Sophie Seidel

This paper introduces a Bayesian framework to improve phylogenetic inference from sparse lineage tracing data by modeling barcode loss, showing it enhances accuracy and recovers higher growth rates than standard filtering methods.

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

SciPhy estimates time-scaled phylogenies and cell population parameters from sequential genetic lineage tracing data using a Bayesian framework, showing improved accuracy over existing methods.

This paper evaluates the accuracy of inferring cell phylogenies and population dynamics from CRISPR lineage recordings using simulations and Bayesian methods.

CloVarS generates synthetic single-cell lineage data to model time-lapse microscopy experiments and test biological hypotheses.

mt-SCITE reconstructs cell lineages from mitochondrial mutations, outperforming existing methods and revealing subclonal relationships in CD8+ T cells post-vaccination.

The paper introduces GABI, a Bayesian framework in BEAST 2 for analyzing lineage tracing data, demonstrating its application to zebrafish development.

TiDeTree estimates time-scaled single-cell phylogenies and population dynamics from genetic lineage tracing data using a Bayesian framework.

This study compares structured coalescent and multitype birth-death models for inferring migration rates between subpopulations using simulated phylogenies, finding MBD outperforms SC in epidemic outbreaks.

The paper examines SARS-CoV-2 genetic diversity within individual patients, finding that a small number of patients carry most of the diversity and that older patients tend to have more diverse viral variants.