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	1. 8563 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. 5735 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
	3. 5210 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
	4. 4614 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. 4452 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
	6. 4419 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. 4012 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
	8. 3816 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.
	9. 3649 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
	10. 3645 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. 3566 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
	12. 3509 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
	13. 3506 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
	14. 3364 Accesses	Review The struggle for life of the genome's selfish architects Aurélie Hua-Van, Arnaud Le Rouzic, Thibaud S Boutin, Jonathan Filée, Pierre Capy Biology Direct 2011, 6:19 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transposable elements are selfish inhabitants of almost all genomes, and maintain with them long-lasting and complex interactions, reviewed here from the point of view of both genomes and transposable elements
	15. 3346 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
	16. 3283 Accesses	Research On origin of genetic code and tRNA before translation Andrei S Rodin, Eörs Szathmáry, Sergei N Rodin Biology Direct 2011, 6:14 (22 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A previously unreported strong bias towards anticodons revealed in published amino acid-binding sites of in vitro selected RNA aptamers unambiguously points to the origin of the genetic code before translation.
	17. 3274 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
	18. 3264 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.
	19. 3218 Accesses	Research Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale Evgeny Shmelkov, Zuojian Tang, Iannis Aifantis, Alexander Statnikov Biology Direct 2011, 6:15 (28 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Rigorous evaluation of ten popular pathway databases reveals that the majority of these databases do not provide high quality and complete lists of transcriptional regulatory targets.
	20. 3207 Accesses	Research The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon Ruben E Valas, Philip E Bourne Biology Direct 2011, 6:16 (28 February 2011) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
	21. 3195 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
	22. 3183 Accesses	Comment Endosymbiont or host: who drove mitochondrial and plastid evolution? Jeferson Gross, Debashish Bhattacharya Biology Direct 2011, 6:12 (19 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An unresolved question in mitochondrial and plastid evolution is whether the establishment of protein topogenesis into the organelles developed primarily under the control of the host or the endosymbiont genome.
	23. 3145 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.
	24. 3030 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.
	25. 3027 Accesses	Hypothesis On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:14 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central