Spatial reconstruction of single-cell gene expression data

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Statistical significance of variables driving systematic variation in high-dimensional data

(2014) Neo Christopher Chung et al.   BIOINFORMATICS

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution

(2014) Robert Durruthy-Durruthy et al.   CELL

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

(2014) Barbara Treutlein et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

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

(2014) D. A. Jaitin et al.   SCIENCE

Genomics: Zebrafish earns its stripes

(2013) Alexander F. Schier   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Full Transcriptome Analysis of Early Dorsoventral Patterning in Zebrafish

(2013) Erika Fodor et al.   PLoS One

Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression

(2013) Peter A. Combs et al.   PLoS One

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

(2012) Andrew McDavid et al.   BIOINFORMATICS

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

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

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

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Gastrulation: Making and Shaping Germ Layers

(2011) Lila Solnica-Krezel et al.   Annual Review of Cell and Developmental Biology

Breaking symmetry: The zebrafish as a model for understanding left-right asymmetry in the developing brain

(2011) Myriam Roussigné et al.   Developmental Neurobiology

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE