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We have developed a portable and easily configurable genome annotation pipeline called MAKER. Its purpose is to allow investigators to independently annotate eukaryotic genomes and create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions, and automatically synthesizes these data into gene(More)
The planarian Schmidtea mediterranea is rapidly emerging as a model organism for the study of regeneration, tissue homeostasis and stem cell biology. The recent sequencing, assembly and annotation of its genome are expected to further buoy the biomedical importance of this organism. In order to make the extensive data associated with the genome sequence(More)
Platyhelminthes are excellent models for the study of stem cell biology, regeneration and the regulation of scale and proportion. In addition, parasitic forms infect millions of people worldwide. Therefore, it is puzzling that they remain relatively unexplored at the molecular level. We present the characterization of approximately 3,000 non-redundant cDNAs(More)
In recent years, interest in planarians as a model system for the study of metazoan regeneration, adult stem cell biology, and the evolution of metazoan body plans has been growing steadily. The availability of RNA interference (RNAi), BrdU-labeling of planarian stem cells, and thousands of planarian cDNA sequences soon to be released into public databases(More)
Planarians have emerged as excellent models for the study of key biological processes such as stem cell function and regulation, axial polarity specification, regeneration, and tissue homeostasis among others. The most widely used organism for these studies is the free-living flatworm Schmidtea mediterranea. In 2007, the Schmidtea mediterranea Genome(More)
Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that(More)
The freshwater planarian Schmidtea mediterranea has emerged as a powerful model system for studying regeneration and adult stem cell (ASC) biology. This is largely due to the developmental plasticity of these organisms and the abundant distribution and experimental accessibility of their ASCs. Techniques such as whole mount in situ hybridization,(More)
Planarian neoblasts are pluripotent, adult somatic stem cells and lineage-primed progenitors that are required for the production and maintenance of all differentiated cell types, including the germline. Neoblasts, originally defined as undifferentiated cells residing in the adult parenchyma, are frequently compared to embryonic stem cells yet their(More)
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