Unravelling cellular relationships during development and regeneration using genetic lineage tracing

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

An Ectoderm-Derived Myeloid-like Cell Population Functions as Antigen Transporters for Langerhans Cells in Zebrafish Epidermis

(2019) Xi Lin et al.   DEVELOPMENTAL CELL

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

(2019) Anna S. Nam et al.   NATURE

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

(2018) Anna K. Casasent et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Clonal analysis of lineage fate in native haematopoiesis

(2018) Alejo E. Rodriguez-Fraticelli 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

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta

(2018) Chloé S. Baron et al.   Nature Communications

Tracing human stem cell lineage during development using DNA methylation

(2018) Lucas A. Salas et al.   GENOME RESEARCH

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Haematopoiesis in the era of advanced single-cell technologies

(2018) Sten Eirik W. Jacobsen et al.   NATURE CELL BIOLOGY

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer

(2017) Marco L. Leung et al.   GENOME RESEARCH

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

(2017) Kirsten L. Frieda et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

In Vivo Tracking of Human Hematopoiesis Reveals Patterns of Clonal Dynamics during Early and Steady-State Reconstitution Phases

(2016) Luca Biasco et al.   Cell Stem Cell

Assessment of megabase-scale somatic copy number variation using single-cell sequencing

(2016) Kristin A. Knouse et al.   GENOME RESEARCH

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development

(2016) Jonathan Henninger et al.   NATURE CELL BIOLOGY

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

Temporal-Spatial Resolution Fate Mapping Reveals Distinct Origins for Embryonic and Adult Microglia in Zebrafish

(2015) Jin Xu et al.   DEVELOPMENTAL CELL

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease

(2015) James B. Stewart et al.   NATURE REVIEWS GENETICS

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Single nucleotide variations: Biological impact and theoretical interpretation

(2014) Panagiotis Katsonis et al.   PROTEIN SCIENCE

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

Quantitative reconstruction of leukocyte subsets using DNA methylation

(2014) William P Accomando et al.   GENOME BIOLOGY

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Mosaic Copy Number Variation in Human Neurons

(2013) M. J. McConnell et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

(2012) Alexej Abyzov et al.   NATURE

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Cell Lineage Analysis of the Mammalian Female Germline

(2012) Yitzhak Reizel et al.   PLoS Genetics

Fate Restriction in the Growing and Regenerating Zebrafish Fin

(2011) Shu Tu et al.   DEVELOPMENTAL CELL

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Germ-layer and lineage-restricted stem/progenitors regenerate the mouse digit tip

(2011) Yuval Rinkevich et al.   NATURE

Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

(2011) Yitzhak Reizel et al.   PLoS Genetics

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Blood stem cells emerge from aortic endothelium by a novel type of cell transition

(2010) Karima Kissa et al.   NATURE

Haematopoietic stem cells derive directly from aortic endothelium during development

(2010) Julien Y. Bertrand et al.   NATURE

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS