[HTML][HTML] Clonal dynamics of haematopoiesis across the human lifespan

E Mitchell, M Spencer Chapman, N Williams… - Nature, 2022 - nature.com
Age-related change in human haematopoiesis causes reduced regenerative capacity,
cytopenias, immune dysfunction and increased risk of blood cancer,–, but the reason for …

The longitudinal dynamics and natural history of clonal haematopoiesis

MA Fabre, JG de Almeida, E Fiorillo, E Mitchell… - Nature, 2022 - nature.com
Clonal expansions driven by somatic mutations become pervasive across human tissues
with age, including in the haematopoietic system, where the phenomenon is termed clonal …

[HTML][HTML] Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in myeloproliferative neoplasms

D Van Egeren, J Escabi, M Nguyen, S Liu, CR Reilly… - Cell stem cell, 2021 - cell.com
Some cancers originate from a single mutation event in a single cell. Blood cancers known
as myeloproliferative neoplasms (MPNs) are thought to originate when a driver mutation is …

Bayesian inference of ancestral dates on bacterial phylogenetic trees

X Didelot, NJ Croucher, SD Bentley… - Nucleic acids …, 2018 - academic.oup.com
The sequencing and comparative analysis of a collection of bacterial genomes from a single
species or lineage of interest can lead to key insights into its evolution, ecology or …

Epidemiological inference from pathogen genomes: a review of phylodynamic models and applications

LA Featherstone, JM Zhang, TG Vaughan… - Virus …, 2022 - academic.oup.com
Phylodynamics requires an interdisciplinary understanding of phylogenetics, epidemiology,
and statistical inference. It has also experienced more intense application than ever before …

[HTML][HTML] Tracking hematopoietic stem cells and their progeny using whole-genome sequencing

H Lee-Six, DG Kent - Experimental hematology, 2020 - Elsevier
Highlights•Using acquired somatic mutations as a genetic barcode allows reconstruction of
a stem cell “family tree” of relatedness.•Understanding HSC clonal dynamics is central to …

Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development

K Liu, S Deng, C Ye, Z Yao, J Wang, H Gong, L Liu… - Nature …, 2021 - nature.com
Mapping the cell phylogeny of a complex multicellular organism relies on somatic mutations
accumulated from zygote to adult. Available cell barcoding methods can record about three …

Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

EM Volz, X Didelot - Systematic Biology, 2018 - academic.oup.com
Nonparametric population genetic modeling provides a simple and flexible approach for
studying demographic history and epidemic dynamics using pathogen sequence data …

Evolutionary and ecological drivers shape the emergence and extinction of foot-and-mouth disease virus lineages

A Di Nardo, L Ferretti, J Wadsworth… - Molecular biology …, 2021 - academic.oup.com
Livestock farming across the world is constantly threatened by the evolutionary turnover of
foot-and-mouth disease virus (FMDV) strains in endemic systems, the underlying dynamics …

Distance metrics for ranked evolutionary trees

J Kim, NA Rosenberg… - Proceedings of the …, 2020 - National Acad Sciences
Genealogical tree modeling is essential for estimating evolutionary parameters in population
genetics and phylogenetics. Recent mathematical results concerning ranked genealogies …