Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

Evolutionary origin of gastrulation: insights from sponge development

(2014) Nagayasu Nakanishi et al.   BMC BIOLOGY

BLIND ordering of large-scale transcriptomic developmental timecourses

(2014) L. Anavy et al.   DEVELOPMENT

Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans

(2014) Sven Leininger et al.   Nature Communications

Characterization of differential transcript abundance through time during Nematostella vectensis development

(2013) Rebecca Helm et al.   BMC GENOMICS

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

(2013) Alex K. Shalek et al.   NATURE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

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

Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

Epithelia, an Evolutionary Novelty of Metazoans

(2011) Sally P. Leys et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

BioMart Central Portal: an open database network for the biological community

(2011) J. M. Guberman et al.   Database-The Journal of Biological Databases and Curation

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

(2010) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

(2009) Bernd Schierwater et al.   PLOS BIOLOGY

ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult

(2008) James D. McGhee et al.   DEVELOPMENTAL BIOLOGY

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

Automated analysis of embryonic gene expression with cellular resolution in C. elegans

(2008) John Isaac Murray et al.   NATURE METHODS