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Rooting the tree of life by transition analyses
Thomas Cavalier-Smith
Biol Direct. 2006; 1: 19. Published online 2006 July 11. doi: 10.1186/1745-6150-1-19
PMCID:
PMC1586193
Abstract Full Text PDF–2.2M

Is Cited by the Following 34 Articles in this Archive:

Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes
Radhey S. Gupta
Antonie Van Leeuwenhoek. 2011 August; 100(2): 171–182. Published online 2011 June 30. doi: 10.1007/s10482-011-9616-8
PMCID:
PMC3133647
Abstract Full Text PDF–762K Supplementary Material
From the scala naturae to the symbiogenetic and dynamic tree of life
Ulrich Kutschera
Biol Direct. 2011; 6: 33. Published online 2011 June 30. doi: 10.1186/1745-6150-6-33
PMCID:
PMC3154191
Abstract Full Text PDF–3.0M
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
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
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
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
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution
Thomas Cavalier-Smith
Biol Direct. 2010; 5: 7. Published online 2010 February 4. doi: 10.1186/1745-6150-5-7
PMCID:
PMC2837639
Abstract Full Text PDF–2.3M
Deep phylogeny, ancestral groups and the four ages of life
Thomas Cavalier-Smith
Philos Trans R Soc Lond B Biol Sci. 2010 January 12; 365(1537): 111–132. doi: 10.1098/rstb.2009.0161
PMCID:
PMC2842702
Abstract Full Text PDF–1.0M
A Modular BAM Complex in the Outer Membrane of the α-Proteobacterium Caulobacter crescentus
Khatira Anwari, Sebastian Poggio, Andrew Perry, Xenia Gatsos, Sri Harsha Ramarathinam, Nicholas A. Williamson, Nicholas Noinaj, Susan Buchanan, Kipros Gabriel, Anthony W. Purcell, Christine Jacobs-Wagner, Trevor Lithgow
PLoS One. 2010; 5(1): e8619. Published online 2010 January 8. doi: 10.1371/journal.pone.0008619
PMCID:
PMC2797634
Abstract Full Text PDF–1.1M Supplementary Material
Deep Phylogeny—How a Tree Can Help Characterize Early Life on Earth
Eric A. Gaucher, James T. Kratzer, Ryan N. Randall
Cold Spring Harb Perspect Biol. 2010 January; 2(1): a002238. doi: 10.1101/cshperspect.a002238
PMCID:
PMC2827910
Abstract Full Text PDF–753K
Evolutionary Triplet Models of Structured RNA
Robert K. Bradley, Ian Holmes
PLoS Comput Biol. 2009 August; 5(8): e1000483. Published online 2009 August 28. doi: 10.1371/journal.pcbi.1000483
PMCID:
PMC2725318
Abstract Full Text PDF–806K Supplementary Material
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
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth
Armen Y Mulkidjanian, Michael Y Galperin
Biol Direct. 2009; 4: 27. Published online 2009 August 24. doi: 10.1186/1745-6150-4-27
PMCID:
PMC2749021
Abstract Full Text PDF–1.0M
The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
Peter G. Foster, Cymon J. Cox, T. Martin Embley
Philos Trans R Soc Lond B Biol Sci. 2009 August 12; 364(1527): 2197–2207. doi: 10.1098/rstb.2009.0034
PMCID:
PMC2873002
Abstract Full Text PDF–500K
Evolution of plant senescence
Howard Thomas, Lin Huang, Mike Young, Helen Ougham
BMC Evol Biol. 2009; 9: 163. Published online 2009 July 14. doi: 10.1186/1471-2148-9-163
PMCID:
PMC2716323
Abstract Full Text PDF–3.1M Supplementary Material
Initial Implementation of a Comparative Data Analysis Ontology
Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli, Julie D. Thompson, Arlin Stoltzfus
Evol Bioinform Online. 2009; 5: 47–66. Published online 2009 July 3.
PMCID:
PMC2747124
Abstract Full Text PDF–6.3M
Phylogenetic Ubiquity and Shuffling of the Bacterial RecBCD and AddAB Recombination Complexes
Gareth A. Cromie
J Bacteriol. 2009 August; 191(16): 5076–5084. Published online 2009 June 19. doi: 10.1128/JB.00254-09
PMCID:
PMC2725590
Abstract Full Text PDF–2.9M Supplementary Material
Nothing about Protein Structure Classification Makes Sense Except in the Light of Evolution
Ruben Valas, Song Yang, Philip E. Bourne
Curr Opin Struct Biol. Author manuscript; available in PMC 2010 June 1.
Published in final edited form as: Curr Opin Struct Biol. 2009 June; 19(3): 329–334. Published online 2009 April 24. doi: 10.1016/j.sbi.2009.03.011
PMCID:
PMC2696554
Abstract Full Text PDF–39K
Origin and Function of Ubiquitin-like Protein Conjugation
Mark Hochstrasser
Nature. Author manuscript; available in PMC 2010 March 26.
Published in final edited form as: Nature. 2009 March 26; 458(7237): 422. doi: 10.1038/nature07958
PMCID:
PMC2819001
Abstract Full Text PDF–1.7M
Co-evolution of primordial membranes and membrane proteins
Armen Y. Mulkidjanian, Michael Y. Galperin, Eugene V. Koonin
Trends Biochem Sci. Author manuscript; available in PMC 2009 September 28.
Published in final edited form as: Trends Biochem Sci. 2009 April; 34(4): 206–215. Published online 2009 March 18. doi: 10.1016/j.tibs.2009.01.005
PMCID:
PMC2752816
Abstract Full Text PDF–1.9M
Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms
Patrick Forterre, Danièle Gadelle
Nucleic Acids Res. 2009 February; 37(3): 679–692. Published online 2009 February. doi: 10.1093/nar/gkp032
PMCID:
PMC2647321
Abstract Full Text PDF–1.5M
Sorting out the mix in microbial genomics
Michael Y Galperin
Environ Microbiol. 2008 December; 10(12): 3187–3192. doi: 10.1111/j.1462-2920.2008.01811.x
PMCID:
PMC2702502
Full Text PDF–85K
Macroamphiphilic Components of Thermophilic Actinomycetes: Identification of Lipoteichoic Acid in Thermobifida fusca
Obaidur Rahman, Markus Pfitzenmaier, Oxana Pester, Siegfried Morath, Stephen P. Cummings, Thomas Hartung, Iain C. Sutcliffe
J Bacteriol. 2009 January; 191(1): 152–160. Published online 2008 October 17. doi: 10.1128/JB.01105-08
PMCID:
PMC2612442
Abstract Full Text PDF–667K Supplementary Material
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
Bastien Boussau, Laurent Guéguen, Manolo Gouy
BMC Evol Biol. 2008; 8: 272. Published online 2008 October 3. doi: 10.1186/1471-2148-8-272
PMCID:
PMC2584045
Abstract Full Text PDF–820K Supplementary Material
Protein secretion and outer membrane assembly in Alphaproteobacteria
Xenia Gatsos, Andrew J Perry, Khatira Anwari, Pavel Dolezal, P Peter Wolynec, Vladimir A Likić, Anthony W Purcell, Susan K Buchanan, Trevor Lithgow
FEMS Microbiol Rev. 2008 November; 32(6): 995–1009. Published online 2008 August 28. doi: 10.1111/j.1574-6976.2008.00130.x
PMCID:
PMC2635482
Abstract Full Text PDF–639K
On the spread of epidemics in a closed heterogeneous population
Artem S Novozhilov
Math Biosci. Author manuscript; available in PMC 2009 October 1.
Published in final edited form as: Math Biosci. 2008 October; 215(2): 177–185. Published online 2008 August 3. doi: 10.1016/j.mbs.2008.07.010
PMCID:
PMC2580825
Abstract Full Text PDF–1.1M
The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner
Nicolas Glansdorff, Ying Xu, Bernard Labedan
Biol Direct. 2008; 3: 29. Published online 2008 July 9. doi: 10.1186/1745-6150-3-29
PMCID:
PMC2478661
Abstract Full Text PDF–738K
Origin of eukaryotic cells as a symbiosis of parasitic α-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes
Matej Vesteg, Juraj Krajčovič
Commun Integr Biol. 2008 Jul-Sep; 1(1): 104–113.
PMCID:
PMC2633810
Abstract Full Text PDF–346K
Rethinking Proteasome Evolution: Two Novel Bacterial Proteasomes
Ruben E. Valas, Philip E. Bourne
J Mol Evol. 2008 May; 66(5): 494–504. Published online 2008 April 4. doi: 10.1007/s00239-008-9075-7
PMCID:
PMC3235984
Abstract Full Text PDF–494K
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