Publications and preprints

S. H. Zhan, Y. Wong*, A. Ignatieva*, K. Eaton, I. Guthrie, B. Jeffery, D. S. Palmer, C. L. Murall, S. P. Otto and J. Kelleher. A pandemic-scale ancestral recombination graph for SARS-CoV-2.
[bioRxiv]

D. Peede, T. Cousins, A. Durvasula, A. Ignatieva, T. G. L. Kovacs, A. Nieto, E. E. Puckett and E. T. Chevy. Not just Ne Ne-more: New applications for SMC from ecology to phylogenies. Genome Biology and Evolution, to appear.
[arXiv]

A. Ignatieva and L. A. F. Ferreira (2025). Phantom epistasis through the lens of genealogies. Genetics, to appear.
[Journal] [bioRxiv]

A. Ignatieva, M. Favero*, J. Koskela*, J. Sant* and S. R. Myers (2025). The length of haplotype blocks and signals of structural variation in reconstructed genealogies. Molecular Biology and Evolution, 42(9):msaf190.
[Journal] [bioRxiv]

Y. Wong, A. Ignatieva*, J. Koskela*, G. Gorjanc, A. W. Wohns, J. Kelleher (2024). A general and efficient representation of ancestral recombination graphs. Genetics, 288(1): iyae100.
[Journal] [bioRxiv]

E. Hayman, A. Ignatieva and J. Hein (2023). Recoverability of ancestral recombination graph topologies. Theoretical Population Biology, 154: 27-39.
[Journal] [bioRxiv]

A. Ignatieva, J. Hein and P. A. Jenkins (2022). Ongoing recombination in SARS-CoV-2 revealed through genealogical reconstruction. Molecular Biology and Evolution, 39(2): msac028.
[Journal]

A. Ignatieva, R. B. Lyngsø, P. A. Jenkins and J. Hein (2021). KwARG: Parsimonious reconstruction of ancestral recombination graphs with recurrent mutation. Bioinformatics, 37(19): 3277-3284.
[Journal] [GitHub]

A. Ignatieva, J. Hein and P. A. Jenkins (2020). A characterisation of the reconstructed birth-death process through time rescaling. Theoretical Population Biology, 134: 61-76.
[Journal]

A. Ignatieva, A. F. Bell and B. J. Worton (2018). Point process models for quasi-periodic volcanic earthquakes. Statistics in Volcanology, 4(2): 1-27.