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Tag metagenomics [205 articles]

Recent papers classified by the tag metagenomics.
  • Microbial oceanography: paradigms, processes and promise
    Nature Reviews Microbiology, Vol. 5, No. 10., pp. 759-769.
    by David M Karl
    posted to metagenomics microorganism review by Yanno on 2007-09-18 09:16:26 as *** along with 1 person vrich
  • Metagenomic Analysis of the Human Distal Gut Microbiome
    Science, Vol. 312, No. 5778. (2 June 2006), pp. 1355-1359.
    by Steven R Gill, Mihai Pop, Robert T Deboy, Paul B Eckburg, Peter J Turnbaugh, Buck S Samuel, Jeffrey I Gordon, David A Relman, Claire M Fraser-Liggett, Karen E Nelson
  • Finding the Needles in the Metagenome Haystack
    Microbial Ecology
    by George A Kowalchuk, Arjen GCL Speksnijder, Kun Zhang, Robert M Goodman, Johannes A van Veen
    posted to metagenomics by Yanno on 2007-11-27 11:57:36 as ** along with 5 people dayjm jmeppley bluto wenhan niallhaslam
  • Metagenomic sorcery and the expanding protein universe
    Nature Biotechnology, Vol. 25, No. 5., pp. 540-542.
    by Eugene V Koonin
    posted to metagenomics reference by Yanno on 2007-05-30 17:24:13 as read
  • Outlook: Metagenomics and industrial applications
    Nature Reviews Microbiology, Vol. 3, No. 6. (01 June 2005), pp. 510-516.
    by Patrick Lorenz, Jurgen Eck
    posted to metagenomics by Yanno on 2007-11-22 09:37:48 as ***** along with 1 person bluto
  • Microbial sciences: The superficial life of microbes
    Nature, Vol. 441, No. 7091. (18 May 2006), pp. 300-302.
    by Roberto Kolter, Peter E Greenberg
  • GenomicsDiscovery in the dirt
    Nature, Vol. 439, No. 7075. (25 January 2006), pp. 384-386.
    by Virginia Gewin
    posted to metagenomics newsviews by Yanno on 2007-10-10 14:54:29 as read along with 1 person dayjm
  • Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
    Nat Methods (29 April 2007)
    by Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C C McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz, Nikos C C Kyrpides
  • Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e82.
    by Jonathan A Eisen
  • A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.
    Proc Natl Acad Sci U S A (13 July 2006)
    by Susanne M D M Goldberg, Justin Johnson, Dana Busam, Tamara Feldblyum, Steve Ferriera, Robert Friedman, Aaron Halpern, Hoda Khouri, Saul A A Kravitz, Federico M M Lauro, Kelvin Li, Yu-Hui H Rogers, Robert Strausberg, Granger Sutton, Luke Tallon, Torsten Thomas, Eli Venter, Marvin Frazier, J Craig C Venter
  • The marine viromes of four oceanic regions.
    PLoS Biol, Vol. 4, No. 11. (November 2006)
    by FE Angly, B Felts, M Breitbart, P Salamon, RA Edwards, C Carlson, AM Chan, M Haynes, S Kelley, H Liu, JM Mahaffy, JE Mueller, J Nulton, R Olson, R Parsons, S Rayhawk, CA Suttle, F Rohwer
  • Microbial diversity in the deep sea and the underexplored "rare biosphere"
    Proc Natl Acad Sci U S A (31 July 2006)
    by Mitchell L L Sogin, Hilary G G Morrison, Julie A A Huber, David Mark M Welch, Susan M M Huse, Phillip R R Neal, Jesus M M Arrieta, Gerhard J J Herndl
  • Using pyrosequencing to shed light on deep mine microbial ecology.
    BMC Genomics, Vol. 7 (2006)
  • Viral metagenomics
    Reviews in Medical Virology, Vol. 17, No. 2. (March 2007), pp. 115-131.
    posted to metagenomics review virology by xingxu on 2008-01-04 17:33:53 as ** along with 1 person bluto
  • Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project
    PLoS Genet, Vol. 4, No. 6. (13 June 2008), e1000095.
    by Yan Zhang, Vadim N Gladyshev
    posted to metagenomics marine by xingxu on 2008-06-26 05:06:50 as ** along with 1 person and 1 group djkt iSEEM
  • Putative novel photosynthetic reaction centre organizations in marine aerobic anoxygenic photosynthetic bacteria: insights from metagenomics and environmental genomics
    Environmental Microbiology, Vol. 7, No. 12. (December 2005), pp. 2027-2033.
    by Natalya Yutin, Oded Beja
  • Metagenomic Analysis of Coastal RNA Virus Communities
    Science, Vol. 312, No. 5781. (23 June 2006), pp. 1795-1798.
    by Alexander I Culley, Andrew S Lang, Curtis A Suttle
  • From the Cover: Microbial community gene expression in ocean surface waters
    Proceedings of the National Academy of Sciences, Vol. 105, No. 10. (11 March 2008), pp. 3805-3810.
    by Jorge Frias-Lopez, Yanmei Shi, Gene W Tyson, Maureen L Coleman, Stephan C Schuster, Sallie W Chisholm, Edward F Delong
  • Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
    Proceedings of the National Academy of Sciences (8 May 2008), 0711303105.
    by Annelie Pernthaler, Anne E Dekas, Titus C Brown, Shana K Goffredi, Tsegereda Embaye, Victoria J Orphan
  • Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell
    Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5555-5560.
    by Yuichi Hongoh, Vineet K Sharma, Tulika Prakash, Satoko Noda, Todd D Taylor, Toshiaki Kudo, Yoshiyuki Sakaki, Atsushi Toyoda, Masahira Hattori, Moriya Ohkuma
  • Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments
    Environmental Microbiology, Vol. 7, No. 7. (July 2005), pp. 1024-1028.
    by Juan M Gonzalez, Carmen C Portillo, Cesareo Saiz-Jimenez
  • Functional metagenomic profiling of nine biomes
    Nature (12 March 2008)
    by Elizabeth A Dinsdale, Robert A Edwards, Dana Hall, Florent Angly, Mya Breitbart, Jennifer M Brulc, Mike Furlan, Christelle Desnues, Matthew Haynes, Linlin Li, Lauren Mcdaniel, Mary A Moran, Karen E Nelson, Christina Nilsson, Robert Olson, John Paul, Beltran R Brito, Yijun Ruan, Brandon K Swan, Rick Stevens, David L Valentine, Rebecca V Thurber, Linda Wegley, Bryan A White, Forest Rohwer
  • Strainer: Software for analysis of population variation in community genomic datasets
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by John Eppley, Gene Tyson, Wayne Getz, Jillian Banfield
  • IMG/M: a data management and analysis system for metagenomes.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    posted to metagenomics by Thaverkamp on 2008-04-14 08:33:46 as *** along with 3 people alexl jyuh jmeppley
  • Genomics, environmental genomics and the issue of microbial species
    Heredity, Vol. aop, No. current.
    by DM Ward, FM Cohan, D Bhaya, JF Heidelberg, M Kühl, A Grossman
  • Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
    Science, Vol. 315, No. 5815. (23 February 2007), pp. 1126-1130.
    by C von Mering, P Hugenholtz, J Raes, SG Tringe, T Doerks, LJ Jensen, N Ward, P Bork
  • A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
    BMC Bioinformatics, Vol. 9 (23 January 2008), 34.
    by Patrick Schloss, Jo Handelsman
  • An analysis of the Sargasso Sea resource and the consequences for database composition.
    BMC Bioinformatics, Vol. 7 (2006)
  • CAMERA: A Community Resource for Metagenomics
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e75.
    by Rekha Seshadri, Saul A Kravitz, Larry Smarr, Paul Gilna, Marvin Frazier
  • The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
    PLoS Biology, Vol. 5, No. 3. (1 March 2007), e77.
    by Douglas B Rusch, Aaron L Halpern, Granger Sutton, Karla B Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A Eisen, Jeff M Hoffman, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freeman, Cynthia Andrews-Pfannkoch, Joseph E Venter, Kelvin Li, Saul Kravitz, John F Heidelberg, Terry Utterback, Yu-Hui Rogers, Luisa I Falcón, Valeria Souza, Germán Bonilla-Rosso, Luis E Eguiarte, David M Karl, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo-Castillo, Michael R Ferrari, Robert L Strausberg, Kenneth Nealson, Robert Friedman, Marvin Frazier, Craig J Venter
  • Assembly of Viral Metagenomes from Yellowstone Hot Springs
    Appl. Environ. Microbiol., Vol. 74, No. 13. (1 July 2008), pp. 4164-4174.
    by Thomas Schoenfeld, Melodee Patterson, Paul M Richardson, Eric K Wommack, Mark Young, David Mead
  • Gene prediction in metagenomic fragments: a large scale machine learning approach
    BMC Bioinformatics, Vol. 9 (28 April 2008), 217.
    by Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke
  • High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment.
    Microb Ecol (2 March 2007)
    by Todd Z Desantis, Eoin L Brodie, Jordan P Moberg, Ingrid X Zubieta, Yvette M Piceno, Gary L Andersen
    posted to metagenomics microarray microbes by srfairclough on 2007-03-08 03:41:23 as ****
  • notes An obesity-associated gut microbiome with increased capacity for energy harvest
    Nature, Vol. 444, No. 7122., pp. 1027-131.
    by Peter J Turnbaugh, Ruth E Ley, Michael A Mahowald, Vincent Magrini, Elaine R Mardis, Jeffrey I Gordon
  • The Airborne Metagenome in an Indoor Urban Environment
    PLoS ONE, Vol. 3, No. 4. (2 April 2008), e1862.
    by Susannah G Tringe, Tao Zhang, Xuguo Liu, Yiting Yu, Wah H Lee, Jennifer Yap, Fei Yao, Sim T Suan, Seah K Ing, Matthew Haynes, Forest Rohwer, Chia L Wei, Patrick Tan, James Bristow, Edward M Rubin, Yijun Ruan
    posted to metagenomics by semrich on 2008-06-21 23:08:34 as **** along with 1 person and 1 group djkt iSEEM
  • Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
    Nature Methods, Vol. 5, No. 3. (10 February 2008), pp. 235-237.
    by Micah Hamady, Jeffrey J Walker, Kirk J Harris, Nicholas J Gold, Rob Knight
  • Evaluating different approaches that test whether microbial communities have the same structure.
    The ISME journal, Vol. 2, No. 3. (March 2008), pp. 265-275.
    by PD Schloss
  • A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases
    N Engl J Med, Vol. 358, No. 10. (6 March 2008), pp. 991-998.
    by Gustavo Palacios, Julian Druce, Lei Du, Thomas Tran, Chris Birch, Thomas Briese, Sean Conlan, Phenix-Lan Quan, Jeffrey Hui, John Marshall, Jan F Simons, Michael Egholm, Christopher D Paddock, Wun-Ju Shieh, Cynthia S Goldsmith, Sherif R Zaki, Mike Catton, Ian W Lipkin
    posted to virus self metagenomics 454 by sconlan on 2008-07-03 20:42:57 as read along with 1 person oelemento
  • A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder.
    Science (6 September 2007)
    by Diana L L Cox-Foster, Sean Conlan, Edward C C Holmes, Gustavo Palacios, Jay D D Evans, Nancy A A Moran, Phenix-Lan L Quan, Thomas Briese, Mady Hornig, David M M Geiser, Vince Martinson, Dennis Vanengelsdorp, Abby L L Kalkstein, Andrew Drysdale, Jeffrey Hui, Junhui Zhai, Liwang Cui, Stephen K K Hutchison, Jan Fredrik F Simons, Michael Egholm, Jeffery S S Pettis, W Ian I Lipkin
  • A diversity profile of the human skin microbiota.
    Genome research (23 May 2008)
    by Elizabeth A A Grice, Heidi H H Kong, Gabriel Renaud, Alice C C Young, , Gerard G G Bouffard, Robert W W Blakesley, Tyra G G Wolfsberg, Maria L L Turner, Julia A A Segre
  • Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data
    Bioinformatics (9 June 2008), btn283.
    by Tiago J Sobreira, Arthur Gruber
  • Bioinformatic Insights from Metagenomics through Visualization.
    Proc IEEE Comput Syst Bioinform Conf, Vol. 4 (2005), pp. 341-350.
    by Susan L Havre, Bobbie-Jo J Webb-Robertson, Anuj Shah, Christian Posse, Banu Gopalan, Fred J Brockman
  • Comparative Metagenomics of Microbial Communities
    Science, Vol. 308, No. 5721. (22 April 2005), pp. 554-557.
    by Susannah G Tringe, Christian von Mering, Arthur Kobayashi, Asaf A Salamov, Kevin Chen, Hwai W Chang, Mircea Podar, Jay M Short, Eric J Mathur, John C Detter, Peer Bork, Philip Hugenholtz, Edward M Rubin
  • Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
    Nature Biotechnology, Vol. 24, No. 10. (24 September 2006), pp. 1263-1269.
    by Héctor G Martín, Natalia Ivanova, Victor Kunin, Falk Warnecke, Kerrie W Barry, Alice C Mchardy, Christine Yeates, Shaomei He, Asaf A Salamov, Ernest Szeto, Eileen Dalin, Nik H Putnam, Harris J Shapiro, Jasmyn L Pangilinan, Isidore Rigoutsos, Nikos C Kyrpides, Linda L Blackall, Katherine D Mcmahon, Philip Hugenholtz
    posted to metagenomics by rabu on 2006-12-08 20:38:29 as **** along with 3 people jmeppley azazello wenhan
  • Metagenomics: application of genomics to uncultured microorganisms.
    Microbiol Mol Biol Rev, Vol. 68, No. 4. (December 2004), pp. 669-685.
  • Mining enzymes from extreme environments.
    Curr Opin Microbiol, Vol. 10, No. 3. (June 2007), pp. 207-214.
    posted to biodiversity biotechnology enzymes metagenomics by operon on 2007-09-24 04:08:29 as ****
  • Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments
    Appl. Environ. Microbiol., Vol. 72, No. 5. (1 May 2006), pp. 3291-3301.
    by Carl B Abulencia, Denise L Wyborski, Joseph A Garcia, Mircea Podar, Wenqiong Chen, Sherman H Chang, Hwai W Chang, David Watson, Eoin L Brodie, Terry C Hazen, Martin Keller
  • Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities
    Appl. Environ. Microbiol., Vol. 73, No. 10. (15 May 2007), pp. 3205-3214.
    by Mircea Podar, Carl B Abulencia, Marion Walcher, Don Hutchison, Karsten Zengler, Joseph A Garcia, Trevin Holland, David Cotton, Loren Hauser, Martin Keller
  • Metagenomics reveals our incomplete knowledge of global diversity.
    Bioinformatics (Oxford, England) (13 July 2008)
    by Miguel Pignatelli, Gabriel Aparicio, Ignacio Blanquer, Vicente Hernández, Andrés Moya, Javier Tamames
    posted to metagenomics by nuin on 2008-07-30 19:05:41 as ** along with 1 person bootsy
  • Metaproteomic analysis of Chesapeake Bay microbial communities.
    Saline Systems, Vol. 1 (19 August 2005)
    by J Kan, TE Hanson, JM Ginter, K Wang, F Chen
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