Verdonk H, Pivirotto A, Pavinato V, Hey J, Kosakovsky Pond SL. (2025 March 25). A new comparative framework for estimating selection on synonymous substitutions. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msaf068.
Weaver, S., Dávila Conn, V. M., Ji, D., Verdonk, H., Ávila-Ríos, S., Leigh Brown, A. J., Wertheim, J. O., & Kosakovsky Pond, S. L. (2024). AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters. Frontiers in Bioinformatics, 4. https://doi.org/10.3389/fbinf.2024.1400003
Colicchio, J. M., Hamm, L. N., Verdonk, H. E., Kooyers, N. J., & Blackman, B. K. (2021). Adaptive and nonadaptive causes of heterogeneity in genetic differentiation across the Mimulus guttatus genome. Molecular Ecology, 30, 6486– 6507.
Verdonk H, Pivirotto A, Pavinato V, Hey J, Pond S.L.K. (2025 July 9). A fresh approach for estimating selection on synonymous codons. SMBE 2025 Conference, Beijing, China. (Selected talk, Graduate Student Excellence symposium)
Verdonk, H., Hey, J., Pond, S.L.K. (2024 July 28). MSS: a codon model with Multiple classes of Synonymous Substitutions. Evolution 2024 Conference, Quebec City, QC, Canada.
Verdonk, H., Hey, J., Pond, S.L.K. (2023, June 24). Repairing the neutral set in codon evolutionary models. Evolution 2023 Conference, Albuquerque, NM, United States.
Verdonk H, Pivirotto A, Pavinato V, Hey J, Pond S.L.K. (2024 July 9). MSS: a codon model with Multiple classes of Synonymous Substitutions. 2024 SMBE 2024 Conference, Puerto Vallarta, México.
Verdonk H, Hey J, Pond S.L.K. (2023 July 25). Redefining the neutral set in codon evolutionary models. 2023 SMBE 2023 Conference, Ferrara, Italy.
Verdonk, H., Hey, J., Pond, S.L.K. (2022). Repairing the neutral set in codon evolutionary models. 2022 MidAtlantic Bioinformatics Conference, Philadelphia, PA, United States. https://www.midatlanticbioinformatics.org/post/repairing-the-neutral-set-in-codon-evolutionary-models