Arthur Zwaenepoel (Gent °1995). I am currently a PhD student in the group of professor Yves Van de Peer, conducting research on the evolutionary importance of polyploidy. In practice I have mainly worked on statistical phylogenetic methods for the inference of genome duplications from comparative genomic data and modeling of gene family evolution, where I have come to prefer a Bayesian approach towards statistics. More broadly, my main research interests are (theoretical) evolutionary genetics and probabilistic modeling in biology. I also take a strong interest in philosophy and mathematics, but claim little expertise there. I enjoy music, literature, computer programming, playing music, long(ish)-distance running and traveling by bicycle.

papers | code | notes | photos | other | phylogenetics-course

Papers

Preprints

A two-type branching process model of gene family evolution. Arthur Zwaenepoel, Yves Van de Peer bioRxiv 2021.03.18.435925; doi: https://doi.org/10.1101/2021.03.18.435925

Published

Model-Based Detection of Whole-Genome Duplications in a Phylogeny. Zwaenepoel, Arthur; Van de Peer, Yves; 2020 – Molecular Biology and Evolution, 37 (9), 2734–2746

The hornwort genome and early land plant evolution. Zhang, Jian; Fu, Xin-Xing; Li, Rui-Qi; Zhao, Xiang; Liu, Yang; Li, Ming-He; Zwaenepoel, Arthur; Ma, Hong; Goffinet, Bernard; Guan, Yan-Long; et al. 2020 – Nature plants 6 (2), 107-118

Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution. Roelofs, Dick; Zwaenepoel, Arthur; Sistermans, Tom; Nap, Joey; Kampfraath, Andries A; Van de Peer, Yves; Ellers, Jacintha; Kraaijeveld, Ken; 2020 – BMC Biology 18 (1), 1-13

Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates. Zwaenepoel, Arthur; Van de Peer, Yves; 2019 – Molecular biology and evolution 36 (7), 1384-1404

Finding evidence for whole genome duplications: a reappraisal. Zwaenepoel, Arthur; Li, Zhen; Lohaus, Rolf; Van de Peer, Yves; 2019 – Molecular plant 12 (2), 133-136

wgd—simple command line tools for the analysis of ancient whole-genome duplications. Zwaenepoel, Arthur; Van de Peer, Yves; 2019 – Bioinformatics 35 (12), 2153-2155

MorphDB: prioritizing genes for specialized metabolism pathways and gene ontology categories in plants Zwaenepoel, Arthur; Diels, Tim; Amar, David; Van Parys, Thomas; Shamir, Ron; Van de Peer, Yves; Tzfadia, Oren; 2018 – Frontiers in plant science 9, 352

Code

All my code that is to some extent usable can be found on github.

Whale: Flexible Bayesian gene tree reconciliation using amalgamated likelihood estimation and probabilistic programming.

DeadBird: Statistical analysis of comparative genomic data using phylogenetic birth-death process models. Still in a quite experimental stage.

TwoTypeDLModel: Inference for a two type continuous-time branching process model of gene family evolution. I did not look for a clever name for this one – it's quite specialized on one thing anyway.

Beluga: Reversible-jump MCMC for model-based inference of ancient WGD events using gene count data.

wgd: simple command line tools for estimating \(K_\mathrm{S}\) distributions, synteny analyses and visualization of these things to unveil ancient WGD events.

Notes

Fisher's geometric model and the cost of complexity

Other

bruine beer, featured on bandcamp daily's 'Best New Ambient Music' here. Also see vuilbak recordlabel, also here.

A particularly nice picture of my cat and me.

discogs, bandcamp

Other biographic trivia: