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

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

(2019) Adam D. Warner et al.   GENOME RESEARCH

A single-cell transcriptional roadmap for cardiopharyngeal fate diversification

(2019) Wei Wang et al.   NATURE CELL BIOLOGY

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

(2018) Arnau Sebé-Pedrós et al.   CELL

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

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

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

(2018) Daniel E. Wagner et al.   SCIENCE

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns

(2018) Annabel Ebbing et al.   DEVELOPMENTAL CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

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

A Transcriptional Lineage of the Early C. elegans Embryo

(2016) Sophia C. Tintori et al.   DEVELOPMENTAL CELL

The time-resolved transcriptome ofC. elegans

(2016) Max E. Boeck et al.   GENOME RESEARCH

A map of terminal regulators of neuronal identity in Caenorhabditis elegans

(2016) Oliver Hobert   Wiley Interdisciplinary Reviews-Developmental Biology

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Single cell dissection of early kidney development: multilineage priming

(2014) E. W. Brunskill et al.   DEVELOPMENT

Extensive Oscillatory Gene Expression during C. elegans Larval Development

(2014) Gert-Jan Hendriks et al.   MOLECULAR CELL

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

(2014) Tamar Hashimshony et al.   NATURE

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

(2013) Danni Yu et al.   BIOINFORMATICS

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

(2012) Mihail Sarov et al.   CELL

The Nkx5/HMX homeodomain protein MLS-2 is required for proper tube cell shape in the C. elegans excretory system

(2012) Ishmail Abdus-Saboor et al.   DEVELOPMENTAL BIOLOGY

A quantitative model of normal Caenorhabditis elegans embryogenesis and its disruption after stress

(2012) Julia L. Richards et al.   DEVELOPMENTAL BIOLOGY

Multidimensional regulation of gene expression in the C. elegans embryo

(2012) J. I. Murray et al.   GENOME RESEARCH

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

(2012) Tamar Hashimshony et al.   Cell Reports

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein

(2011) M. Harterink et al.   DEVELOPMENT

The homeodomain protein hmbx-1 maintains asymmetric gene expression in adult C. elegans olfactory neurons

(2010) B. J. Lesch et al.   GENES & DEVELOPMENT

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

Six and Eya promote apoptosis through direct transcriptional activation of the proapoptotic BH3-only gene egl-1 in Caenorhabditis elegans

(2010) T. Hirose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The NK-2 class homeodomain factor CEH-51 and the T-box factor TBX-35 have overlapping function in C. elegans mesoderm development

(2009) G. Broitman-Maduro et al.   DEVELOPMENT

Fast unfolding of communities in large networks

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