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Prediction of effective genome size in metagenomic samples
Jeroen Raes, Jan O Korbel, Martin J Lercher, Christian von Mering, Peer Bork
Genome Biol. 2007; 8(1): R10. Published online 2007 January 15. doi: 10.1186/gb-2007-8-1-r10
PMCID:
PMC1839125
Abstract Full Text PDF–622K Supplementary Material

Is Cited by the Following 30 Articles in this Archive:

Bacterial Niche-Specific Genome Expansion Is Coupled with Highly Frequent Gene Disruptions in Deep-Sea Sediments
Yong Wang, Jiang Ke Yang, On On Lee, Tie Gang Li, Abdulaziz Al-Suwailem, Antoine Danchin, Pei-Yuan Qian
PLoS One. 2011; 6(12): e29149. Published online 2011 December 21. doi: 10.1371/journal.pone.0029149
PMCID:
PMC3244439
Abstract Full Text PDF–601K Supplementary Material
Open resource metagenomics: a model for sharing metagenomic libraries
J.D. Neufeld, K. Engel, J. Cheng, G. Moreno-Hagelsieb, D.R. Rose, T.C. Charles
Stand Genomic Sci. 2011 November 30; 5(2): 203–210. Published online 2011 November 23. doi: 10.4056/sigs.1974654
PMCID:
PMC3235511
Abstract Full Text PDF–1.0M
Potential for phosphite and phosphonate utilization by Prochlorococcus
Roi Feingersch, Alon Philosof, Tom Mejuch, Fabian Glaser, Onit Alalouf, Yuval Shoham, Oded Béjà
ISME J. 2012 April; 6(4): 827–834. Published online 2011 October 20. doi: 10.1038/ismej.2011.149
PMCID:
PMC3309357
Free in PMC on 2013/04/01
A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments
Othilde Elise Håvelsrud, Thomas HA Haverkamp, Tom Kristensen, Kjetill S Jakobsen, Anne Gunn Rike
BMC Microbiol. 2011; 11: 221. Published online 2011 October 4. doi: 10.1186/1471-2180-11-221
PMCID:
PMC3197505
Abstract Full Text PDF–568K Supplementary Material
Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes
Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg, Frank Oliver Glöckner
Microb Inform Exp. 2011; 1: 9. Published online 2011 September 7. doi: 10.1186/2042-5783-1-9
PMCID:
PMC3351728
Abstract Full Text PDF–444K Supplementary Material
Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem
Seungdae Oh, Alejandro Caro-Quintero, Despina Tsementzi, Natasha DeLeon-Rodriguez, Chengwei Luo, Rachel Poretsky, Konstantinos T. Konstantinidis
Appl Environ Microbiol. 2011 September; 77(17): 6000–6011. doi: 10.1128/AEM.00107-11
PMCID:
PMC3165412
Abstract Full Text PDF–2.2M Supplementary Material
Going Deeper: Metagenome of a Hadopelagic Microbial Community
Emiley A. Eloe, Douglas W. Fadrosh, Mark Novotny, Lisa Zeigler Allen, Maria Kim, Mary-Jane Lombardo, Joyclyn Yee-Greenbaum, Shibu Yooseph, Eric E. Allen, Roger Lasken, Shannon J. Williamson, Douglas H. Bartlett
PLoS One. 2011; 6(5): e20388. Published online 2011 May 24. doi: 10.1371/journal.pone.0020388
PMCID:
PMC3101246
Abstract Full Text PDF–1.2M Supplementary Material
Quantitative Metagenomic Analyses Based on Average Genome Size Normalization
Jeremy A. Frank, Søren J. Sørensen
Appl Environ Microbiol. 2011 April; 77(7): 2513–2521. Published online 2011 February 11. doi: 10.1128/AEM.02167-10
PMCID:
PMC3067418
Abstract Full Text PDF–477K Supplementary Material
Novel Analysis of Oceanic Surface Water Metagenomes Suggests Importance of Polyphosphate Metabolism in Oligotrophic Environments
Ben Temperton, Jack A. Gilbert, John P. Quinn, John W. McGrath
PLoS One. 2011; 6(1): e16499. Published online 2011 January 28. doi: 10.1371/journal.pone.0016499
PMCID:
PMC3030594
Abstract Full Text PDF–1.9M Supplementary Material
Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams
Tatiana A. Vishnivetskaya, Jennifer J. Mosher, Anthony V. Palumbo, Zamin K. Yang, Mircea Podar, Steven D. Brown, Scott C. Brooks, Baohua Gu, George R. Southworth, Meghan M. Drake, Craig C. Brandt, Dwayne A. Elias
Appl Environ Microbiol. 2011 January; 77(1): 302–311. Published online 2010 November 5. doi: 10.1128/AEM.01715-10
PMCID:
PMC3019708
Abstract Full Text PDF–1.1M
Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities
J. Jacob Parnell, Giovanni Rompato, Leigh C. Latta, IV, Michael E. Pfrender, Joy D. Van Nostrand, Zhili He, Jizhong Zhou, Gary Andersen, Patti Champine, Balasubramanian Ganesan, Bart C. Weimer
PLoS One. 2010; 5(9): e12919. Published online 2010 September 23. doi: 10.1371/journal.pone.0012919
PMCID:
PMC2950788
Abstract Full Text PDF–1.7M Supplementary Material
MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
Manuel Stark, Simon A Berger, Alexandros Stamatakis, Christian von Mering
BMC Genomics. 2010; 11: 461. Published online 2010 August 5. doi: 10.1186/1471-2164-11-461
PMCID:
PMC3091657
Abstract Full Text PDF–3.6M
Microbial Community Changes in Response to Ethanol or Methanol Amendments for U(VI) Reduction
Tatiana A. Vishnivetskaya, Craig C. Brandt, Andrew S. Madden, Meghan M. Drake, Joel E. Kostka, Denise M. Akob, Kirsten Küsel, Anthony V. Palumbo
Appl Environ Microbiol. 2010 September; 76(17): 5728–5735. Published online 2010 July 2. doi: 10.1128/AEM.00308-10
PMCID:
PMC2935046
Abstract Full Text PDF–532K
A global network of coexisting microbes from environmental and whole-genome sequence data
Samuel Chaffron, Hubert Rehrauer, Jakob Pernthaler, Christian von Mering
Genome Res. 2010 July; 20(7): 947–959. doi: 10.1101/gr.104521.109
PMCID:
PMC2892096
Abstract Full Text PDF–2.1M
Enigmatic, ultrasmall, uncultivated Archaea
Brett J. Baker, Luis R. Comolli, Gregory J. Dick, Loren J. Hauser, Doug Hyatt, Brian D. Dill, Miriam L. Land, Nathan C. VerBerkmoes, Robert L. Hettich, Jillian F. Banfield
Proc Natl Acad Sci U S A. 2010 May 11; 107(19): 8806–8811. Published online 2010 April 26. doi: 10.1073/pnas.0914470107
PMCID:
PMC2889320
Abstract Full Text PDF–1.1M Supplementary Material
A Primer on Metagenomics
John C. Wooley, Adam Godzik, Iddo Friedberg
PLoS Comput Biol. 2010 February; 6(2): e1000667. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000667
PMCID:
PMC2829047
Abstract Full Text PDF–360K
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer
PLoS Comput Biol. 2009 December; 5(12): e1000593. Published online 2009 December 11. doi: 10.1371/journal.pcbi.1000593
PMCID:
PMC2781106
Abstract Full Text PDF–1016K Supplementary Material
The impact of long-distance horizontal gene transfer on prokaryotic genome size
Otto X. Cordero, Paulien Hogeweg
Proc Natl Acad Sci U S A. 2009 December 22; 106(51): 21748–21753. Published online 2009 December 9. doi: 10.1073/pnas.0907584106
PMCID:
PMC2799812
Abstract Full Text PDF–1.0M Supplementary Material
The genomic basis of trophic strategy in marine bacteria
Federico M. Lauro, Diane McDougald, Torsten Thomas, Timothy J. Williams, Suhelen Egan, Scott Rice, Matthew Z. DeMaere, Lily Ting, Haluk Ertan, Justin Johnson, Steven Ferriera, Alla Lapidus, Iain Anderson, Nikos Kyrpides, A. Christine Munk, Chris Detter, Cliff S. Han, Mark V. Brown, Frank T. Robb, Staffan Kjelleberg, Ricardo Cavicchioli
Proc Natl Acad Sci U S A. 2009 September 15; 106(37): 15527–15533. Published online 2009 September 8. doi: 10.1073/pnas.0903507106
PMCID:
PMC2739866
Abstract Full Text PDF–867K Supplementary Material
Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre
Konstantinos T. Konstantinidis, Jennifer Braff, David M. Karl, Edward F. DeLong
Appl Environ Microbiol. 2009 August; 75(16): 5345–5355. Published online 2009 June 19. doi: 10.1128/AEM.00473-09
PMCID:
PMC2725473
Abstract Full Text PDF–1.7M Supplementary Material
Methods for comparative metagenomics
Daniel H Huson, Daniel C Richter, Suparna Mitra, Alexander F Auch, Stephan C Schuster
BMC Bioinformatics. 2009; 10(Suppl 1): S12. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S12
PMCID:
PMC2648729
Abstract Full Text PDF–539K
Quantifying environmental adaptation of metabolic pathways in metagenomics
Tara A. Gianoulis, Jeroen Raes, Prianka V. Patel, Robert Bjornson, Jan O. Korbel, Ivica Letunic, Takuji Yamada, Alberto Paccanaro, Lars J. Jensen, Michael Snyder, Peer Bork, Mark B. Gerstein
Proc Natl Acad Sci U S A. 2009 February 3; 106(5): 1374–1379. Published online 2009 January 22. doi: 10.1073/pnas.0808022106
PMCID:
PMC2629784
Abstract Full Text PDF–1.3M Supplementary Material
Metagenomics: Facts and Artifacts, and Computational Challenges*
John C. Wooley, Yuzhen Ye
J Comput Sci Technol. Author manuscript; available in PMC 2010 July 19.
Published in final edited form as: J Comput Sci Technol. 2009 January; 25(1): 71–81. doi: 10.1007/s11390-010-9306-4
PMCID:
PMC2905821
Abstract Full Text PDF–62K
A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data
Konrad U. Foerstner, Tobias Doerks, Christopher J. Creevey, Anja Doerks, Peer Bork
PLoS ONE. 2008; 3(10): e3515. Published online 2008 October 27. doi: 10.1371/journal.pone.0003515
PMCID:
PMC2568958
Abstract Full Text PDF–306K Supplementary Material
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat
Victor Kunin, Jeroen Raes, J Kirk Harris, John R Spear, Jeffrey J Walker, Natalia Ivanova, Christian von Mering, Brad M Bebout, Norman R Pace, Peer Bork, Philip Hugenholtz
Mol Syst Biol. 2008; 4: 198. Published online 2008 June 3. doi: 10.1038/msb.2008.35
PMCID:
PMC2483411
Abstract Full Text PDF–341K Supplementary Material
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, Albin Sandelin
Nucleic Acids Res. 2008 January; 36(Database issue): D102–D106. Published online 2008 January. doi: 10.1093/nar/gkm955
PMCID:
PMC2238834
Abstract Full Text PDF–6.5M
Compressing Proteomes: The Relevance of Medium Range Correlations
Dario Benedetto, Emanuele Caglioti, Claudia Chica
EURASIP J Bioinform Syst Biol. 2007; 2007(1): 60723. Published online 2007 October 30. doi: 10.1155/2007/60723
PMCID:
PMC3171345
Abstract Full Text PDF–632K
Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments
Marc Mußmann, Fen Z Hu, Michael Richter, Dirk de Beer, André Preisler, Bo B Jørgensen, Marcel Huntemann, Frank Oliver Glöckner, Rudolf Amann, Werner J. H Koopman, Roger S Lasken, Benjamin Janto, Justin Hogg, Paul Stoodley, Robert Boissy, Garth D Ehrlich
PLoS Biol. 2007 September; 5(9): e230. Published online 2007 August 28. doi: 10.1371/journal.pbio.0050230
PMCID:
PMC1951784
Abstract Full Text PDF–870K Supplementary Material
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
E. D. Harrington, A. H. Singh, T. Doerks, I. Letunic, C. von Mering, L. J. Jensen, J. Raes, P. Bork
Proc Natl Acad Sci U S A. 2007 August 28; 104(35): 13913–13918. Published online 2007 August 23. doi: 10.1073/pnas.0702636104
PMCID:
PMC1955820
Abstract Full Text PDF–353K Supplementary Material
Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
Yann Marcy, Cleber Ouverney, Elisabeth M. Bik, Tina Lösekann, Natalia Ivanova, Hector Garcia Martin, Ernest Szeto, Darren Platt, Philip Hugenholtz, David A. Relman, Stephen R. Quake
Proc Natl Acad Sci U S A. 2007 July 17; 104(29): 11889–11894. Published online 2007 July 9. doi: 10.1073/pnas.0704662104
PMCID:
PMC1924555
Abstract Full Text PDF–936K Supplementary Material
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