoftAlign: End-to-end protein structures alignmentPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-14 · 1 citations

• Evaluation of Metagenome Binning: Advances and ChallengesPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-21 · 2 citations

• Rapid and sensitive protein complex alignment with Foldseek-Multimer

  Nature Methods · 2025-02-05 · 59 citations

• Stochastic Variational Inference for Structured Additive Distributional RegressionPreprint

  arXiv (Cornell University) · 2024-12-13

• Aggregating gut: on the link between neurodegeneration and bacterial functional amyloidsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-28 · 2 citations

• UniOP: a universal operon prediction for high-throughput prokaryotic (meta-)genomic data using intergenic distancePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-11 · 1 citations