Lineage tracing meets single-cell omics: opportunities and challenges

In vitro characterization of the human segmentation clock

(2020) Margarete Diaz-Cuadros et al.   NATURE

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements

(2019) Byungjin Hwang et al.   Nature Communications

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

(2019) Blanca Pijuan-Sala et al.   NATURE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng 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

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

The bone marrow microenvironment at single-cell resolution

(2019) Anastasia N. Tikhonova et al.   NATURE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice

(2019) Weike Pei et al.   Nature Protocols

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

(2019) Jin Xu et al.   eLife

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects

(2019) T. Yvanka de Soysa et al.   NATURE

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

Comprehensive single-cell transcriptome lineages of a proto-vertebrate

(2019) Chen Cao et al.   NATURE

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution

(2019) Stefan Siebert et al.   SCIENCE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

(2019) Huidong Chen et al.   Nature Communications

NASC-seq monitors RNA synthesis in single cells

(2019) Gert-Jan Hendriks et al.   Nature Communications

Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

(2019) Dylan Kotliar et al.   eLife

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

(2019) Jonathan S. Packer et al.   SCIENCE

Prospectively Isolated Tetraspanin + Neoblasts Are Adult Pluripotent Stem Cells Underlying Planaria Regeneration

(2018) An Zeng et al.   CELL

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

(2018) Arnau Sebé-Pedrós et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

(2018) Kaia Achim et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells

(2018) Robert J. Ihry et al.   NATURE MEDICINE

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

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

(2018) Jihwan Park et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

(2018) Ino D. Karemaker et al.   TRENDS IN BIOTECHNOLOGY

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

High-throughput chromatin accessibility profiling at single-cell resolution

(2018) Anja Mezger et al.   Nature Communications

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level

(2018) Katie McDole et al.   CELL

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT

(2018) Bushra Raj et al.   Nature Protocols

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

(2017) Kyung Yeon Han 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

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn 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

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Discovering sparse transcription factor codes for cell states and state transitions during development

(2017) Leon A Furchtgott et al.   eLife

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

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

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

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

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

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

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

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

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Universal patterns of stem cell fate in cycling adult tissues

(2011) A. M. Klein et al.   DEVELOPMENT

The Endoderm of the Mouse Embryo Arises by Dynamic Widespread Intercalation of Embryonic and Extraembryonic Lineages

(2008) Gloria S. Kwon et al.   DEVELOPMENTAL CELL

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE