Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Tracing cell-type evolution by cross-species comparison of cell atlases

(2021) Jingjing Wang et al.   Cell Reports

Fibroblast dedifferentiation as a determinant of successful regeneration

(2021) Tzi-Yang Lin et al.   DEVELOPMENTAL CELL

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Cellular diversity of the regenerating caudal fin

(2020) Yiran Hou et al.   Science Advances

Single-Cell Transcriptomics Uncovers Glial Progenitor Diversity and Cell Fate Determinants during Development and Gliomagenesis

(2019) Qinjie Weng et al.   Cell Stem Cell

Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell

(2019) Arshad Ayyaz et al.   NATURE

Identification of a regeneration-organizing cell in the Xenopus tail

(2019) C. Aztekin et al.   SCIENCE

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Model systems for regeneration: zebrafish

(2019) Ines J. Marques et al.   DEVELOPMENT

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

(2019) Jonathan S. Packer et al.   SCIENCE

A single-cell transcriptome atlas for zebrafish development

(2019) Dylan R. Farnsworth et al.   DEVELOPMENTAL BIOLOGY

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

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

(2018) Arnau Sebé-Pedrós et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

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

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

Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles

(2018) Maria Antonietta Tosches et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

Zebrafish Infection: From Pathogenesis to Cell Biology

(2018) Vincenzo Torraca et al.   TRENDS IN CELL BIOLOGY

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

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

(2018) Lindsey W. Plasschaert et al.   NATURE

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

(2018) Tobias Gerber et al.   SCIENCE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

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

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

Unraveling the transcriptional regulation of TWIST1 in limb development

(2018) Naama Hirsch et al.   PLoS Genetics

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing

(2017) Qin Tang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish

(2017) Neil I Bower et al.   NATURE NEUROSCIENCE

The Molecular and Cellular Choreography of Appendage Regeneration

(2016) Elly M. Tanaka   CELL

Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration

(2016) Chi-Chung Wu et al.   DEVELOPMENTAL CELL

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

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

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Sufficient Numbers of Early Germ Cells Are Essential for Female Sex Development in Zebrafish

(2015) Xiangyan Dai et al.   PLoS One

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling

(2014) Mansi Srivastava et al.   CURRENT BIOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Dynamic gene expression by putative hair-cell progenitors during regeneration in the zebrafish lateral line

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

The zebrafish as a model for complex tissue regeneration

(2013) Matthew Gemberling et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

HMGB factors are required for posterior digit development through integrating signaling pathway activities

(2011) Junji Itou et al.   DEVELOPMENTAL DYNAMICS

Expression of Hairy/enhancer of split genes in neural progenitors and neurogenesis domains of the adult zebrafish brain

(2011) Prisca Chapouton et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Comparative Transcriptome Analyses Indicate Molecular Homology of Zebrafish Swimbladder and Mammalian Lung

(2011) Weiling Zheng et al.   PLoS One

The ziwi promoter drives germline-specific gene expression in zebrafish

(2010) David H. Leu et al.   DEVELOPMENTAL DYNAMICS

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols