A RESTful API for accessing microbial community data for MG-RAST.

Autor: Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M Glass, Narayan Desai, Folker Meyer

Publikováno v: PLoS Computational Biology, Vol 11, Iss 1, p e1004008 (2015)

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adopt

Externí odkaz: https://doaj.org/article/46e0a4e84f954269980eda5df0a06231

KBase: The United States Department of Energy Systems Biology Knowledgebase

Autor: Shinjae Yoo, Matthew L. Henderson, Sarah S. Poon, Pavel S. Novichkov, Mark Mills, Roy T. Kamimura, Adam P. Arkin, Rick Stevens, Holly L. Haun, Shinnosuke Kondo, Meghan M Drake, Aaron A. Best, José P. Faria, Fernando Perez, Matthew DeJongh, Gang Fang, Thomas Brettin, Sergei Maslov, Janaka N. Edirisinghe, Folker Meyer, Jer Ming Chia, Scott Devoid, Doreen Ware, Steven E. Brenner, Paul M. Frybarger, Miriam Land, Dan Gunter, Fei He, John-Marc Chandonia, Hyunseung Yoo, Marcin P. Joachimiak, Dantong Yu, Christopher S. Henry, Mark Gerstein, Christopher Bun, Michael W. Sneddon, Samuel M. D. Seaver, Rashmi Jain, Stephen Y. Chan, Robert W. Cottingham, James J. Davis, Annette Greiner, Inna Dubchak, Vivek Kumar, Priya Ranjan, Daifeng Wang, Neal Conrad, James Thomason, Fangfang Xia, Maulik Shukla, Gavin Price, Nathan L. Tintle, Gary J. Olsen, Shiran Pasternak, Shane Canon, Roman A. Sutormin, William J. Riehl, Nomi L. Harris, Dan Murphy-Olson, Jason K. Baumohl, Wolfgang Gerlach, Benjamin H. Allen, Pamela C. Ronald, Michael C. Schatz, Mustafa H Syed, Brian H. Davison, Taeyun Oh, Dylan Chivian, Elizabeth M. Glass, R. L. Colasanti, Erik Pearson, David J. Weston, Sunita Kumari, Kevin P. Keegan, Emily M. Dietrich, Robert Olson, Srividya Ramakrishnan, James Gurtowski, Benjamin P. Bowen, Paramvir S. Dehal, Bruce Parrello

Publikováno v: Nature biotechnology, vol 36, iss 7
Nature Biotechnology
Arkin, AP; Cottingham, RW; Henry, CS; Harris, NL; Stevens, RL; Maslov, S; et al.(2018). KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7), 566-569. doi: 10.1038/nbt.4163. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/7p39r37f

Author(s): Arkin, Adam P; Cottingham, Robert W; Henry, Christopher S; Harris, Nomi L; Stevens, Rick L; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W; Henderson, Matthew L; Riehl, William J; Murphy-Ol

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c789b3716f923398ce5518911fb65ab7
https://doi.org/10.1038/nbt.4163

The complete genome sequence for putative H2- and S-oxidizerCandidatusSulfuricurvum sp., assembledde novofrom an aquifer-derived metagenome

Autor: Jack A. Gilbert, Edward J. O'Loughlin, William L. Trimble, Kelly A. Skinner, Dionysios A. Antonopoulos, Andreas Wilke, Tobias Paczian, Kim M. Handley, Kenneth H. Williams, Kenneth M. Kemner, Narayan Desai, Folker Meyer, Daniela Bartels, Elizabeth M. Glass

Publikováno v: Environmental Microbiology. 16:3443-3462

Summary We reconstructed the complete 2.4 Mb-long genome of a previously uncultivated epsilonproteobacterium, Candidatus Sulfuricurvum sp. RIFRC-1, via assembly of short-read shotgun metagenomic data using a complexity reduction approach. Genome-base

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::dff4a8fdd47853c50d3e0dd338d105b5
https://doi.org/10.1111/1462-2920.12453

Metagenomic Design and Sequencing

Autor: Elizabeth M. Glass, William L. Trimble, Sarah M. Owens, Folker Meyer, Stephanie M. Greenwald

Publikováno v: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing ISBN: 9783319313481

Metagenomics, shotgun metagenomics in particular, is a field that has disproportionately benefited from advances in high-throughput sequencing technologies. This chapter discusses the choice of sample number, depth, and sequencing technology, the she

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::7a5468ec36149f65adc9677f52dd6f85
https://doi.org/10.1007/978-3-319-31350-4_12

The DOE Systems Biology Knowledgebase (KBase)

Autor: Seaver Smd, Erik Pearson, José P. Faria, Gary J. Olsen, Olson B, Sarah S. Poon, Jason K. Baumohl, Christopher Bun, Emily M. Dietrich, Pamela C. Ronald, Nathan L. Tintle, Fei He, Paramvir S. Dehal, Marcin P. Joachimiak, Benjamin H. Allen, Thomas Brettin, Benjamin P. Bowen, Folker Meyer, Steven E. Brenner, Holly L. Haun, Shinjae Yoo, Fernando Perez, Matthew DeJongh, R. L. Colasanti, Maulik Shukla, Wolfgang Gerlach, Kevin P. Keegan, Jer Ming Chia, Michael C. Schatz, Taeyun Oh, Dylan Chivian, James Thomason, Sergei Maslov, Roman A. Sutormin, John-Marc Chandonia, Nomi L. Harris, Dan Murphy-Olson, James J. Davis, Hyunseung Yoo, Matthew L. Henderson, Roy T. Kamimura, Shane Canon, Michael W. Sneddon, Christopher S. Henry, Stephen Y. Chan, Pavel S. Novichkov, Inna Dubchak, Mark Mills, Adam P. Arkin, Neal Conrad, Fangfang Xia, Gang Fang, Scott Devoid, Janaka N. Edirisinghe, Brian H. Davison, Bruce Parrello, Shinnosuke Kondo, William J. Riehl, Paul M. Frybarger, Doreen Ware, Miriam Land, Dan Gunter, Rashmi Jain, Rick Stevens, Meghan M Drake, Gavin Price, Shiran Pasternak, Mustafa H Syed, Mark Gerstein, David J. Weston, Sunita Kumari, Kumar, Robert W. Cottingham, Elizabeth M. Glass, James Gurtowski, Aaron A. Best, Daifeng Wang, Srividya Ramakrishnan, Priya Ranjan

The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small sca

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a42f71091420946234b6e35b826e316f
https://escholarship.org/uc/item/4058b7v5