Author

Alessio Milanese

SIB Swiss Institute of BioinformaticsORCID 0000-0002-7050-2239Unclaimed 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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Assay:metagenomics· 3 Approach:statistical model· 3 Approach:benchmark study· 2 Research Focus:benchmarking· 2 Research Focus:software / tool· 2 Organism:bacteria (other)· 1 Research Focus:database / resource· 1 Research Focus:deconvolution· 1

Frequent Co-Authors

Georg ZelleriD· 3 shared Daniel R. MendeiD· 2 shared Hans‐Joachim RuscheweyhiD· 2 shared Lucas PaoliiD· 2 shared Shinichi SunagawaiD· 2 shared Aaron E. DarlingiD· 1 shared Adrian FritziD· 1 shared Alexandru Cristian· 1 shared

Activity by Year

2021-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBioinformatics

Georg ZellerORCID

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Author profile →

3 papers

Recent·Most cited

Critical Assessment of Metagenome Interpretation - the second round of challenges

Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey A. Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline Brito, C. Titus Brown, Jan P. Buchmann, Aydın Buluç, , Till Strowig

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Nature Methods · Apr 1, 2022Peer-reviewedBioinformatics

Accurate de novo identification of biosynthetic gene clusters with GECCO

Laura M. Carroll, Martin F. Larralde, Jonas Simon Fleck, Ruby Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller

A linear conditional random field over ordered protein-domain annotations finds biosynthetic gene clusters de novo more precisely than DeepBGC and runs over three times faster on one CPU.

bioRxiv · May 3, 2021 · PreprintBioinformatics✦ In-depth digest

Reference genome-independent taxonomic profiling of microbiomes with mOTUs3

Hans‐Joachim Ruscheweyh, Alessio Milanese, Lucas Paoli, Nicolai Karcher, Quentin Clayssen, Marisa Isabell Metzger, Jakob Wirbel, Peer Bork B, Daniel R. Mende, Georg Zeller, Shinichi Sunagawa

The paper introduces mOTUs3, a tool for reference genome-independent taxonomic profiling of metagenomes, improving accuracy and coverage for underexplored microbiomes.

bioRxiv · Apr 20, 2021 · PreprintBioinformatics