Recording development with single cell dynamic lineage tracing

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

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

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

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

Exploring single cells in space and time during tissue development, homeostasis and regeneration

(2019) Urs Mayr et al.   DEVELOPMENT

Defining Adult Stem Cells by Function, not by Phenotype

(2018) Hans Clevers et al.   Annual Review of Biochemistry

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

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

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

(2018) Tsung-Li Liu et al.   SCIENCE

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang 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

Tracing human stem cell lineage during development using DNA methylation

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

Hierarchically related lineage-restricted fates of multipotent haematopoietic stem cells

(2018) Joana Carrelha et al.   NATURE

Population dynamics of normal human blood inferred from somatic mutations

(2018) Henry Lee-Six et al.   NATURE

CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window

(2018) Shakked O. Halperin et al.   NATURE

Erratum: Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration

(2018) Tobias Gerber et al.   SCIENCE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

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

(2018) Katie McDole et al.   CELL

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

(2018) Andrea Attardi et al.   DEVELOPMENT

A Regeneration Toolkit

(2018) Mayssa H. Mokalled et al.   DEVELOPMENTAL CELL

Quantification of somatic mutation flow across individual cell division events by lineage sequencing

(2018) Yehuda Brody et al.   GENOME RESEARCH

Transcriptional recording by CRISPR spacer acquisition from RNA

(2018) Florian Schmidt et al.   NATURE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Cellular barcoding: lineage tracing, screening and beyond

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

Changing concepts in hematopoietic stem cells

(2018) Ryo Yamamoto et al.   SCIENCE

Loss of embryonic neural crest derived cardiomyocytes causes adult onset hypertrophic cardiomyopathy in zebrafish

(2018) Sarah Abdul-Wajid et al.   Nature Communications

Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution

(2018) Nicholas D. Leigh et al.   Nature Communications

Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis

(2018) Fernando G. Osorio et al.   Cell Reports

A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation

(2017) Michal Rabani et al.   MOLECULAR CELL

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

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

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

The evolution of tumour phylogenetics: principles and practice

(2017) Russell Schwartz et al.   NATURE REVIEWS GENETICS

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Multiplex recording of cellular events over time on CRISPR biological tape

(2017) Ravi U. Sheth et al.   SCIENCE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Advances in Decoding Axolotl Limb Regeneration

(2017) Brian J. Haas et al.   TRENDS IN GENETICS

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

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

Lineage tracing of genome-edited alleles reveals high fidelity axolotl limb regeneration

(2017) Grant Parker Flowers et al.   eLife

The Molecular and Cellular Choreography of Appendage Regeneration

(2016) Elly M. Tanaka   CELL

Tet-On Systems For Doxycycline-inducible Gene Expression

(2016) Atze T. Das et al.   CURRENT GENE THERAPY

Plasticity in the Adult: How Should the Waddington Diagram Be Applied to Regenerating Tissues?

(2016) Jayaraj Rajagopal et al.   DEVELOPMENTAL CELL

Emerging Imaging and Genomic Tools for Developmental Systems Biology

(2016) Zhe Liu et al.   DEVELOPMENTAL CELL

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Adult cell plasticity in vivo: de-differentiation and transdifferentiation are back in style

(2016) Allyson J. Merrell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Molecular recordings by directed CRISPR spacer acquisition

(2016) Seth L. Shipman et al.   SCIENCE

Review Paper: The Shape of Phylogenetic Treespace

(2016) St. John Katherine   SYSTEMATIC BIOLOGY

Retroviral integration: Site matters

(2015) Jonas Demeulemeester et al.   BIOESSAYS

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

(2015) Jaehoon Shin et al.   Cell Stem Cell

A pathway from chromosome transfer to engineering resulting in human and mouse artificial chromosomes for a variety of applications to bio-medical challenges

(2015) Mitsuo Oshimura et al.   CHROMOSOME RESEARCH

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish

(2015) Eric J. Horstick et al.   NUCLEIC ACIDS RESEARCH

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

Cell lineage tracing in human epithelial tissues using mitochondrial DNA mutations as clonal markers

(2015) Viola Walther et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

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

(2014) Sean C. Bendall et al.   CELL

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

In vivo generation of DNA sequence diversity for cellular barcoding

(2014) Ian D. Peikon et al.   NUCLEIC ACIDS RESEARCH

Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

(2014) James A. Gagnon et al.   PLoS One

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

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

(2013) Y. Albert Pan et al.   DEVELOPMENT

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Limited dedifferentiation provides replacement tissue during zebrafish fin regeneration

(2012) Scott Stewart et al.   DEVELOPMENTAL BIOLOGY

The neural crest in cardiac congenital anomalies

(2012) Anna Keyte et al.   DIFFERENTIATION

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Fate Restriction in the Growing and Regenerating Zebrafish Fin

(2011) Shu Tu et al.   DEVELOPMENTAL CELL

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

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Decoding cell lineage from acquired mutations using arbitrary deep sequencing

(2011) Cheryl A Carlson et al.   NATURE METHODS

Flybow: genetic multicolor cell labeling for neural circuit analysis in Drosophila melanogaster

(2011) Dafni Hadjieconomou et al.   NATURE METHODS