Johannes Söding

 

 

Johannes Söding

MaxPlanck Institute for Biophysical Chemistry

Quantitative and Computational Biology

Germany

(ORCID)

New tools for protein structure and sequence searching and metagenome assembly

I will give an update on Foldseek, which can perform structural similarity searches and alignment through the Uniprot50 and MGnify/ESM30 database of 95M structures in a few seconds on a single core, at a sensitivity similar to TMalign (search.foldseek.com). I also present SpaceDust, a tool for fast sequence- and structure-based searches of clusters of “positional orthologs” between genomes. Finally, I will introduce PenguiN, our  new tool for strain-resolved metatranscriptomic and -genomic assemby, which assembles multiple times more strain variation than the state of the art.

Short bio

Johannes Söding obtained his PhD in 1996 in laser cooling of neutral atoms at the MaxPlanck Institute for Nuclear Physics and did postdoctoral experimental work on Bose-Einstein condensation of neutral atoms at the École Normale Supérieure in Paris. After three years as consultant at the Boston Consulting Group, he returned to science in 2002. He started his career in bioinformatics with Andrei Lupas at the Max Planck Institute for Developmental Biology in Tübingen, working on protein evolution, remote homology detection and structure prediction. In 2007 he became an independent research group leader at the Gene Center of the University of Munich (LMU). Since 2014 he leads the research group Quantitative and Computational Biology at the MaxPlanck Institute for Biophysical Chemistry. His group develops statistical and computational methods for analyzing data from high-throughput biological experiments, in particular for protein function and structure prediction, sequence search and assembly in metagenomics, transcription regulation, gene regulatory networks, and systems medicine. He is married and has three children (2002, 2004, 2008). 

Group website