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2005
Li, S., Dai, M., He, X., Zhang, Y., Ruan, J., Burt, D., Yu, J., Wang, J., Yang, H., Hu, Y., Liu, B., Wong, G., Ye, C., Chen, J., Cong, L., Fang, L.
Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling...
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Freshwater Sponges Have Functional, Sealing Epithelia with High Transepithelial Resistance and Negative Transepithelial Potential
Download2010
Leys, S.P., Goss, G.G., Adams, E.D.M.
Epithelial tissue — the sealed and polarized layer of cells that regulates transport of ions and solutes between the environment and the internal milieu — is a defining characteristic of the Eumetazoa. Sponges, the most ancient metazoan phylum [1], [2], are generally believed to lack true...
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2007
Wang, W., Wang, H., Wong, G.K.S., Zheng, H., Clark, T., Zhang, G., Kang, L., Wang, J., Shi, J., Wang, X.
Background Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade depends on specific components in its proteome that give rise to specialized...
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PolySearch: A web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Download2008
Stothard, P., Damaraju, S., Wishart, D.S., Young, N., Cheng, D., Knox, C.
A particular challenge in biomedical text mining is to find ways of handling ‘comprehensive’ or ‘associative’ queries such as ‘Find all genes associated with breast cancer’. Given that many queries in genomics, proteomics or metabolomics involve these kind of comprehensive searches we believe...
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ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
Download2005
Ye, C., Wang, J., Li, S., Li, R., Wong, G.K.S., Ye, J., Yang, H., Han, Y., Yu, J.
We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer...
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2005
Xia, Q., Chen, J., Dai, M., Ye, C., Wang, J., Li, S., Li, R., Zhou, Z., Ruan, J., Hu, Y., Yu, G., Yang, H., He, X., Yu, Jun, Xiang, Z., Yuan, H., Lu, C., Feng, T.
The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ~6X draft genome sequence of the domestic silkworm (Bombyx mori ), SilkDB provides an integrated representation of the...
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The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: Evidence for programmed translational frameshifting
Download2008
Rosengarten, R.D., Sperling, E.A., Leys, S.P., Dellaporta, S.L., Moreno, M.A.
Background: Mitochondrial genomes (mtDNA) of numerous sponges have been sequenced as part of an ongoing effort to resolve the class-level phylogeny of the Porifera, as well as to place the various lower metazoan groups on the animal-kingdom tree. Most recently, the partial mtDNA of two glass...
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2006
Li, R., Zheng, W., Durbin, R., Liu, T., Bolund, L., Dehal, P., Coin, L.J., Coghlan, A., Osmotherly, L., Heriche, J.K., Ruan, J., Li, H., Wang, J., Wong, G., Zhang, Z.
TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively,...