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The Genome of the Sea Urchin Strongylocentrotus purpuratus
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combinedExpand
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Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis.
Complete genome doubling has long-term consequences for the genome structure and the subsequent evolution of an organism. It has been suggested that two genome duplications occurred at the origin ofExpand
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Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention.
Animal genomes possess highly conserved cis-regulatory sequences that are often found near genes that regulate transcription and development. Researchers have proposed that the strong conservation ofExpand
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A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks
BackgroundThe genome of the sea urchin Strongylocentrotus purpuratus has recently been sequenced because it is a major model system for the study of gene regulatory networks. Embryonic expressionExpand
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Evolution of a Core Gene Network for Skeletogenesis in Chordates
The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are centralExpand
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New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes.
The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to theExpand
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Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement.
Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have importantExpand
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The amphioxus Hairy family: differential fate after duplication
Vertebrate Hairy genes are highly pleiotropic and have been implicated in numerous functions, such as somitogenesis, neurogenesis and endocrine tissue development. In order to gain insight into theExpand
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The globin gene family of the cephalochordate amphioxus: implications for chordate globin evolution
BackgroundThe lancelet amphioxus (Cephalochordata) is a close relative of vertebrates and thus may enhance our understanding of vertebrate gene and genome evolution. In this context, the globins areExpand
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Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network
TLDR
We developed a heuristic to assess the completeness of large GRNs, using ODE simulations under different conditions and randomly sampled parameter sets to detect parameter-invariant effects. Expand
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