Author

Ruoshi Zhang

Max Planck Institute for Multidisciplinary SciencesORCID 0000-0002-1982-4793Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 3 Assay:metagenomics· 3 Approach:statistical model· 3 Research Focus:gene regulatory network inference· 2 Research Focus:database / resource· 1 Organism:virus· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Johannes SödingiD· 3 shared Milot MirditaiD· 2 shared Clovis GalieziD· 1 shared Clovis Norroy· 1 shared Eli Levy KariniD· 1 shared Hong Su· 1 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 11 mutual co-author links

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3 shared papersBioinformatics

Johannes SödingORCID

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3 papers

Recent·Most cited

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

Ruoshi Zhang, Milot Mirdita, Johannes Söding

Spacedust identifies conserved gene clusters in microbial genomes using structure comparison and statistical methods, recovering most known antiviral defense systems.

Nature Methods · Sep 15, 2025Peer-reviewedBioinformatics

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

Hong Su, Ruoshi Zhang, Johannes Söding

UniOP predicts operons in prokaryotic genomic and metagenomic data using intergenic distances, outperforming existing methods across multiple genomes and metagenomes.

bioRxiv · Nov 11, 2024 · PreprintBioinformatics

SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts

Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, Johannes Söding

SpacePHARER identifies phage-host relationships by matching CRISPR spacers to phage genomes in genomic or metagenomic data, improving sensitivity through protein-level comparisons and multiple match evidence.

Bioinformatics · Mar 31, 2021Peer-reviewedBioinformatics