Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

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

(2017) Kirsten L. Frieda et al.   NATURE

Cell diversity and network dynamics in photosensitive human brain organoids

(2017) Giorgia Quadrato et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

(2017) Abbas H Rizvi et al.   NATURE BIOTECHNOLOGY

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib 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

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

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

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

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

(2017) Leon A Furchtgott et al.   eLife

Genetic targeting and anatomical registration of neuronal populations in the zebrafish brain with a new set of BAC transgenic tools

(2017) Dominique Förster et al.   Scientific Reports

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

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

Disentangling neural cell diversity using single-cell transcriptomics

(2016) Jean-Francois Poulin et al.   NATURE NEUROSCIENCE

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques 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

Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development

(2016) Summer B. Thyme et al.   Cell Reports

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

A CRISPR/Cas9 Vector System for Tissue-Specific Gene Disruption in Zebrafish

(2015) Julien Ablain et al.   DEVELOPMENTAL CELL

Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs

(2015) Linlin Yin et al.   GENETICS

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Coexpression analysis of nine neuropeptides in the neurosecretory preoptic area of larval zebrafish

(2015) Ulrich Herget et al.   Frontiers in Neuroanatomy

Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs

(2015) Linlin Yin et al.   GENETICS

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2013) Y. Albert Pan et al.   DEVELOPMENT

Neurogenesis in zebrafish – from embryo to adult

(2013) Rebecca Schmidt et al.   Neural Development

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

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

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