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. …
LineageOT is a unified framework for lineage tracing and trajectory inference
A Forrow, G Schiebinger - Nature communications, 2021 - nature.com
… collection of data on cell state and cell lineage. The two types … Our results show a path towards
realizing the substantial … , when we use an entropy parameter proportional to the inferred …
realizing the substantial … , when we use an entropy parameter proportional to the inferred …
From single-cell variability to population growth
J Lin, A Amir - Physical Review E, 2020 - APS
… results provide a recipe to infer the population growth rate based on single-lineage data, eg,
data … The same argument also applies to the size-additive noise and we also do the same …
data … The same argument also applies to the size-additive noise and we also do the same …
Effects of cell cycle variability on lineage and population measurements of messenger RNA abundance
R Perez-Carrasco, C Beentjes… - Journal of the Royal …, 2020 - royalsocietypublishing.org
… relevant to the experimental inference of kinetic parameters, we aim … Furthermore, we apply
our results to a genome-wide … This is of particular relevance for current data analysis where …
our results to a genome-wide … This is of particular relevance for current data analysis where …
Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: theory and experimental validation
… infer the temperaturedependent gene expression parameters, … of the burst size distribution
allows us to analyze both bursty … better understood using our analytical results. Recall that the …
allows us to analyze both bursty … better understood using our analytical results. Recall that the …
Linking branch lengths across sets of loci provides the highest statistical support for phylogenetic inference
… In this study, we examined the effects of linking and unlinking branch-length parameters …
Our results suggest that the variation in rates across loci and lineages will often be well …
Our results suggest that the variation in rates across loci and lineages will often be well …
CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data
… FN rate parameters, we built an error model with two free parameters, … Our results suggest
that CellPhy is an efficient tool for … output, is the estimation of cell lineage trees. Our extensive …
that CellPhy is an efficient tool for … output, is the estimation of cell lineage trees. Our extensive …
Generalized and scalable trajectory inference in single-cell omics data with VIA
… to discovering elusive lineages and less populous cell fates … We first generate and analyze
simulated datasets (see … that these biological findings are robust to user parameter tuning, we …
simulated datasets (see … that these biological findings are robust to user parameter tuning, we …
Measuring single cell divisions in human tissues from multi-region sequencing data
B Werner, J Case, MJ Williams, K Chkhaidze… - Nature …, 2020 - nature.com
… account for cell death or differentiation, leading to lineage loss. … of n cell divisions into r
divisions that result in two surviving … We want to infer the microscopic evolutionary parameters μ …
divisions that result in two surviving … We want to infer the microscopic evolutionary parameters μ …
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 …