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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EpiPAMPAS: Rapid detection of intra-protein epistasis via parsimonious ancestral state reconstruction and counting mutations
bioRxiv, December 20, 2024
Dabbaghie F*, Thedinga K*, Bazykin G A, Marschall T†, Kallinina O K†
Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B
The American Journal of Human Genetics, August 8, 2024
Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O’Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE
Locityper: targeted genotyping of complex polymorphic genes
bioRxiv, May 6, 2024
Prodanov T, Plender EG, Seebohm G, Meuth SG, Eichler EE, Marschall T

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

A tool for computing statistics for GFA-formatted pangenome graphs

PanGenie

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

GraphAligner

A tool to align long reads to genome graphs.

MBG

Minimizer based sparse de Bruijn Graph constructor

BubbleGun

A general-purpose tool for detecting Bubbles and Superbubbles in genome graphs.

gaftools

General purpose utility related to GAF files

PanPA

Generation and alignment of panproteome graphs

WhatsHap

A tool for read-based phasing.