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LinRace: single cell lineage reconstruction using paired lineage barcode and gene expression data

https://doi.org/10.1101/2023.04.12.536601

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/aama.2001.0759openalex-snapshot

Geometry of the Space of Phylogenetic Trees

inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot

Comparison of phylogenetic trees

inferredcites →https://doi.org/10.1016/j.cell.2008.02.007openalex-snapshot

Mechanisms of Asymmetric Stem Cell Division

inferredcites →https://doi.org/10.1016/j.cell.2009.08.044openalex-snapshot

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

inferredcites →https://doi.org/10.1016/j.cell.2012.01.002openalex-snapshot

Lineage Tracing

inferredcites →https://doi.org/10.1016/j.cels.2021.05.008openalex-snapshot

Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

inferredcites →https://doi.org/10.1021/acssynbio.6b00309openalex-snapshot

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

inferredcites →https://doi.org/10.1038/nature04956openalex-snapshot

Asymmetric and symmetric stem-cell divisions in development and cancer

inferredcites →https://doi.org/10.1038/nature25969openalex-snapshot

Whole-organism clone tracing using single-cell sequencing

inferredcites →https://doi.org/10.1038/nbt.4103openalex-snapshot

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

inferredcites →https://doi.org/10.1038/nbt.4124openalex-snapshot

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

inferredcites →https://doi.org/10.1038/ng1005-1027openalex-snapshot

Stem cells, asymmetric division and cancer

inferredcites →https://doi.org/10.1038/s41467-020-16821-5openalex-snapshot

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

inferredcites →https://doi.org/10.1038/s41576-020-0223-2openalex-snapshot

Lineage tracing meets single-cell omics: opportunities and challenges

inferredcites →https://doi.org/10.1038/s41576-020-0233-0openalex-snapshot

Phylogenetic tree building in the genomic age

inferredcites →https://doi.org/10.1038/s41586-019-1184-5openalex-snapshot

Molecular recording of mammalian embryogenesis

inferredcites →https://doi.org/10.1038/s41587-019-0071-9openalex-snapshot

A comparison of single-cell trajectory inference methods

inferredcites →https://doi.org/10.1093/bioinformatics/btaa614openalex-snapshot

Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/bti720openalex-snapshot

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/btv325openalex-snapshot

Diffusion maps for high-dimensional single-cell analysis of differentiation data

inferredcites →https://doi.org/10.1093/molbev/msv150openalex-snapshot

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

inferredcites →https://doi.org/10.1093/nar/gkab301openalex-snapshot

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

inferredcites →https://doi.org/10.1093/nar/gkab325openalex-snapshot

CeLaVi: an interactive cell lineage visualization tool

inferredcites →https://doi.org/10.1093/nar/gkac235openalex-snapshot

TedSim: temporal dynamics simulation of single-cell RNA sequencing data and cell division history

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

inferredcites →https://doi.org/10.1098/rsob.190229openalex-snapshot

High-throughput dense reconstruction of cell lineages

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.aat9804openalex-snapshot

Developmental barcoding of whole mouse via homing CRISPR

inferredcites →https://doi.org/10.1126/science.aax1971openalex-snapshot

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

inferredcites →https://doi.org/10.1186/s12859-022-04633-xopenalex-snapshot

Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR

inferredcites →https://doi.org/10.1186/s12864-018-4772-0openalex-snapshot

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

inferredcites →https://doi.org/10.1186/s13059-019-1663-xopenalex-snapshot

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

inferredcites →https://doi.org/10.1186/s13059-020-02000-8openalex-snapshot

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia

inferredcites →https://doi.org/10.1214/009117906000000034openalex-snapshot

Subtree prune and regraft: A reversible real tree-valued Markov process

inferredcites →https://doi.org/10.1242/dev.175620openalex-snapshot

Correction: Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics (doi: 10.1242/dev.166728)

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/10.1007/s12551-023-01090-5openalex-snapshot

Studying temporal dynamics of single cells: expression, lineage and regulatory networks

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.