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	1. 9068 Accesses	Hypothesis The ancient Virus World and evolution of cells Eugene V Koonin, Tatiana G Senkevich, Valerian V Dolja Biology Direct 2006, 1:29 (19 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology
	2. 6918 Accesses	Research A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses Geoffrey S Diemer, Kenneth M Stedman Biology Direct 2012, 7:13 (19 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The discovery of a previously unknown viral genome, the apparent result of a recombination event between unrelated RNA and DNA viruses, has implications for theories of viral evolution.
	3. 6246 Accesses	Research Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution Thomas Cavalier-Smith Biology Direct 2010, 5:7 (4 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	4. 6054 Accesses	Review Early evolution without a tree of life William F Martin Biology Direct 2011, 6:36 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
	5. 5282 Accesses	Research Transcript length bias in RNA-seq data confounds systems biology Alicia Oshlack, Matthew J Wakefield Biology Direct 2009, 4:14 (16 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	6. 4776 Accesses	Research Rooting the tree of life by transition analyses Thomas Cavalier-Smith Biology Direct 2006, 1:19 (11 July 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	7. 4601 Accesses	Research Energetics and genetics across the prokaryote-eukaryote divide Nick Lane Biology Direct 2011, 6:35 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
	8. 4344 Accesses	Research The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms Avshalom Zoossmann-Diskin Biology Direct 2010, 5:57 (6 October 2010) Abstract \| Full text \| PDF \| PubMed
	9. 4289 Accesses	Hypothesis The public goods hypothesis for the evolution of life on Earth James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell Biology Direct 2011, 6:41 (23 August 2011) Abstract \| Full text \| PDF \| PubMed
	10. 4157 Accesses	Research The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner Nicolas Glansdorff, Ying Xu, Bernard Labedan Biology Direct 2008, 3:29 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Last Universal Common Ancestor developed in a protoeukaryotic, promiscuous and genetically redundant community of cells with a broad, moderate thermal profile and an RNA genome enclosed in a protonucleus.
	11. 4141 Accesses	Review Exosomal transfer of proteins and RNAs at synapses in the nervous system Neil R Smalheiser Biology Direct 2007, 2:35 (30 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	12. 4078 Accesses	Research Evolution before genes Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman, Eörs Szathmáry Biology Direct 2012, 7:1 (5 January 2012) Abstract \| Full text \| PDF \| PubMed
	13. 4068 Accesses	Review How stands the Tree of Life a century and a half after The Origin? Maureen A O'Malley, Eugene V Koonin Biology Direct 2011, 6:32 (30 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	14. 4061 Accesses	Hypothesis On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth Armen Y Mulkidjanian Biology Direct 2009, 4:26 (24 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Life may have emerged owing to the ability of porous, hydrothermal zinc sulfide precipitates to store solar energy and reduce atmospheric carbon dioxide, providing nourishment and shelter for the first organisms.
	15. 3988 Accesses	Opinion Is evolution Darwinian or/and Lamarckian? Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:42 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Darwinian and Lamarckian mechanisms are both important for evolution and seem to belong to different parts of the broad range of complex interactions between genotypes and environment.
	16. 3977 Accesses	Review The new biology: beyond the Modern Synthesis Michael R Rose, Todd H Oakley Biology Direct 2007, 2:30 (24 November 2007) Abstract \| Full text \| PDF \| PubMed
	17. 3970 Accesses	Research Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin Biology Direct 2011, 6:38 (14 July 2011) Abstract \| Full text \| PDF \| PubMed
	18. 3891 Accesses	Review Prokaryotic evolution and the tree of life are two different things Eric Bapteste, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, François-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher, William Martin Biology Direct 2009, 4:34 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary From philosophical, scientific and epistemological perspectives, we argue that the tree of life can not successfully account for prokaryotic evolution, and we briefly set out alternative models to study their evolution.
	19. 3700 Accesses	Review Trees and networks before and after Darwin Mark A Ragan Biology Direct 2009, 4:43 (16 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology
	20. 3685 Accesses	Research Telling the whole story in a 10,000-genome world Robert G Beiko Biology Direct 2011, 6:34 (30 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	21. 3586 Accesses	Research The advantages and disadvantages of horizontal gene transfer and the emergence of the first species Aaron A Vogan, Paul G Higgs Biology Direct 2011, 6:1 (3 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Horizontal gene transfer is likely to be advantageous in the earliest organisms but disadvantageous in modern prokaryotes; hence evolution passes through a Darwinian threshold.
	22. 3529 Accesses	Hypothesis The Biological Big Bang model for the major transitions in evolution Eugene V Koonin Biology Direct 2007, 2:21 (20 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
	23. 3522 Accesses	Opinion From the scala naturae to the symbiogenetic and dynamic tree of life Ulrich Kutschera Biology Direct 2011, 6:33 (30 June 2011) Abstract \| Full text \| PDF \| PubMed
	24. 3517 Accesses	Research Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome Manfredo J Seufferheld, Kyung Kim, James Whitfield, Alejandro Valerio, Gustavo Caetano-Anollés Biology Direct 2011, 6:50 (5 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The universality of volutin granules and presence of the vacuolar pyrophosphatase in the three superkingdoms of life reveals that the acidocalcisomes may have originated in the Last Universal Common Ancestor.
	25. 3433 Accesses	Research A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin Biology Direct 2006, 1:7 (16 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Computational analysis shows that CRISPR repeats and associated Cas proteins in prokaryotes might act in conjunction as a RNA-silencing mechanism against plasmids and viruses, similar to the eukaryotic RNA-interference system.