@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 {1542,
	title = {PlanMine {\textendash} a mineable resource of planarian biology and biodiversity},
	journal = {Nucleic Acids Research},
	volume = {44},
	year = {2016},
	month = {2016/01/04},
	pages = {D764 - D773},
	publisher = {Oxford University Press},
	abstract = {<p>Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history traits. PlanMine (http://planmine.mpi-cbg.de/) aims to accomplish two primary missions: First, to provide an easily accessible platform for sharing, comparing and value-added mining of planarian sequence data. Second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. Currently, PlanMine houses transcriptomes independently assembled by our lab and community contributors. Detailed assembly/annotation statistics, a custom-developed BLAST viewer and easy export options enable comparisons at the contig and assembly level. Consistent annotation of all transcriptomes by an automated pipeline, the integration of published gene expression information and inter-relational query tools provide opportunities for mining planarian gene sequences and functions. For inter-species comparisons, we include transcriptomes of, so far, six planarian species, along with images, expert-curated information on their biology and pre-calculated cross-species sequence homologies. PlanMine is based on the popular InterMine system in order to make the rich biology of planarians accessible to the general life sciences research community.</p>
},
	isbn = {0305-10481362-4962},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702831/},
	author = {Brandl, Holger and Moon, HongKee and Vila-Farr{\'e}, Miquel and Liu, Shang-Yun and Henry, Ian and Rink, Jochen C}
}
