Author

Jakob Russel

University of CopenhagenORCID 0000-0002-0565-3161Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:metagenomics· 3 Research Focus:benchmarking· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Organism:human· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Søren Johannes SørenseniD· 3 shared Asker BrejnrodiD· 2 shared Jonathan ThorseniD· 2 shared Shiraz Ali ShahiD· 2 shared Aron Charles EklundiD· 1 shared Charisse PeterseniD· 1 shared David Mayo-MuñoziD· 1 shared Gisle VestergaardiD· 1 shared

Activity by Year

2018-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersBioinformatics

Søren Johannes SørensenORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome

Sara Pita, Pernille Neve Myers, Joachim Johansen, Jakob Russel, Mads Cort Nielsen, Aron Charles Eklund, Henrik Bjørn Nielsen

CHAMP provides accurate taxonomic profiling of prokaryotes, eukaryotes, and viruses in the human microbiome, outperforming existing tools in recall, F1 score, and false positive reduction.

Frontiers in Microbiology · Oct 17, 2024Peer-reviewedBioinformatics

MAGinator enables strain-level quantification of de novo MAGs

Trine Zachariasen, Jakob Russel, Charisse Petersen, Gisle Vestergaard, Shiraz Ali Shah, Stuart E. Turvey, Søren Johannes Sørensen, Ole Lund, Jakob Stokholm, Asker Brejnrod, Jonathan Thorsen

MAGinator quantifies strain-level abundance of metagenome-assembled genomes and infers their functional and phylogenetic profiles from shotgun metagenomics data.

bioRxiv · Aug 28, 2023 · PreprintBioinformatics

CRISPRCasTyper: An automated tool for the identification, annotation and classification of CRISPR-Cas loci

Jakob Russel, Rafael Pinilla‐Redondo, David Mayo-Muñoz, Shiraz Ali Shah, Søren Johannes Sørensen

CRISPRCasTyper is a tool that identifies and classifies CRISPR-Cas loci in prokaryotic sequences using machine learning, achieving high accuracy in subtyping and handling fragmented data.

The CRISPR Journal · Dec 1, 2020Peer-reviewedBioinformatics

DAtest: a framework for choosing differential abundance or expression method

Jakob Russel, Jonathan Thorsen, Asker Brejnrod, Hans Flinker Bisgaard, Søren Johannes Sørensen, Mette Burmølle

DAtest is an R package that empirically compares statistical methods for differential expression or abundance directly on a user's own dataset across diverse omics types.

bioRxiv · Jan 2, 2018 · PreprintBioinformatics