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. Besides my aspirations in science, I take a strong interest in philosophy, music and literature. I enjoy computer programming, playing music, long(ish)-distance running and traveling by bicycle.

notes | publications | code | other


Notes

Fisher’s geometric model and the cost of complexity


Publications

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 (nan), 352


Code

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

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

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

… and more on github


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:


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