Filtering for highly variable genes and high quality spots improves phylogenetic analysis of cancer spatial transcriptomics Visium data
Alexandra “Sasha” Gavryushkina, Holly R. Pinkney, Sarah D. Diermeier, Alex Gavryushkin
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University of CanterburyORCID 0000-0002-1885-1108Unclaimed ORCID profile · follow to get notified of new preprints
3 papers
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Alexandra “Sasha” Gavryushkina, Holly R. Pinkney, Sarah D. Diermeier, Alex Gavryushkin
Ugnė Stolz, Alexandra “Sasha” Gavryushkina, Timothy G. Vaughan…·Bethany J. Allen
This paper introduces the SRFBD model to improve phylogenetic inference by incorporating stratigraphic range data, showing it produces older divergence times and higher sampling proportions compared to the FBD model.
Kate Truman, Timothy G. Vaughan, Alex Gavryushkin, Alexandra “Sasha” Gavryushkina
The paper proves that time-dependent fossilised birth-death models are identifiable, but shows that adding a removal after sampling parameter makes them unidentifiable.