Author

René Kallies

Helmholtz Centre for Environmental ResearchORCID 0000-0002-9195-0276Unclaimed 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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Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Assay:metagenomics· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Research Focus:genome assembly· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Ulisses Nunes da RochaiD· 3 shared J. SaraivaiD· 2 shared Jonas Coelho KasmanasiD· 2 shared Marcos Fleming Bicalho· 2 shared Peter Florian StadleriD· 2 shared Alexander BartholomäusiD· 1 shared Alexander J. ProbstiD· 1 shared Antonis ChatzinotasiD· 1 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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3 shared papersBioinformatics

Ulisses Nunes da RochaORCID

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3 papers

Recent·Most cited

PhaGAMeToo: A semi-automated workflow for merging structural and functional annotation of phage genomes and generation of a GenBank file

Ebrar Demircioğlu, Martin Bole, Ulisses Nunes da Rocha, René Kallies

PhaGAMeToo merges functional annotations from phage genomes and generates submission-ready GenBank files using Pharokka, VIBRANT, and BLASTP.

bioRxiv · Aug 18, 2026 · PreprintBioinformatics

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Ulisses Nunes da Rocha, Jonas Coelho Kasmanas, René Kallies, J. Saraiva, Rodolfo Brizola Toscan, Polonca Štefanič, Marcos Fleming Bicalho, Felipe Borim Corrêa, Merve Nida Baştürk, Efthymios Fousekis, Luiz Miguel Viana Barbosa, Julia Plewka, Alexander J. Probst, Petr Baldrián, Peter Florian Stadler

MuDoGeR simplifies genome recovery from metagenomes for non-experts, demonstrating effectiveness across various sample sizes.

bioRxiv · Jun 21, 2022 · PreprintBioinformatics

OrtSuite - from genomes to prediction of microbial interactions within targeted ecosystem processes

J. Saraiva, Alexander Bartholomäus, René Kallies, Marta Gomes, Marcos Fleming Bicalho, Jonas Coelho Kasmanas, Carsten Vogt, Antonis Chatzinotas, Peter Florian Stadler, Óscar Dias, Ulisses Nunes da Rocha

OrtSuite predicts microbial interactions based on genomic content for specific ecosystem processes using ortholog clustering and user-defined functions.

Life Science Alliance · Sep 27, 2021Peer-reviewedBioinformatics