Paul G. Cantalupo, Byron Calgua, Guoyan Zhao, Ayalkibet Hundesa, Adam D. Wier, Josh P. Katz, Michael Grabe, Roger W. Hendrix, Rosina Girones, David Wang, James M. Pipas

mBio. 2011 Sep-Oct; 2(5): e00180-11. Published online 2011 October 4. doi: 10.1128/mBio.00180-11

PMCID:: PMC3187576

Abstract Full Text PDF–2.2M Supplementary Material

Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes

Philippe Colson, Natalya Yutin, Svetlana A. Shabalina, Catherine Robert, Ghislain Fournous, Bernard La Scola, Didier Raoult, Eugene V. Koonin

Genome Biol Evol. 2011; 3: 737–742. Published online 2011 June 24. doi: 10.1093/gbe/evr048

PMCID:: PMC3163472

Abstract Full Text PDF–795K

Planktonic Microbes in the Gulf of Maine Area

William K. W. Li, Robert A. Andersen, Dian J. Gifford, Lewis S. Incze, Jennifer L. Martin, Cynthia H. Pilskaln, Juliette N. Rooney-Varga, Michael E. Sieracki, William H. Wilson, Nicholas H. Wolff

PLoS One. 2011; 6(6): e20981. Published online 2011 June 15. doi: 10.1371/journal.pone.0020981

PMCID:: PMC3115965

Abstract Full Text PDF–507K Supplementary Material

Virophage control of antarctic algal host–virus dynamics

Sheree Yau, Federico M. Lauro, Matthew Z. DeMaere, Mark V. Brown, Torsten Thomas, Mark J. Raftery, Cynthia Andrews-Pfannkoch, Matthew Lewis, Jeffrey M. Hoffman, John A. Gibson, Ricardo Cavicchioli

Proc Natl Acad Sci U S A. 2011 April 12; 108(15): 6163–6168. Published online 2011 March 28. doi: 10.1073/pnas.1018221108

PMCID:: PMC3076838

Abstract Full Text PDF–1.0M Supplementary Material

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

Yu-Wei Wu, Yuzhen Ye

J Comput Biol. 2011 March; 18(3): 523–534. doi: 10.1089/cmb.2010.0245

PMCID:: PMC3123841

Abstract Full Text PDF–318K Supplementary Material

Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

Francis C Weng, Chien-Hao Su, Ming-Tsung Hsu, Tse-Yi Wang, Huai-Kuang Tsai, Daryi Wang

BMC Bioinformatics. 2010; 11: 565. Published online 2010 November 18. doi: 10.1186/1471-2105-11-565

PMCID:: PMC3098102

Abstract Full Text PDF–1.1M Supplementary Material

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

Frederick A Matsen, Robin B Kodner, E Virginia Armbrust

BMC Bioinformatics. 2010; 11: 538. Published online 2010 October 30. doi: 10.1186/1471-2105-11-538

PMCID:: PMC3098090

Abstract Full Text PDF–1.7M Supplementary Material

Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses

Eugene V. Koonin, Natalya Yutin

Intervirology. 2010 June; 53(5): 284–292. Published online 2010 June 15. doi: 10.1159/000312913

PMCID:: PMC2895762

Abstract Full Text PDF–207K

Integration of open access literature into the RCSB Protein Data Bank using BioLit

Andreas Prlić, Marco A Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T Yukich, Peter W Rose, Philip E Bourne, J Lynn Fink

BMC Bioinformatics. 2010; 11: 220. Published online 2010 April 29. doi: 10.1186/1471-2105-11-220

PMCID:: PMC2880030

Abstract Full Text PDF–1.2M

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

Natalya Yutin, Yuri I Wolf, Didier Raoult, Eugene V Koonin

Virol J. 2009; 6: 223. Published online 2009 December 17. doi: 10.1186/1743-422X-6-223

PMCID:: PMC2806869

Abstract Full Text PDF–1.1M Supplementary Material

New dimensions of the virus world discovered through metagenomics

David M. Kristensen, Arcady R. Mushegian, Valerian V. Dolja, Eugene V. Koonin

Trends Microbiol. Author manuscript; available in PMC 2012 March 5.

Published in final edited form as: Trends Microbiol. 2010 January; 18(1): 11–19. Published online 2009 November 26. doi: 10.1016/j.tim.2009.11.003

PMCID:: PMC3293453

Abstract Full Text PDF–1.3M

Isolation of Prasinoviruses of the Green Unicellular Algae Ostreococcus spp. on a Worldwide Geographical Scale

Laure Bellec, Nigel Grimsley, Yves Desdevises

Appl Environ Microbiol. 2010 January; 76(1): 96–101. Published online 2009 November 6. doi: 10.1128/AEM.01799-09

PMCID:: PMC2798645

Abstract Full Text PDF–369K Supplementary Material

Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus

Hiroyuki Ogata, Kensuke Toyoda, Yuji Tomaru, Natsuko Nakayama, Yoko Shirai, Jean-Michel Claverie, Keizo Nagasaki

Virol J. 2009; 6: 178. Published online 2009 October 27. doi: 10.1186/1743-422X-6-178

PMCID:: PMC2777158

Abstract Full Text PDF–1.5M Supplementary Material

The not so universal tree of life or the place of viruses in the living world

Harald Brüssow

Philos Trans R Soc Lond B Biol Sci. 2009 August 12; 364(1527): 2263–2274. doi: 10.1098/rstb.2009.0036

PMCID:: PMC2873004

Abstract Full Text PDF–255K

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