Browsing by Author "Zhang, F."

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    PATRIC: The VBI PathoSystems Resource Integration Center
    Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, Maulik; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, Joseph L.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, Stephen M.; Khudyakov, Y.; Meng, Xiang-Jin; Rupprecht, C.; Vinje, J.; Crasta, Oswald R.; Czar, M. J.; Dickerman, Allan W.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, Joao C.; Sobral, Bruno (2007-01)
    The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: 'breadth first' beginning with whole-genome and proteome curation using standardized protocols, a 'targeted' approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website (https://patric.vbi.vt.edu) will continually grow with the addition of data, analysis and functionality over the course of the project.
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    Recent advances in understanding the terminal Ediacaran Earth-life system in South China and Arctic Siberia
    Cui, H.; Kaufman, Alan J.; Xiao, S.; Grazhdankin, D. V.; Peek, S.; Martin, A. J.; Bykova, N. V.; Rogov, V. I.; Liu, X. M.; Zhang, F.; Romaniello, S. J.; Anbar, A. D.; Peng, Y.; Cai, Y.; Schiffbauer, J. D.; Meyer, M.; Gilleaudeau, Geoffrey J.; Plummer, Rebecca E.; Sievers, N. E.; Goderis, S.; Claeys, P. (2019-11-22)
    The terminal Ediacaran contains dramatic changes in biogeochemical cycles, many of which are closely coupled with evolutionary transitions in the corresponding fossil records. Dynamic redox conditions may have caused a profound impact on early animal evolution. Our work highlights the significance of integrated bio-, litho-, and chemo-stratigraphy in geobiology research of the deep time.
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    A vanished history of skeletonization in Cambrian comb jellies
    Ou, Q.; Xiao, S.; Han, J.; Sun, G.; Zhang, F.; Zhang, Z.; Shu, D. (2015-07)
    Ctenophores are traditionally regarded as "lower" metazoans, sharing with cnidarians a diploblastic grade of organization. Unlike cnidarians, where skeletonization (biomineralization and sclerotization) evolved repeatedly among ecologically important taxa (for example, scleractinians and octocorals), living ctenophores are characteristically soft-bodied animals. We report six sclerotized and armored ctenophores from the early Cambrian period. They have diagnostic ctenophore features (for example, an octamerous symmetry, oral-aboral axis, aboral sense organ, and octaradially arranged ctene rows). Unlike most modern counterparts, however, they lack tentacles, have a sclerotized framework, and have eight pairs of ctene rows. They are resolved as a monophyletic group (Scleroctenophora new class) within the ctenophores. This clade reveals a cryptic history and sheds new light on the early evolution of this basal animal phylum. Skeletonization also occurs in some other Cambrian animal groups whose extant members are exclusively soft-bodied, suggesting the ecological importance of skeletonization in the Cambrian explosion.