The Marschall Lab

Our research group, headed by Prof. Dr. Tobias Marschall, mainly works on genome data science, with a focus on novel algorithms and software tools for computational genomics. We address computational challenges arising from latest sequencing technologies to further our understanding of genomic variation and their consequences on phenotypic variation and disease. Over the past years, a special emphasis has been on methods for haplotype reconstruction, genome assembly, structural variation analysis, pangenomics and single-cell genomics.

People
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Publications
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PanPA: generation and alignment of panproteome graphs
Bioinformatics Advances, November 24, 2023
Dabbaghie F, Sikakulam S K, Marschall T, Kallinina O K
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Cell Rep Methods, August 28, 2023
Lee H, Greer SU, Pavlichin DS, Zhou B, Urban AE, Weissman T, Human Pangenome Reference Consortium, Ji HP
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Nature, August 23, 2023
Hallast P*, Ebert P*, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K, Human Genome Structural Variation Consortium (HGSVC), O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C

Legend: * joint first author; † joint last author
Software
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PanGenie

A short-read genotyper for various types of genetic variants (such as SNPs, indels and structural variants) represented in a pangenome graph.

WhatsHap

A tool for read-based phasing.

GraphAligner

A tool to align long reads to genome graphs.

MBG

Minimizer based sparse de Bruijn Graph constructor