Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Orthogonal muscle fibres have different instructive roles in planarian regeneration

(2017) M. Lucila Scimone et al.   NATURE

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

(2017) Kirsten L. Frieda et al.   NATURE

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

(2017) Abbas H Rizvi et al.   NATURE BIOTECHNOLOGY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

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

(2016) Dominic Grün et al.   Cell Stem Cell

Single-cell states versus single-cell atlases — two classes of heterogeneity that differ in meaning and method

(2016) Kevin A Janes   CURRENT OPINION IN BIOTECHNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan 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

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

(2016) Jinmiao Chen et al.   Nature Communications

Hedgehog signaling regulates gene expression in planarian glia

(2016) Irving E Wang et al.   eLife

A functional genomics screen in planarians reveals regulators of whole-brain regeneration

(2016) Rachel H Roberts-Galbraith et al.   eLife

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians

(2016) Jordi Solana et al.   eLife

Light-induced depigmentation in planarians models the pathophysiology of acute porphyrias

(2016) Bradford M Stubenhaus et al.   eLife

Forkhead containing transcription factor Albino controls tetrapyrrole-based body pigmentation in planarian

(2016) Chen Wang et al.   Cell Discovery

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 Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians

(2015) Omri Wurtzel et al.   DEVELOPMENTAL CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

PlanMine – a mineable resource of planarian biology and biodiversity

(2015) Holger Brandl et al.   NUCLEIC ACIDS RESEARCH

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

(2015) F. Notta et al.   SCIENCE

Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment

(2014) Josien C. van Wolfswinkel et al.   Cell Stem Cell

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein 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

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

COE Loss-of-Function Analysis Reveals a Genetic Program Underlying Maintenance and Regeneration of the Nervous System in Planarians

(2014) Martis W. Cowles et al.   PLoS Genetics

The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation

(2013) Jordi Solana et al.   PLoS Genetics

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells

(2012) Pinar Önal et al.   EMBO JOURNAL

A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

(2012) Roselyne M. Labbé et al.   STEM CELLS

Transcriptome Analysis of the Planarian Eye Identifies ovo as a Specific Regulator of Eye Regeneration

(2012) Sylvain W. Lapan et al.   Cell Reports

Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach

(2012) Jordi Solana et al.   GENOME BIOLOGY

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

The maintenance and regeneration of the planarian excretory system are regulated by EGFR signaling

(2011) J. C. Rink et al.   DEVELOPMENT

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Clonogenic Neoblasts Are Pluripotent Adult Stem Cells That Underlie Planarian Regeneration

(2011) D. E. Wagner et al.   SCIENCE

Planarian regeneration involves distinct stem cell responses to wounds and tissue absence

(2010) Danielle Wenemoser et al.   DEVELOPMENTAL BIOLOGY

Genome-Wide Analyses Reveal a Role for Peptide Hormones in Planarian Germline Development

(2010) James J. Collins et al.   PLOS BIOLOGY

Molecular Analysis of Stem Cells and Their Descendants during Cell Turnover and Regeneration in the Planarian Schmidtea mediterranea

(2008) George T. Eisenhoffer et al.   Cell Stem Cell

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT