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	1. 43687 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. 34131 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
	3. 25925 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
	4. 23771 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.
	5. 19840 Accesses	Discovery notes Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites Sebastian Maurer-Stroh, Jianmin Ma, Raphael Lee, Fernanda L Sirota, Frank Eisenhaber Biology Direct 2009, 4:18 (20 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Sequence variation analysis and 3D modeling of the 2009 H1N1 influenza virus indicate that antiviral drugs currently in use should remain effective for treatment.
	6. 18977 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
	7. 17972 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
	8. 17042 Accesses	Research Origin and evolution of the peroxisomal proteome Toni Gabaldón, Berend Snel, Frank van Zimmeren, Wieger Hemrika, Henk Tabak, Martijn A Huynen Biology Direct 2006, 1:8 (23 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	9. 16356 Accesses	Research Proteomic and bioinformatic analysis of epithelial tight junction reveals an unexpected cluster of synaptic molecules Vivian W Tang Biology Direct 2006, 1:37 (8 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	10. 16096 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. 14948 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
	12. 14763 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
	13. 14643 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
	14. 14508 Accesses	Hypothesis The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life Eugene V Koonin Biology Direct 2007, 2:15 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	15. 14309 Accesses	Hypothesis The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Eugene V Koonin Biology Direct 2006, 1:22 (14 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	16. 13051 Accesses	Research Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data Larry J Wilhelm, H James Tripp, Scott A Givan, Daniel P Smith, Stephen J Giovannoni Biology Direct 2007, 2:27 (7 November 2007) Abstract \| Full text \| PDF \| PubMed
	17. 12949 Accesses	Research Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus Yuri I Wolf, Cecile Viboud, Edward C Holmes, Eugene V Koonin, David J Lipman Biology Direct 2006, 1:34 (26 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human influenza virus evolution shifts from long stasis periods with minimal antigenic drift to brief intervals of rapid Darwinian evolution, when a new dominant virus rapidly eliminates most other variants.
	18. 11982 Accesses	Review A survey of motif discovery methods in an integrated framework Geir Sandve, Finn Drabløs Biology Direct 2006, 1:11 (6 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19. 11628 Accesses	Research The stochastic behavior of a molecular switching circuit with feedback Supriya Krishnamurthy, Eric Smith, David Krakauer, Walter Fontana Biology Direct 2007, 2:13 (31 May 2007) Abstract \| Full text \| PDF \| PubMed
	20. 11574 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.
	21. 10811 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.
	22. 10770 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.
	23. 10693 Accesses	Research Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution Jesse D Bloom, Philip A Romero, Zhongyi Lu, Frances H Arnold Biology Direct 2007, 2:17 (28 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	24. 9889 Accesses	Research Component retention in principal component analysis with application to cDNA microarray data Richard Cangelosi, Alain Goriely Biology Direct 2007, 2:2 (17 January 2007) Abstract \| Full text \| PDF \| PubMed
	25. 9724 Accesses	Review Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla Joseph F Ryan, Andreas D Baxevanis Biology Direct 2007, 2:37 (13 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central