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

The axolotl genome and the evolution of key tissue formation regulators

(2018) Sergej Nowoshilow et al.   NATURE

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

(2017) Grant Parker Flowers et al.   eLife

Live Imaging of Axolotl Digit Regeneration Reveals Spatiotemporal Choreography of Diverse Connective Tissue Progenitor Pools

(2016) Joshua D. Currie et al.   DEVELOPMENTAL CELL

Modulation of tissue repair by regeneration enhancer elements

(2016) Junsu Kang et al.   NATURE

FGF8 and SHH substitute for anterior–posterior tissue interactions to induce limb regeneration

(2016) Eugeniu Nacu et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Asymmetric division of clonal muscle stem cells coordinates muscle regeneration in vivo

(2016) D. B. Gurevich et al.   SCIENCE

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

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Cellular dynamics underlying regeneration of appropriate segment number during axolotl tail regeneration

(2015) Carr D. Vincent et al.   BMC DEVELOPMENTAL BIOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Optimized axolotl (Ambystoma mexicanum) husbandry, breeding, metamorphosis, transgenesis and tamoxifen-mediated recombination

(2014) Shahryar Khattak et al.   Nature Protocols

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

(2014) Simone Picelli et al.   Nature Protocols

Germline Transgenic Methods for Tracking Cells and Testing Gene Function during Regeneration in the Axolotl

(2014) Shahryar Khattak et al.   Stem Cell Reports

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers

(2013) Gabriel Renaud et al.   BIOINFORMATICS

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

(2013) Y. Albert Pan et al.   DEVELOPMENT

Connective tissue cells, but not muscle cells, are involved in establishing the proximo-distal outcome of limb regeneration in the axolotl

(2013) E. Nacu et al.   DEVELOPMENT

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

(2013) Simone Picelli et al.   NATURE METHODS

Comparative Transcriptional Profiling of the Axolotl Limb Identifies a Tripartite Regeneration-Specific Gene Program

(2013) Dunja Knapp et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Limb Regeneration: A New Development?

(2011) Eugen Nacu et al.   Annual Review of Cell and Developmental Biology

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

Regulatory elements of Xenopus col2a1 drive cartilaginous gene expression in transgenic frogs

(2009) Ryan Kerney et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Cells keep a memory of their tissue origin during axolotl limb regeneration

(2009) Martin Kragl et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Comparative Aspects of Animal Regeneration

(2008) Jeremy P. Brockes et al.   Annual Review of Cell and Developmental Biology

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH