Publication – Schneeberger Lab

PUBLICATIONS

Selected publications and research output from our group. Find all our research here.

PubMed Google Scholar bioRxiv

2026

Tracing modern breeding introgressions in European potato

Craig I Dent, Lisa C Baus, Sergio Tusso, Klaus J Dehmer, Ronald C B Hutten, Herman J van Eck, Korbinian Schneeberger

DOI: 10.1007/s00122-025-05143-z

2025

The phased pan-genome of tetraploid European potato

Hequan Sun, Sergio Tusso, Craig I Dent, Manish Goel, Raúl Y Wijfjes, Lisa C Baus, Xiao Dong, José A Campoy, Ana Kurdadze, Birgit Walkemeier, Christine Sänger, Bruno Huettel, Ronald C B Hutten, Herman J van Eck, Klaus J Dehmer, Korbinian Schneeberger

DOI: 10.1038/s41586-025-08843-0

Scalable eQTL mapping using single-nucleus RNA-sequencing of recombined gametes from a small number of individuals

Matthew T Parker, Samija Amar, José A Campoy, Kristin Krause, Sergio Tusso, Magdalena Marek, Bruno Huettel, Korbinian Schneeberger

DOI: 10.1371/journal.pbio.3003085

2024

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

Hequan Sun, Patrik Abeli, José Antonio Campoy, Thea Rütjes, Kristin Krause, Wen-Biao Jiao, Randy Beaudry, Korbinian Schneeberger

DOI: 10.1186/s12870-024-05628-x

The vast majority of somatic mutations in plants are layer-specific

Manish Goel, José A. Campoy, Kristin Krause, Lisa C. Baus, Anshupa Sahu, Hequan Sun, Birgit Walkemeier, Magdalena Marek, Randy Beaudry, David Ruiz, Bruno Huettel & Korbinian Schneeberger

DOI: 10.1186/s13059-024-03337-0

A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Qichao Lian, Bruno Huettel, Birgit Walkemeier, Baptiste Mayjonade, Céline Lopez-Roques, Lisa Gil, Fabrice Roux, Korbinian Schneeberger, Raphaël Mercier

DOI: 10.1038/s41588-024-01715-9

2023

Gamete Binning to Achieve Haplotype-Resolved Genome Assembly

Hequan Sun, José Campoy, Korbinian Schneeberger

DOI: 10.1007/978-1-0716-2819-5_13

2022

Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge

Vidya Oruganti, Helena Toegelová, Aleš Pečinka, Andreas Madlung, Korbinian Schneeberger

DOI: 10.1093/genetics/iyac132

plotsr: visualizing structural similarities and rearrangements between multiple genomes

Manish Goel, Korbinian Schneeberger

DOI: 10.1093/bioinformatics/btac196

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Hequan Sun, Wen-Biao Jiao, Kristin Krause, José A. Campoy, Manish Goel, Kat Folz-Donahue, Christian Kukat, Bruno Huettel, Korbinian Schneeberger

DOI: 10.1038/s41588-022-01015-0

2020

The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana

Wen-Biao Jiao, Vipul Patel, Jonas Klasen, Fang Liu, Petra Pecinkova, Marina Ferrand, Isabelle Gy, Christine Camilleri, Sigi Effgen, Maarten Koornneef, Ales Pecinka, Olivier Loudet, Korbinian Schneeberger

DOI: 10.1093/molbev/msaa306

Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes

José A. Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Christian Kukat, Manuel Rubio, David Ruiz, Bruno Huettel, Korbinian Schneeberger

DOI: 10.1186/s13059-020-02235-5

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

Jiao WB, Schneeberger K.

DOI: 10.1038/s41467-020-14779-y

2019

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Goel M, Sun H, Jiao WB, Schneeberger K.

DOI: 10.1186/s13059-019-1911-0

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

Hequan Sun, Beth A Rowan, Pádraic J Flood, Ronny Brandt, Janina Fuss, Angela M Hancock, Richard W Michelmore, Bruno Huettel, Korbinian Schneeberger

DOI: 10.1038/s41467-019-12209-2

Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation

Kiefer C, Willing EM, Jiao WB, Sun H, Piednoël M, Hümann U, Hartwig B, Koch MA, Schneeberger K.

DOI: 10.1038/s41477-019-0486-9

2018

findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies

Sun H, Ding J, Piednoël M, Schneeberger K.

DOI: 10.1093/bioinformatics/btx637

2017

The impact of third generation genomic technologies on plant genome assembly

Jiao WB, Schneeberger K.

DOI: 10.1016/j.pbi.2017.02.002

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

Jiao WB, Accinelli GG, Hartwig B, Kiefer C, Baker D, Severing E, Willing EM, Piednoël M, Woetzel S, Madrid-Herrero E, Huettel B, Hümann U, Reinhard R, Koch MA, Swan D, Clavijo B, Coupland G, Schneeberger K.

DOI: 10.1101/gr.213652.116