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

Imaging cell lineage with a synthetic digital recording system

(2021) Ke-Huan K. Chow et al.   SCIENCE

A community effort to create standards for evaluating tumor subclonal reconstruction

(2020) Adriana Salcedo et al.   NATURE BIOTECHNOLOGY

Embracing the dropouts in single-cell RNA-seq analysis

(2020) Peng Qiu   Nature Communications

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

(2020) Sarah Bowling et al.   CELL

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

A programmable sequence of reporters for lineage analysis

(2020) Jorge Garcia-Marques et al.   NATURE NEUROSCIENCE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

(2018) F. Lemoine et al.   NATURE

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

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

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

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

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Cellular barcoding: lineage tracing, screening and beyond

(2018) Justus M. Kebschull et al.   NATURE METHODS

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

eSTGt: a programming and simulation environment for population dynamics

(2016) Adam Spiro et al.   BMC BIOINFORMATICS

Crowdsourcing biomedical research: leveraging communities as innovation engines

(2016) Julio Saez-Rodriguez et al.   NATURE REVIEWS GENETICS

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Continuous genetic recording with self-targeting CRISPR-Cas in human cells

(2016) S. D. Perli et al.   SCIENCE

Triplet MaxCut: a new toolkit for rooted supertree

(2016) Gur Sevillya et al.   Methods in Ecology and Evolution

Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis

(2015) Tamily A. Weissman et al.   GENETICS

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

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis

(2015) Tamily A. Weissman et al.   GENETICS

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines

(2014) S. Becattini et al.   SCIENCE

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One