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We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most(More)
BACKGROUND The evolution of complex sub-cellular structures such as the synapse requires the assembly of multiple proteins, each conferring added functionality to the integrated structure. Tracking the early evolution of synapses has not been possible without genomic information from the earliest branching animals. As the closest extant relatives to the(More)
High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions-particularly those expressed with low abundance- is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping(More)
MOTIVATION Gene duplications and losses (GDLs) are important events in genome evolution. They result in expansion or contraction of gene families, with a likely role in phenotypic evolution. As more genomes become available and their annotations are improved, software programs capable of rapidly and accurately identifying the content of ancestral genomes(More)
PDZ domains are protein-protein interaction modules widely used to assemble membranous signaling complexes including those found in the neuronal synapse. PDZ-containing genes encoded in metazoan genomes vastly outnumber those in prokaryotes, plants, and fungi. By comparing 40 proteomes to track the evolutionary history of the PDZ domain, we observed that(More)
Ion channels establish and regulate membrane potentials in excitable and non-excitable cells. How functional diversification of ion channels contributed to the evolution of nervous systems may be understood by studying organisms at key positions in the evolution of animal multicellularity. We have carried out the first analysis of ion channels cloned from a(More)
Microarray technology provides cell-scale expression data, however , analyzing this data is notoriously difficult. It is becoming clear that system-oriented methods are needed in order to best interpret this data. Combining microarray expression data with previously built pathway models may provide useful insight about the cellular machinery and reveal(More)
Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are(More)
  • Santa Barbara, Ali Umut Irturk, Ryan Kastner, Ronald A Iltis, Li-C Wang, Firat Kart +5 others
  • 2007
iv ACKNOWLEDGEMENTS It is a pleasure to thank everybody who made this thesis possible. It is difficult to overstate my gratitude to my advisor, Professor Ryan Kastner. With his inspiration, enthusiasm, and great efforts to explain things simply and clearly, he helped to make computer architecture fun for me. I also thank to Professor Ronald Iltis and(More)
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