Author

Tom Kitak

SIB Swiss Institute of BioinformaticsORCID 0009-0004-1529-4459Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Research Focus:database / resource· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:dimensionality reduction· 1

Frequent Co-Authors

Izaskun MallonaiD· 2 shared Aidan Meara· 1 shared Atreya ChoudhuryiD· 1 shared Ben CarrilloiD· 1 shared David WisseliD· 1 shared M LehmanniD· 1 shared Mark D. RobinsoniD· 1 shared Martin EmonsiD· 1 shared

Activity by Year

2026-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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2 shared papersGenomics

Izaskun MallonaORCID

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2 papers

Recent·Most cited

fastder: fast, annotation-agnostic detection of expressed regions from RNA-seq coverage and splicing data

M Lehmann, Tom Kitak, Izaskun Mallona

fastder detects expressed regions from RNA-seq data without relying on annotations, achieving high accuracy and speed for large-scale analysis.

bioRxiv · Jun 25, 2026 · PreprintGenomics

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

Atreya Choudhury, Tom Kitak, Ben Carrillo, Pauline Busch, Martin Emons, Samuel Gunz, Maruša Koderman, Siyuan Luo, Izaskun Mallona, Aidan Meara, David Wissel, Mark D. Robinson

The paper evaluates five single-cell RNA sequencing pipelines using Omnibenchmark, highlighting differences in parameter implementation across tools.

bioRxiv · May 5, 2026 · PreprintBioinformatics