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.


New publication: Constructing founder sets under allelic and non-allelic homologous recombination

October 2, 2023

We present a simple but powerful computational model of homologous allelic and non-allelic recombination which leverages pangenome graphs, capable of representing large structural variants including duplications, deletions and inversions. We formulated and provided solutions for two founder set problems under it and described exact methods for characterizing the number of recombinations.

The Marschall Lab website is online

September 12, 2021

Our new group website is online! Thanks to free software and the work of Adam Phillippy’s lab, the “perfect wheel” already existed and we did not have to reinvent anything!

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
Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia
Hemasphere, July 17, 2023
Brandes D, Yasin L, Nebral K, Ebler J, Schinnerl D, Picard D, Bergmann AK, Alam J, Köhrer S, Haas OA, Attarbaschi A, Marschall T, Stanulla M, Borkhardt A, Brozou T, Fischer U, Wagener R
Pangenome graph construction from genome alignments with Minigraph-Cactus
Nat Biotechnol, May 10, 2023
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B

Legend: * joint first author; joint last author


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


A tool for read-based phasing.


A tool to align long reads to genome graphs.


Minimizer based sparse de Bruijn Graph constructor