Gene expression across mammalian organ development

M Cardoso-Moreira, J Halbert, D Valloton, B Velten… - Nature, 2019 - nature.com
The evolution of gene expression in mammalian organ development remains largely
uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum …

De novo prediction of stem cell identity using single-cell transcriptome data

D Grün, MJ Muraro, JC Boisset, K Wiebrands… - Cell stem cell, 2016 - cell.com
Adult mitotic tissues like the intestine, skin, and blood undergo constant turnover throughout
the life of an organism. Knowing the identity of the stem cell is crucial to understanding …

The mid-developmental transition and the evolution of animal body plans

M Levin, L Anavy, AG Cole, E Winter, N Mostov, S Khair… - Nature, 2016 - nature.com
Animals are grouped into~ 35 'phyla'based upon the notion of distinct body plans,,,.
Morphological and molecular analyses have revealed that a stage in the middle of …

What to compare and how: comparative transcriptomics for evo‐devo

J Roux, M Rosikiewicz… - Journal of Experimental …, 2015 - Wiley Online Library
Evolutionary developmental biology has grown historically from the capacity to relate
patterns of evolution in anatomy to patterns of evolution of expression of specific genes …

Entropy as a measure of variability and stemness in single-cell transcriptomics

O Gandrillon, M Gaillard, T Espinasse… - Current Opinion in …, 2021 - Elsevier
Entropy as a measure of variability and stemness in single-cell transcriptomics -
ScienceDirect Skip to main contentSkip to article Elsevier logo Journals & Books Search …

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer

T Hashimshony, M Feder, M Levin, BK Hall, I Yanai - Nature, 2015 - nature.com
The concept of germ layers has been one of the foremost organizing principles in
developmental biology, classification, systematics and evolution for 150 years (refs,,). Of the …

Real age prediction from the transcriptome with RAPToR

R Bulteau, M Francesconi - Nature Methods, 2022 - nature.com
Transcriptomic data is often affected by uncontrolled variation among samples that can
obscure and confound the effects of interest. This variation is frequently due to unintended …

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica

SL Fernandez-Valverde, AD Calcino, BM Degnan - BMC genomics, 2015 - Springer
Abstract Background The demosponge Amphimedon queenslandica is amongst the few
early-branching metazoans with an assembled and annotated draft genome, making it an …

Draft Genomes Shed Light on the Dual Bacterial Symbiosis that Dominates the Microbiome of the Coral Reef Sponge Amphimedon queenslandica

MEA Gauthier, JR Watson, SM Degnan - Frontiers in Marine Science, 2016 - frontiersin.org
Amphimedon queenslandica is a coral reef demosponge that houses a low complexity and
low abundance microbiota dominated by a proteobacterial duo for which draft genomes are …

Ontogenetic Changes in the Bacterial Symbiont Community of the Tropical Demosponge Amphimedon queenslandica: Metamorphosis Is a New Beginning

RA Fieth, MEA Gauthier, J Bayes, KM Green… - Frontiers in Marine …, 2016 - frontiersin.org
Vertical transmission of bacterial symbionts, which is known in many species of sponge
(Porifera), is expected to promote strong fidelity between the partners. Combining 16S rRNA …