Research

Our group works on the evolution of fungal interactions, both sexual and social. We aim to integrate genetics with evolutionary biology to answer the question “how and why do fungi interact?”.

Some examples of recent publications can be found below.

Highlighted

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Manubot

Manuscript Source

Website

open-science collaboration

All

2025

Evolutionary divergence in sympatric populations of the fungal pathogen Alternaria alternata across wild tomato hosts

Tamara Schmey, Ben Auxier, Stefan Krebs, Satish Kumar Patneedi, Farooq Ahmad, Michael Habig, Remco Stam

openRxiv  ·  01 Oct 2025  ·  doi:10.1101/2025.10.01.678058

Genetic mapping and nuclear interactions of an incompatibility response in Agaricus bisporus

K. Scholtmeijer, B. Auxier, Patrick Hendrickx, B Lavrijssen, A.J.M. Debets, JJP. Baars, DK Aanen, A. van Peer

openRxiv  ·  21 Aug 2025  ·  doi:10.1101/2025.08.15.670591

Land use drives drug resistance in an airborne human fungal pathogen

Hylke H Kortenbosch, Bo Briggeman, Francisca Reyes Marquez, Ben Auxier, Sytze de Bruin, Bas J Zwaan, Eveline Snelders

The ISME Journal  ·  01 Jan 2025  ·  doi:10.1093/ismejo/wraf246

2024

The Narrow Footprint of Ancient Balancing Selection Revealed by Heterokaryon Incompatibility Genes in Aspergillus fumigatus

Ben Auxier, Jianhua Zhang, Francisca Reyes Marquez, Kira Senden, Joost van den Heuvel, Duur K Aanen, Eveline Snelders, Alfons J M Debets

Molecular Biology and Evolution  ·  23 Apr 2024  ·  doi:10.1093/molbev/msae079

2023

Community diversity affects functionality and species sorting during propagation of a natural microbial community

Alanna Leale, Ben Auxier, Eddy J. Smid, Sijmen Schoustra

openRxiv  ·  24 Feb 2023  ·  doi:10.1101/2023.02.24.529839

2022

Identification of heterokaryon incompatibility genes in Aspergillus fumigatus highlights a narrow footprint of ancient balancing selection

Ben Auxier, Jianhua Zhang, Francisca Reyes Marquez, Kira Senden, Joost van den Heuvel, Duur K. Aanen, Eveline Snelders, Alfons J.M. Debets

openRxiv  ·  25 Nov 2022  ·  doi:10.1101/2022.11.25.517501

Modeling the consequences of the dikaryotic life cycle of mushroom-forming fungi on genomic conflict

Benjamin Auxier, Tamás L Czárán, Duur K Aanen

eLife  ·  20 Apr 2022  ·  doi:10.7554/eLife.75917

Meiosis in the human pathogen Aspergillus fumigatus has the highest known number of crossovers

Ben Auxier, Frank Becker, Reindert Nijland, Alfons J. M. Debets, Joost van den Heuvel, Eveline Snelders

openRxiv  ·  15 Jan 2022  ·  doi:10.1101/2022.01.14.476329

2021

Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces

Lennart J.J. van de Peppel, Mathijs Nieuwenhuis, Benjamin Auxier, Alexey A. Grum-Grzhimaylo, Martha E. Cárdenas, …, Matthew E. Smith, Thomas W. Kuyper, Ana E. Franco-Molano, Timothy J. Baroni, Duur K. Aanen

Current Biology  ·  01 Oct 2021  ·  doi:10.1016/j.cub.2021.07.070

Cytoplasmic Mixing, Not Nuclear Coexistence, Can Explain Somatic Incompatibility in Basidiomycetes

Ben Auxier, Karin Scholtmeijer, Arend F. van Peer, Johan J. P. Baars, Alfons J. M. Debets, Duur K. Aanen

Microorganisms  ·  08 Jun 2021  ·  doi:10.3390/microorganisms9061248

2020

Open collaborative writing with Manubot

Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter

PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Manubot

Manuscript Source

Website

open-science collaboration

Living apart together: modelling the consequences of the dikaryotic life cycle of mushroom-forming fungi for genomic conflict

Ben Auxier, Tamás Czaran, Duur K. Aanen

openRxiv  ·  30 May 2020  ·  doi:10.1101/2020.05.28.103697

Constructing knowledge graphs and their biomedical applications

David N. Nicholson, Casey S. Greene

Computational and Structural Biotechnology Journal  ·  01 Jan 2020  ·  doi:10.1016/j.csbj.2020.05.017

2019

Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'

Benjamin Auxier, Anna Bazzicalupo

eLife  ·  25 Oct 2019  ·  doi:10.7554/eLife.47301

Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs

Benjamin Auxier, Jaclyn Dee, Mary L. Berbee, Michelle Momany

BMC Evolutionary Biology  ·  07 Jan 2019  ·  doi:10.1186/s12862-018-1297-8

2018

Sci-Hub provides access to nearly all scholarly literature

Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene

eLife  ·  01 Mar 2018  ·  doi:10.7554/eLife.32822

Evolutionary genetics of nonself recognition regarding social and sexual interactions of fungi

Ben Auxier

Wageningen University and Research  ·  [no date info]  ·  doi:10.18174/587592