Inference of single-cell phylogenies from lineage tracing data using Cassiopeia
… simulation parameters (as determined by the experimental data… CRISPR-recorders, our
results suggest that with adequate … size distribution described in the manufacturer’s protocol. …
results suggest that with adequate … size distribution described in the manufacturer’s protocol. …
SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
… score for k-medoids clustering of the cells based on a distance matrix obtained from the inferred
cell lineage tree… As the values of the error rate parameters α, β and the parameters of the …
cell lineage tree… As the values of the error rate parameters α, β and the parameters of the …
Phylodynamics for cell biologists
… cell lineages within tissues and organisms. Large amounts of … to infer dynamical behavior
from experimental single-cell data. … parameters can be inferred by use of standard statistical …
from experimental single-cell data. … parameters can be inferred by use of standard statistical …
Characterization of cell fate probabilities in single-cell data with Palantir
… is also used to infer terminal states from the data. Palantir … Our results suggest continuity in
early hematopoietic lineage … with different parameters and the robustness of the results was …
early hematopoietic lineage … with different parameters and the robustness of the results was …
Inferring population dynamics from single-cell RNA-sequencing time series data
DS Fischer, AK Fiedler, EM Kernfeld, RMJ Genga… - Nature …, 2019 - nature.com
… robustness of the parameter estimation in multiple simulation … z-scores of sliding window
expression estimates across cell … of the drift parameter on the T-cell lineage across cell state (…
expression estimates across cell … of the drift parameter on the T-cell lineage across cell state (…
A comparison of single-cell trajectory inference methods
… inference approaches analyze genome-wide omics data … of single cells and computationally
infer the order of these cells … has a parameter γ, which was fixed at 0.1 to make the scores …
infer the order of these cells … has a parameter γ, which was fixed at 0.1 to make the scores …
Analytical distributions for detailed models of stochastic gene expression in eukaryotic cells
… A recent application of the model is its use to infer the promoter-… to a forward lineage, ie,
either of the two daughter cells is … (A) Using parameters typical of mammalian cells, we find that …
either of the two daughter cells is … (A) Using parameters typical of mammalian cells, we find that …
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
K Chkhaidze, T Heide, B Werner… - PLoS computational …, 2019 - journals.plos.org
… Our results indicate that spatial constrains can introduce … the ancestral history of cancer
cell lineages [6]. However, one … For Fig 4 and parameter inference framework with single cell …
cell lineages [6]. However, one … For Fig 4 and parameter inference framework with single cell …
A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution
… in gene expression can result in discontinuous trajectories. Thus… parameters. Finally, for most
discontinuous trajectories, … above analysis, we find that the extent to which lineage predicts …
discontinuous trajectories, … above analysis, we find that the extent to which lineage predicts …
Lineage tracing meets single-cell omics: opportunities and challenges
… The challenge of data analysis is then to infer the continuum … the results of more powerful
forms of data analysis. … 5 we have detailed two parameters that can strongly influence the …
forms of data analysis. … 5 we have detailed two parameters that can strongly influence the …