@article {1899,
	title = {PlanMine 3.0{\textemdash}improvements to a mineable resource of flatworm biology and biodiversity},
	journal = {Nucleic Acids Researchnar},
	volume = {47},
	year = {2018},
	month = {2018},
	pages = {D812 - D820},
	abstract = {Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine (http://planmine.mpi-cbg.de/) has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective. Building on the recent availability of a high quality genome assembly of the planarian model species Schmidtea mediterranea, we provide a gene prediction set that now assign existing transcripts to defined genomic coordinates. The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information. Further, we add transcriptomes from a broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary species comparisons accessible to non-experts. At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons. Overall, PlanMine 3.0 thus provides a host of new features that makes the fascinating biology of flatworms accessible to the wider research community.},
	isbn = {0305-1048},
	url = {https://doi.org/10.1093/nar/gky1070},
	author = {Rozanski, Andrei and Brandl, Holger and Moon, HongKee and Grohme, Markus A and Henry, Ian and Rink, Jochen C and Martin-Duran, Jose M and H{\"u}ttner, Katja and Bartscherer, Kerstin}
}
@article {21194483,
	title = {Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea},
	journal = {BMC Genomics},
	volume = {11},
	number = {1},
	year = {2010},
	pages = {731},
	abstract = {BACKGROUND:Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system.RESULTS:In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function.CONCLUSIONS:We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-11-731},
	url = {http://www.biomedcentral.com/1471-2164/11/731},
	author = {Abril, Josep and Cebria, Francesc and Rodriguez-Esteban, Gustavo and Horn, Thomas and Fraguas, Susanna and Calvo, Beatriz and Bartscherer, Kerstin and Salo, Emili}
}
