CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

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 Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

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

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

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han 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

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

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

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

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

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

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

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

Robust lineage reconstruction from high-dimensional single-cell data

(2016) Gregory Giecold et al.   NUCLEIC ACIDS RESEARCH

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

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

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

(2016) Jinmiao Chen et al.   Nature Communications

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita 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

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet

(2014) Samantha A. Morris et al.   CELL

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

(2014) Sean C. Bendall et al.   CELL

The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress

(2014) Peter van Galen 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

A Chimeric HS4-SAR Insulator (IS2) That Prevents Silencing and Enhances Expression of Lentiviral Vectors in Pluripotent Stem Cells

(2014) Karim Benabdellah et al.   PLoS One

Microfluidic single-cell whole-transcriptome sequencing

(2014) A. M. Streets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo

(2014) Shaina N Porter et al.   GENOME BIOLOGY

Induction of Multipotential Hematopoietic Progenitors from Human Pluripotent Stem Cells via Respecification of Lineage-Restricted Precursors

(2013) Sergei Doulatov et al.   Cell Stem Cell

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

A ubiquitous chromatin opening element prevents transgene silencing in pluripotent stem cells and their differentiated progeny

(2013) Nils Pfaff et al.   STEM CELLS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Generation of high-titer viral preparations by concentration using successive rounds of ultracentrifugation

(2011) Christine V Ichim et al.   Journal of Translational Medicine

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

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Lentiviral Vectors and Protocols for Creation of Stable hESC Lines for Fluorescent Tracking and Drug Resistance Selection of Cardiomyocytes

(2009) Hiroko Kita-Matsuo et al.   PLoS One