Author

Verena Esther Kutschera

Stockholm UniversityORCID 0000-0002-8930-534XUnclaimed 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· 5 Assay:whole-genome sequencing· 5 Research Focus:database / resource· 3 Approach:experimental assay· 3 Organism:fungi (other)· 2 Research Focus:variant calling· 2 Research Focus:benchmarking· 1 Research Focus:genome assembly· 1

Frequent Co-Authors

Tom van der ValkiD· 3 shared Anna RoslingiD· 2 shared Benjamin GuinetiD· 2 shared Claudia BerginiD· 2 shared David Díez‐del‐MolinoiD· 2 shared Edana LordiD· 2 shared Hanna JohannessoniD· 2 shared Love DaléniD· 2 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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3 shared papersBioinformatics

Tom van der ValkORCID

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Author profile →

7 papers

Recent·Most cited

DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

Muhammad Bilal Sharif, Verena Esther Kutschera, Nikolay Oskolkov, Benjamin Guinet, Edana Lord, Juan Camilo Chacón-Duque, Jonas Oppenheimer, Tom van der Valk, David Díez‐del‐Molino, Peter D. Heintzman, Love Dalén

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

bioRxiv · Sep 12, 2026 · PreprintBioinformatics

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

Simon Jacobsen Ellerstrand, Allison M. Churcher, Verena Esther Kutschera, Bengt Hansson

PhaseWY is a pipeline that identifies sex-chromosomal regions and extracts Y/W sequences from whole-genome sequencing data, demonstrating its utility in non-model organisms.

bioRxiv · Jun 22, 2026 · PreprintBioinformatics

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Francisco J. Ruíz-Ruano, Stephen A. Schlebusch, Niki Vontzou, Hugo Moreno, Matthew T. Biegler, Verena Esther Kutschera, Diana Stark Ekman, Inês Borges, Yifan Pei, Roberto Rossini, Tomáš Albrecht, Jesper Boman, Павел Михайлович Бородин, Reto Burri, Kristal Elaine Cain, , Alexander Suh

The paper identifies germline-restricted chromosomes (GRCs) in 6,700 passerine species, showing rapid evolution and functional gene retention despite programmed DNA elimination.

bioRxiv · Jul 16, 2025 · PreprintGenomics

Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data

Nikolay Oskolkov, Chenyu Jin, Samantha López Clinton, Benjamin Guinet, Flore Wijnands, Ernst Johnson, Verena Esther Kutschera, Cormac M. Kinsella, Peter D. Heintzman, Tom van der Valk

The paper presents a method to identify and mask microbial-like sequences in eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data.

bioRxiv · Mar 19, 2025 · PreprintGenomics

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Verena Esther Kutschera, Marcin Kierczak, Tom van der Valk, Johanna von Seth, Nicolás Dussex, Edana Lord, Marianne Dehasque, David W. G. Stanton, Payam Emami Khoonsari, Björn Nystedt, Love Dalén, David Díez‐del‐Molino

GenErode provides a pipeline to analyze genomic erosion by comparing ancient and modern whole-genome re-sequencing data, producing standardized erosion indices.

BMC Bioinformatics · Jun 13, 2022Peer-reviewedBioinformatics

In-depth phylogenomic analysis of arbuscular mycorrhizal fungi based on a comprehensive set of de novo genome assemblies

Mercè Montoliu-Nerin, Marisol Sánchez‐García, Claudia Bergin, Verena Esther Kutschera, Hanna Johannesson, James D. Bever, Anna Rosling

The paper presents a phylogenomic analysis of arbuscular mycorrhizal fungi using de novo genome assemblies, revealing new evolutionary relationships among families.

Frontiers in Fungal Biology · Sep 29, 2021Peer-reviewedGenomics

From single nuclei to whole genome assembly

Mercè Montoliu-Nerin, Marisol Sánchez‐García, Claudia Bergin, Manfred G. Grabherr, Barbara Ellis, Verena Esther Kutschera, Marcin Kierczak, Hanna Johannesson, Anna Rosling

The paper introduces a novel single nuclei sequencing and assembly workflow to generate reference genomes from arbuscular mycorrhizal fungi, bypassing the need for culturing.

Scientific Reports · Jan 28, 2020Peer-reviewedGenomics