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Group: microbiology_nijmegen - library [471 articles]

Recent papers posted by members of the microbiology_nijmegen group
  • Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2 — PNAS
    Proceedings of the National Academy of Sciences of the USA, Vol. 105, No. 28. (July 2008), pp. 10203-10208.
    by Mohamed Baani, Werner Liesack
    posted to pmmo monooxygenase methylotrophy methanotrophy methane biochemistry by Katje to the group microbiology_nijmegen on 2008-07-17 12:11:18 as **
  • Stable carbon isotope fractionation between substrates and products of Methanosarcina barkeri
    Organic Geochemistry, Vol. 39, No. 5. (May 2008), pp. 608-621.
    by Kathleen L Londry, Kathleen G Dawson, Heather D Grover, Roger E Summons, Alexander S Bradley
    posted to stable_isotopes methylotrophy methanotrophy methanogenesis by Katje to the group microbiology_nijmegen on 2008-07-15 18:48:30 as read
  • Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification
    Mol Biol Evol (8 July 2008), msn146.
    by Christopher M Jones, Blaz Stres, Magnus Rosenquist, Sara Hallin
    posted to horizontal_gene_transfer evolution denitrification by Katje to the group microbiology_nijmegen on 2008-07-14 09:27:38 as **
  • Formate as the Main Branch Point for Methylotrophic Metabolism in Methylobacterium extorquens AM1
    J. Bacteriol., Vol. 190, No. 14. (15 July 2008), pp. 5057-5062.
    by Gregory J Crowther, George Kosaly, Mary E Lidstrom
    posted to methylotroph biochemistry by kinestetika to the group microbiology_nijmegen on 2008-07-13 20:16:24 as **
  • Preferential Use of an Anode as an Electron Acceptor by an Acidophilic Bacterium in the Presence of Oxygen
    Appl. Environ. Microbiol., Vol. 74, No. 14. (15 July 2008), pp. 4472-4476.
    by Moustafa Malki, Antonio L De Lacey, Nuria Rodriguez, Ricardo Amils, Victor M Fernandez
    posted to microbial_fuel_cells by kinestetika to the group microbiology_nijmegen on 2008-07-13 20:10:55 as **
  • Genetic Determinants of Self Identity and Social Recognition in Bacteria
    Science, Vol. 321, No. 5886. (11 July 2008), pp. 256-259.
    by Karine A Gibbs, Mark L Urbanowski, Peter E Greenberg
    posted to eco_micro by kinestetika to the group microbiology_nijmegen on 2008-07-13 20:07:43 as ** along with 1 person stevanspringer
  • Calling on a million minds for community annotation in WikiProteins
    Genome Biology, Vol. 9, No. 5. (2008)
    by Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert J van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch
    posted to proteomics proteome genome annotation by Katje to the group microbiology_nijmegen on 2008-07-03 13:26:38 as ** along with 12 people ChrisEvelo sjc fpattyn jamselem chad_davis yas renatomilani dullhunk tharris thomaskelder AlexanderPico neils
  • notes Reactive Oxygen Species Special Feature: Oxygen-regulated isoforms of cytochrome c oxidase have differential effects on its nitric oxide production and on hypoxic signaling
    Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8203-8208.
    by Pablo R Castello, Dong K Woo, Kerri Ball, Jay Wojcik, Laura Liu, Robert O Poyton
    posted to nitric denitrification cytochrome cytc biochemistry anaerobic by Katje to the group microbiology_nijmegen on 2008-06-18 10:01:34 as **
  • Selectivity of bacterial proteome fractionation based on differential solubility: A mass spectrometry evaluation
    Analytical Biochemistry, Vol. 377, No. 2. (15 June 2008), pp. 134-140.
    by Yassel Ramos, Yairet García, Alexey Llopiz, Lila Castellanos-Serra
    posted to no-tag by Huub_odc to the group microbiology_nijmegen on 2008-06-13 08:02:44 as **
  • Characterization and expression analysis of the cytochrome bd oxidase operon from Desulfovibrio gigas.
    Current microbiology, Vol. 52, No. 4. (April 2006), pp. 274-281.
    by P Machado, R Félix, R Rodrigues, S Oliveira, C Rodrigues-Pousada
    posted to rt-pcr oxygen oxide nitroc by mjetten to the group microbiology_nijmegen on 2008-06-03 19:23:05 as **
  • Desulfovibrio gigas flavodiiron protein affords protection against nitrosative stress in vivo.
    Journal of bacteriology, Vol. 188, No. 8. (April 2006), pp. 2745-2751.
    by R Rodrigues, JB Vicente, R Félix, S Oliveira, M Teixeira, C Rodrigues-Pousada
    posted to stress oxygen oxide nitrosative nitric flavoprotein by mjetten to the group microbiology_nijmegen on 2008-06-03 19:21:40 as ** along with 1 group anammox
  • Cholest-4-en-3-one-delta 1-dehydrogenase, a flavoprotein catalyzing the second step in anoxic cholesterol metabolism.
    Applied and environmental microbiology, Vol. 74, No. 1. (January 2008), pp. 107-113.
    by YR Chiang, W Ismail, S Gallien, D Heintz, A Van Dorsselaer, G Fuchs
    posted to sterol denitrification by mjetten to the group microbiology_nijmegen on 2008-06-03 19:19:53 as **
  • Study of anoxic and oxic cholesterol metabolism by Sterolibacterium denitrificans.
    Journal of bacteriology, Vol. 190, No. 3. (February 2008), pp. 905-914.
    by YR Chiang, W Ismail, D Heintz, C Schaeffer, A Van Dorsselaer, G Fuchs
    posted to sterol pathway oxygen denitrification by mjetten to the group microbiology_nijmegen on 2008-06-03 19:19:11 as **
  • Initial steps in the anoxic metabolism of cholesterol by the denitrifying Sterolibacterium denitrificans.
    The Journal of biological chemistry, Vol. 282, No. 18. (4 May 2007), pp. 13240-13249.
    by YR Chiang, W Ismail, M Müller, G Fuchs
    posted to oxygen n-damo denitrification by mjetten to the group microbiology_nijmegen on 2008-06-03 19:18:12 as **
  • Structure of the monooxygenase component of a two-component flavoprotein monooxygenase.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 4. (23 January 2007), pp. 1177-1182.
    by A Alfieri, F Fersini, N Ruangchan, M Prongjit, P Chaiyen, A Mattevi
    posted to peroxy oxygenase n-damo flavoprotein by mjetten to the group microbiology_nijmegen on 2008-06-03 19:16:49 as **
  • Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase.
    Journal of molecular biology, Vol. 376, No. 2. (15 February 2008), pp. 453-465.
    by L Li, X Liu, W Yang, F Xu, W Wang, L Feng, M Bartlam, L Wang, Z Rao
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 19:15:40 as **
  • Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 13. (27 March 2007), pp. 5602-5607.
    by L Feng, W Wang, J Cheng, Y Ren, G Zhao, C Gao, Y Tang, X Liu, W Han, X Peng, R Liu, L Wang
    posted to proteome oxygenase genome alkane by mjetten to the group microbiology_nijmegen on 2008-06-03 19:15:23 as ** along with 1 group anammox
  • TPR domain of NrfG mediates complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia coli O157:H7.
    Proteins, Vol. 70, No. 3. (15 February 2008), pp. 900-914.
    by D Han, K Kim, J Oh, J Park, Y Kim
    posted to tpr protein-protein nrf nitrite interaction ammonia by mjetten to the group microbiology_nijmegen on 2008-06-03 19:13:48 as ** along with 1 group anammox
  • Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California.
    ISME J (24 January 2008)
    by Shana K K Goffredi, Regina Wilpiszeski, Ray Lee, Victoria J J Orphan
    posted to n-damo methane diversity by mjetten to the group microbiology_nijmegen on 2008-06-03 19:12:45 as ** along with 2 people vrich Katje
  • Analysis of the respiratory chain in Ethanologenic Zymomonas mobilis with a cyanide-resistant bd-type ubiquinol oxidase as the only terminal oxidase and its possible physiological roles.
    Journal of molecular microbiology and biotechnology, Vol. 14, No. 4. (2008), pp. 163-175.
    by K Sootsuwan, N Lertwattanasakul, P Thanonkeo, K Matsushita, M Yamada
    posted to oxygen oxidase n-damo bd by mjetten to the group microbiology_nijmegen on 2008-06-03 19:11:59 as **
  • Cytochrome bd oxidase, oxidative stress, and dioxygen tolerance of the strictly anaerobic bacterium Moorella thermoacetica.
    Journal of bacteriology, Vol. 187, No. 6. (March 2005), pp. 2020-2029.
    by A Das, R Silaghi-Dumitrescu, LG Ljungdahl, DM Kurtz
    posted to oxygen n-damo anaerobe by mjetten to the group microbiology_nijmegen on 2008-06-03 19:09:36 as **
  • Presence and expression of terminal oxygen reductases in strictly anaerobic sulfate-reducing bacteria isolated from salt-marsh sediments.
    Anaerobe (25 March 2008)
    by Margarida Santana
    posted to oxygen n-damo cytochrome bd anaerobic by mjetten to the group microbiology_nijmegen on 2008-06-03 19:08:31 as **
  • NOX family NADPH oxidases: not just in mammals.
    Biochimie, Vol. 89, No. 9. (September 2007), pp. 1107-1112.
    by K Bedard, B Lardy, KH Krause
    posted to oxygen n-damo by mjetten to the group microbiology_nijmegen on 2008-06-03 19:06:38 as **
  • Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox) family of enzymes
    BMC Evolutionary Biology, Vol. 7 (06 July 2007), 109.
    by Tsukasa Kawahara, Mark T Quinn, David J Lambeth
    posted to reactive oxygen n-damo by mjetten to the group microbiology_nijmegen on 2008-06-03 19:05:59 as ** along with 1 person pbarker
  • Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species.
    The FEBS journal (30 May 2008)
    by Hideki Sumimoto
    posted to reactive oxygen oxidase n-damo methane by mjetten to the group microbiology_nijmegen on 2008-06-03 19:04:34 as ** along with 1 person pbarker
  • Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers
    BioEssays, Vol. 29, No. 1. (2007), pp. 11-14.
    by Ricardo Cavicchioli, Matthew Z Demaere, Torsten Thomas
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:19:41 as ** along with 1 person jmeppley
  • Building on basic metagenomics with complementary technologies
    Genome Biology, Vol. 8 (28 December 2007), 231.
    by Falk Warnecke, Philip Hugenholtz
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:19:19 as ** along with 2 people and 2 groups jlgreen alexisfjdufresne iSEEM Green Lab
  • Tracking microbial biodiversity through molecular and genomic ecology.
    Research in microbiology, Vol. 159, No. 1. (b 2008), pp. 67-73.
    by P López-García, D Moreira
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:18:51 as ** along with 1 person and 2 groups jlgreen iSEEM Green Lab
  • Bacterial carbon processing by generalist species in the coastal ocean
    Nature (27 January 2008)
    by Xiaozhen Mou, Shulei Sun, Robert A Edwards, Robert E Hodson, Mary A Moran
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:18:24 as ** along with 2 people vrich cmzmasek
  • Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation.
    Omics : a journal of integrative biology (16 April 2008)
    by Samuel V V Angiuoli, Aaron Gussman, William Klimke, Guy Cochrane, Dawn Field, George Garrity, Chinnappa D D Kodira, Nikos Kyrpides, Ramana Madupu, Victor Markowitz, Tatiana Tatusova, Nick Thomson, Owen White
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:17:03 as **
  • MEGAN analysis of metagenomic data.
    Genome Res, Vol. 17, No. 3. (March 2007), pp. 377-386.
    by DH Huson, AF Auch, J Qi, SC Schuster
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:15:06 as ** along with 4 people and 1 group alexl carpi azazello wenhan anammox
  • 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
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:14:44 as ** along with 9 people and 4 groups jlgreen alexl carlk Yanno oamg jmeppley bluto azazello GustavoLacerda iSEEM Green Lab Glimcher_Lab Bioinformatics
  • Binning sequences using very sparse labels within a metagenome
    BMC Bioinformatics, Vol. 9 (28 April 2008), 215.
    by Chon-Kit K Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:14:15 as ** along with 1 person alexl
  • 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
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:11:50 as ** along with 2 people and 2 groups alexl stajich anammox Berkeley Mycology
  • Metagenomics is not enough.
    DNA and cell biology, Vol. 27, No. 5. (May 2008), pp. 219-221.
    by J Handelsman
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 13:11:15 as ** along with 1 group anammox
  • Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
    Science, Vol. 311, No. 5760. (27 January 2006), pp. 496-503.
    by Edward F Delong, Christina M Preston, Tracy Mincer, Virginia Rich, Steven J Hallam, Niels-Ulrik Frigaard, Asuncion Martinez, Matthew B Sullivan, Robert Edwards, Beltran R Brito, Sallie W Chisholm, David M Karl
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:57:53 as ** along with 10 people and 3 groups jlgreen vrich mcox eoghanharr dayjm jmeppley michC bluto jdelcampo beatrizfernandez iSEEM Green Lab Microbial-Ecology
  • Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities
    FEMS Microbiology Letters, Vol. 275, No. 2. (2007), pp. 183-190.
    by Stanley CK Lau, Wen T Liu
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:57:10 as ** along with 1 person Olaf_Ilzins
  • 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
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:56:41 as ** along with 11 people and 6 groups jlgreen ana nickluscombe michC bluto agg19954 TaqSys azazello Thaverkamp larsjuhljensen rvgomes iSEEM Green Lab structural_bioinformatics Bioinformatics EBI-regulation Microbial-Ecology
  • 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
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:56:07 as ** along with 10 people and 3 groups jlgreen sanchezbuelna vrich mcox bluto jmeppley AaronDarling azazello wenhan sgoetz iSEEM Green Lab anammox
  • Proteogenomic approaches for the molecular characterization of natural microbial communities.
    OMICS, Vol. 9, No. 4. (2005), pp. 301-333.
    by JF Banfield, NC Verberkmoes, RL Hettich, MP Thelen
    posted to proteomeics metagenomics by mjetten to the group microbiology_nijmegen on 2008-06-03 12:55:01 as ** along with 2 people and 1 group jmeppley nitiniitk anammox
  • Toward a census of bacteria in soil.
    PLoS Comput Biol, Vol. 2, No. 7. (21 July 2006)
    by PD Schloss, J Handelsman
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:53:43 as ** along with 2 people and 1 group fornstar azazello anammox
  • A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
    BMC Bioinformatics, Vol. 9 (23 January 2008), 34.
    by Patrick Schloss, Jo Handelsman
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:53:15 as ** along with 5 people and 3 groups djkt bluto alexisfjdufresne jmeppley Thaverkamp iSEEM anammox Microbial-Ecology
  • Opinion: Whither or wither geomicrobiology in the era of 'community metagenomics'
    Nature Reviews Microbiology, Vol. 3, No. 7. (01 July 2005), pp. 572-578.
    by Ronald S Oremland, Douglas G Capone, John F Stolz, Jed Fuhrman
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:52:40 as ** along with 1 group anammox
  • Signature, a web server for taxonomic characterization of sequence samples using signature genes.
    Nucleic acids research (23 May 2008)
    by Bas E E Dutilh, Ying He, Maarten L L Hekkelman, Martijn A A Huynen
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:52:09 as ** along with 1 group anammox
  • Signature Genes as a Phylogenomic Tool.
    Molecular biology and evolution (19 May 2008)
    by Bas E E Dutilh, Berend Snel, Thijs J G J Ettema, Martijn A A Huynen
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:51:49 as ** along with 1 group anammox
  • Metagenomics: Exploring unseen communities
    Nature, Vol. 453, No. 7195. (28 May 2008), pp. 687-690.
    by Nathan Blow
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:51:15 as ** along with 1 person and 1 group reyez anammox
  • The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.
    PLoS Biol, Vol. 5, No. 3. (13 March 2007)
    by Shibu Yooseph, Granger Sutton, Douglas B B Rusch, Aaron L L Halpern, Shannon J J Williamson, Karin Remington, Jonathan A A Eisen, Karla B B Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S S Miller, Huiying Li, Susan T T Mashiyama, Marcin P P Joachimiak, Christopher van Belle, John-Marc M Chandonia, David A A Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J J Raphael, Vineet Bafna, Robert Friedman, Steven E E Brenner, Adam Godzik, David Eisenberg, Jack E E Dixon, Susan S S Taylor, Robert L L Strausberg, Marvin Frazier, J Craig C Venter
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:50:04 as read along with 5 people and 3 groups jlgreen vrich jmeppley kaspermunch michC iSEEM Green Lab Bioinformatics
  • Analysis of microbial gene transcripts in environmental samples.
    Applied and environmental microbiology, Vol. 71, No. 7. (July 2005), pp. 4121-4126.
    by RS Poretsky, N Bano, A Buchan, G LeCleir, J Kleikemper, M Pickering, WM Pate, MA Moran, JT Hollibaugh
    posted to rt-pcr mrna metagenomics by mjetten to the group microbiology_nijmegen on 2008-06-03 12:49:05 as ** along with 1 person mcox
  • 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
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:47:09 as ** along with 3 people and 2 groups jlgreen vaulot tmmurali iSEEM Green Lab
  • The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.
    PLoS ONE, Vol. 3, No. 1. (2008)
    by SJ Williamson, DB Rusch, S Yooseph, AL Halpern, KB Heidelberg, JI Glass, C Andrews-Pfannkoch, D Fadrosh, CS Miller, G Sutton, M Frazier, JC Venter
    posted to no-tag by mjetten to the group microbiology_nijmegen on 2008-06-03 12:45:09 as ** along with 1 person and 1 group jdelcampo Microbial-Ecology
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