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On the statistical analysis of single cell lineage trees
(2018)Journal of Theoretical BiologyStem cells play a central role in the regeneration and repair of multicellular organisms. However, it remains far from trivial to reliably identify them. Despite decades of work, current techniques to isolate hematopoietic stem cells (HSCs) based on cell-surface markers only result in 50% purity, i.e. half of the sorted cells are not stem cells when functionally tested. Modern microscopy techniques allow us to follow single cells and their ...Journal Article -
Impact of the tree prior on estimating clock rates during epidemic outbreaks
(2018)Proceedings of the National Academy of Sciences of the United States of AmericaBayesian phylogenetics aims at estimating phylogenetic trees together with evolutionary and population dynamic parameters based on genetic sequences. It has been noted that the clock rate, one of the evolutionary parameters, decreases with an increase in the sampling period of sequences. In particular, clock rates of epidemic outbreaks are often estimated to be higher compared with the long-term clock rate. Purifying selection has been ...Journal Article -
Tuberculosis outbreak investigation using phylodynamic analysis
(2018)EpidemicsThe fast evolution of pathogenic viruses has allowed for the development of phylodynamic approaches that extract information about the epidemiological characteristics of viral genomes. Thanks to advances in whole genome sequencing, they can be applied to slowly evolving bacterial pathogens like Mycobacterium tuberculosis. In this study, we investigate and compare the epidemiological dynamics underlying two M. tuberculosis outbreaks using ...Journal Article -
The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes
(2018)Journal of Theoretical BiologyA birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting “birth” as branching speciation, “death” as extinction, and “sampling” as fossil preservation and recovery, this model – also referred to as the fossilized birth-death (FBD) model – gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range ...Journal Article