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Bayesian phylodynamics of early vertebrate development in BEAST 2
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells
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Variability of an Early Developmental Cell Population Underlies Stochastic Laterality Defects
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Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees
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Emergence of Neuronal Diversity during Vertebrate Brain Development
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Clonal dynamics of native haematopoiesis
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Whole-organism clone tracing using single-cell sequencing
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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain
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Methods and applications for single-cell and spatial multi-omics
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Unravelling cellular relationships during development and regeneration using genetic lineage tracing
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Molecular recording of mammalian embryogenesis
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Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT
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Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
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Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution
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Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing
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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
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Phylodynamic Model Adequacy Using Posterior Predictive Simulations
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TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data
inferredcites →https://doi.org/10.1098/rstb.1925.0002openalex-snapshot
II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S
inferredcites →https://doi.org/10.1098/rstb.1994.0068openalex-snapshot
The reconstructed evolutionary process
inferredcites →https://doi.org/10.1098/rstb.1995.0087openalex-snapshot
Inferring population history from molecular phylogenies
inferredcites →https://doi.org/10.1101/2020.04.16.045245openalex-snapshot
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts
inferredcites →https://doi.org/10.1111/j.1558-5646.1965.tb01722.xopenalex-snapshot
A METHOD FOR DEDUCING BRANCHING SEQUENCES IN PHYLOGENY
inferredcites →https://doi.org/10.1126/science.aaf7907openalex-snapshot
Whole-organism lineage tracing by combinatorial and cumulative genome editing
inferredcites →https://doi.org/10.1126/science.aah6266openalex-snapshot
Phylodynamics for cell biologists
inferredcites →https://doi.org/10.1126/science.abb3099openalex-snapshot
Imaging cell lineage with a synthetic digital recording system
inferredcites →https://doi.org/10.1144/sp549-2023-174openalex-snapshot
Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth–death skyline model
inferredcites →https://doi.org/10.1161/circresaha.116.305097openalex-snapshot
Cellular Origin and Developmental Program of Coronary Angiogenesis
inferredcites →https://doi.org/10.1186/1471-2148-7-214openalex-snapshot
BEAST: Bayesian evolutionary analysis by sampling trees
inferredcites →https://doi.org/10.1186/1741-7007-8-114openalex-snapshot
Bayesian random local clocks, or one rate to rule them all
inferredcites →https://doi.org/10.1186/s12859-022-04633-xopenalex-snapshot
Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR
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Long-read-based human genomic structural variation detection with cuteSV
inferredcites →https://doi.org/10.1214/20-aoas1400openalex-snapshot
Estimation of cell lineage trees by maximum-likelihood phylogenetics
inferredcites →https://doi.org/10.1242/dev.169730openalex-snapshot
Recording development with single cell dynamic lineage tracing
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pbio.1000015openalex-snapshot
Cell Lineages and the Logic of Proliferative Control
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.2307/1535879openalex-snapshot
ORGAN-FORMING SUBSTANCES IN THE EGGS OF ASCIDIANS
inferredcites →https://doi.org/10.7554/elife.40292openalex-snapshot
Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1093/genetics/iyaf112openalex-snapshot
Learning evolutionary parameters from genealogies using allelic trees
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