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Search for a 'Tree of Life' in the thicket of the phylogenetic forest
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
J Biol. 2009; 8(6): 59. Published online 2009 July 13. doi: 10.1186/jbiol159
PMCID:
PMC2737373
Abstract Full Text PDF–3.3M Supplementary Material

Is Cited by the Following 32 Articles in this Archive:

The Emergence and Early Evolution of Biological Carbon-Fixation
Rogier Braakman, Eric Smith
PLoS Comput Biol. 2012 April; 8(4): e1002455. Published online 2012 April 19. doi: 10.1371/journal.pcbi.1002455
PMCID:
PMC3334880
Abstract Full Text PDF–740K Supplementary Material
Genome Sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary
Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
J Bacteriol. 2012 April; 194(8): 2119–2120. doi: 10.1128/JB.00007-12
PMCID:
PMC3318456
Free in PMC on 2012/10/01
Genome Sequence of “Candidatus Nitrosopumilus salaria” BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary
Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
J Bacteriol. 2012 April; 194(8): 2121–2122. doi: 10.1128/JB.00013-12
PMCID:
PMC3318490
Free in PMC on 2012/10/01
A Rooted Net of Life
David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam, J Peter Gogarten
Biol Direct. 2011; 6: 45. Published online 2011 September 21. doi: 10.1186/1745-6150-6-45
PMCID:
PMC3189188
Abstract Full Text PDF–845K
The public goods hypothesis for the evolution of life on Earth
James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell
Biol Direct. 2011; 6: 41. Published online 2011 August 23. doi: 10.1186/1745-6150-6-41
PMCID:
PMC3179745
Abstract Full Text PDF–796K
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste
Biol Direct. 2011; 6: 39. Published online 2011 July 20. doi: 10.1186/1745-6150-6-39
PMCID:
PMC3160433
Abstract Full Text PDF–977K Supplementary Material
Split-based computation of majority-rule supertrees
Anne Kupczok
BMC Evol Biol. 2011; 11: 205. Published online 2011 July 13. doi: 10.1186/1471-2148-11-205
PMCID:
PMC3169514
Abstract Full Text PDF–574K
How stands the Tree of Life a century and a half after The Origin?
Maureen A O'Malley, Eugene V Koonin
Biol Direct. 2011; 6: 32. Published online 2011 June 30. doi: 10.1186/1745-6150-6-32
PMCID:
PMC3158114
Abstract Full Text PDF–521K
Telling the whole story in a 10,000-genome world
Robert G Beiko
Biol Direct. 2011; 6: 34. Published online 2011 June 30. doi: 10.1186/1745-6150-6-34
PMCID:
PMC3158115
Abstract Full Text PDF–3.8M
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
Priya Narasingarao, Sheila Podell, Juan A Ugalde, Céline Brochier-Armanet, Joanne B Emerson, Jochen J Brocks, Karla B Heidelberg, Jillian F Banfield, Eric E Allen
ISME J. 2012 January; 6(1): 81–93. Published online 2011 June 30. doi: 10.1038/ismej.2011.78
PMCID:
PMC3246234
Free in PMC on 2013/01/01
Evaluating Phylogenetic Congruence in the Post-Genomic Era
Jessica W. Leigh, François-Joseph Lapointe, Philippe Lopez, Eric Bapteste
Genome Biol Evol. 2011; 3: 571–587. Published online 2011 June 28. doi: 10.1093/gbe/evr050
PMCID:
PMC3156567
Abstract Full Text PDF–1000K
Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes
Iain Anderson, Carmen Scheuner, Markus Göker, Kostas Mavromatis, Sean D. Hooper, Iris Porat, Hans-Peter Klenk, Natalia Ivanova, Nikos Kyrpides
PLoS One. 2011; 6(5): e20237. Published online 2011 May 25. doi: 10.1371/journal.pone.0020237
PMCID:
PMC3102087
Abstract Full Text PDF–436K Supplementary Material
Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula
Adam C. Jones, Emily A. Monroe, Sheila Podell, Wolfgang R. Hess, Sven Klages, Eduardo Esquenazi, Sherry Niessen, Heather Hoover, Michael Rothmann, Roger S. Lasken, John R. Yates, III, Richard Reinhardt, Michael Kube, Michael D. Burkart, Eric E. Allen, Pieter C. Dorrestein, William H. Gerwick, Lena Gerwick
Proc Natl Acad Sci U S A. 2011 May 24; 108(21): 8815–8820. Published online 2011 May 9. doi: 10.1073/pnas.1101137108
PMCID:
PMC3102346
Abstract Full Text PDF–606K Supplementary Material
Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts
David M. Kristensen, Xixu Cai, Arcady Mushegian
J Bacteriol. 2011 April; 193(8): 1806–1814. doi: 10.1128/JB.01311-10
PMCID:
PMC3133016
Abstract Full Text PDF–614K
The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon
Ruben E Valas, Philip E Bourne
Biol Direct. 2011; 6: 16. Published online 2011 February 28. doi: 10.1186/1745-6150-6-16
PMCID:
PMC3056875
Abstract Full Text PDF–1.0M Supplementary Material
Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction
Cécile Ané
Genome Biol Evol. 2011; 3: 246–258. Published online 2011 February 28. doi: 10.1093/gbe/evr013
PMCID:
PMC3070431
Abstract Full Text PDF–326K
The advantages and disadvantages of horizontal gene transfer and the emergence of the first species
Aaron A Vogan, Paul G Higgs
Biol Direct. 2011; 6: 1. Published online 2011 January 3. doi: 10.1186/1745-6150-6-1
PMCID:
PMC3043529
Abstract Full Text PDF–381K
Assembling networks of microbial genomes using linear programming
Catherine Holloway, Robert G Beiko
BMC Evol Biol. 2010; 10: 360. Published online 2010 November 20. doi: 10.1186/1471-2148-10-360
PMCID:
PMC3224671
Abstract Full Text PDF–2.7M Supplementary Material
The Tree and Net Components of Prokaryote Evolution
Pere Puigbò, Yuri I. Wolf, Eugene V. Koonin
Genome Biol Evol. 2010; 2: 745–756. Published online 2010 October 1. doi: 10.1093/gbe/evq062
PMCID:
PMC2997564
Abstract Full Text PDF–1.7M
Evolution and Multiplicity of Arginine Decarboxylases in Polyamine Biosynthesis and Essential Role in Bacillus subtilis Biofilm Formation
Matthew Burrell, Colin C. Hanfrey, Ewan J. Murray, Nicola R. Stanley-Wall, Anthony J. Michael
J Biol Chem. 2010 December 10; 285(50): 39224–39238. Published online 2010 September 27. doi: 10.1074/jbc.M110.163154
PMCID:
PMC2998088
Abstract Full Text Supplementary Material
Save the tree of life or get lost in the woods
Ruben E Valas, Philip E Bourne
Biol Direct. 2010; 5: 44. Published online 2010 July 1. doi: 10.1186/1745-6150-5-44
PMCID:
PMC2910001
Abstract Full Text PDF–1000K Supplementary Material
Biased gene transfer mimics patterns created through shared ancestry
Cheryl P. Andam, David Williams, J. Peter Gogarten
Proc Natl Acad Sci U S A. 2010 June 8; 107(23): 10679–10684. Published online 2010 May 21. doi: 10.1073/pnas.1001418107
PMCID:
PMC2890805
Abstract Full Text PDF–3.1M Supplementary Material
Genome Networks Root the Tree of Life between Prokaryotic Domains
Tal Dagan, Mayo Roettger, David Bryant, William Martin
Genome Biol Evol. 2010; 2: 379–392. Published online 2010 May 18. doi: 10.1093/gbe/evq025
PMCID:
PMC2997548
Abstract Full Text PDF–1017K
Phylogeny of Gammaproteobacteria
Kelly P. Williams, Joseph J. Gillespie, Bruno W. S. Sobral, Eric K. Nordberg, Eric E. Snyder, Joshua M. Shallom, Allan W. Dickerman
J Bacteriol. 2010 May; 192(9): 2305–2314. Published online 2010 March 5. doi: 10.1128/JB.01480-09
PMCID:
PMC2863478
Abstract Full Text PDF–1.9M Supplementary Material
Top ten in Journal of Biology in 2009: stem cells, influenza, pit bulls, Darwin, and more
Miranda Robertson
J Biol. 2009; 8(12): 102. Published online 2009 December 31. doi: 10.1186/jbiol210
PMCID:
PMC2804281
Full Text PDF–59K
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
Mapping the Tree of Life: Progress and Prospects
Norman R. Pace
Microbiol Mol Biol Rev. 2009 December; 73(4): 565–576. doi: 10.1128/MMBR.00033-09
PMCID:
PMC2786576
Abstract Full Text PDF–1.4M
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
Talima Pearson, Philip Giffard, Stephen Beckstrom-Sternberg, Raymond Auerbach, Heidie Hornstra, Apichai Tuanyok, Erin P Price, Mindy B Glass, Benjamin Leadem, James S Beckstrom-Sternberg, Gerard J Allan, Jeffrey T Foster, David M Wagner, Richard T Okinaka, Siew Hoon Sim, Ofori Pearson, Zaining Wu, Jean Chang, Rajinder Kaul, Alex R Hoffmaster, Thomas S Brettin, Richard A Robison, Mark Mayo, Jay E Gee, Patrick Tan, Bart J Currie, Paul Keim
BMC Biol. 2009; 7: 78. Published online 2009 November 18. doi: 10.1186/1741-7007-7-78
PMCID:
PMC2784454
Abstract Full Text PDF–1.4M Supplementary Material
The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum
Eugene V Koonin, Yuri I Wolf
Biol Direct. 2009; 4: 33. Published online 2009 September 29. doi: 10.1186/1745-6150-4-33
PMCID:
PMC2761301
Abstract Full Text PDF–647K
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life
Ruben E Valas, Philip E Bourne
Biol Direct. 2009; 4: 30. Published online 2009 August 25. doi: 10.1186/1745-6150-4-30
PMCID:
PMC3224940
Abstract Full Text PDF–1017K
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