Author

Matthew R. Huska

Robert Koch InstituteORCID 0000-0002-0912-745XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Assay:whole-genome sequencing· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Organism:human· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Marie LataretuiD· 2 shared Roland F. SchwarziD· 2 shared Abay SisayiD· 1 shared Adrian Baez‐OrtegaiD· 1 shared Adrian ViehwegeriD· 1 shared Akinyemi I. OjesinaiD· 1 shared Alexander DiltheyiD· 1 shared Alvis Brazma· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersBioinformatics

Marie LataretuORCID

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4 papers

Recent·Most cited

BioinformaticsNature MethodsPeer-reviewedFeb 9, 2026

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Martin Hunt, Angie S. Hinrichs, Daniel Anderson…·Djin-Ye Oh

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

19 citationstop 1%

viruswhole-genome sequencing

𝕏 PostBluesky

BioinformaticsNAR Genomics and BioinformaticsPeer-reviewedJul 4, 2025

Targeted decontamination of sequencing data with CLEAN

Marie Lataretu, Sebastian Krautwurst, Matthew R. Huska…·Martin Hölzer

The paper introduces CLEAN, a pipeline to remove contaminants from sequencing data, improving reproducibility and analysis quality.

9 citations

long-read sequencingbulk RNA-seq

𝕏 PostBluesky

BioinformaticsPLoS Computational BiologyPeer-reviewedOct 23, 2023

Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity

Thomas B.K. Watkins, Emma Colliver, Matthew R. Huska…·Roland F. Schwarz

Refphase uses multi-sample reference phasing to infer haplotype-specific copy numbers and reveal intra-tumour heterogeneity in cancer samples.

15 citations

humanwhole-genome sequencing

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GenomicsNature CommunicationsPeer-reviewedFeb 5, 2020

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

Yiqun Zhang, Fengju Chen, Nuno A. Fonseca…·Paul Alan Edwards

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

77 citationstop 2%

humanwhole-genome sequencing

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