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

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

(2017) Kirsten L. Frieda et al.   NATURE

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

(2017) Young Seok Ju et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

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

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

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

(2017) Stephanie Tzouanas Schmidt et al.   ACS Synthetic Biology

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution

(2015) Andrei Y. Kobitski et al.   Scientific Reports

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

Hematopoiesis

(2013) M. Jagannathan-Bogdan et al.   DEVELOPMENT

Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish

(2013) Y. Albert Pan et al.   DEVELOPMENT

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

(2012) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

Microhomology Directs Diverse DNA Break Repair Pathways and Chromosomal Translocations

(2012) Diana D. Villarreal et al.   PLoS Genetics

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS