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	1. 54425 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. 37781 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. 29660 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. 28111 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. 24611 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
	6. 23030 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 \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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.
	7. 22573 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
	8. 22523 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.
	9. 22490 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
	10. 21504 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. 19996 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
	12. 19799 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
	13. 18997 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
	14. 18147 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
	15. 17264 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
	16. 17006 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
	17. 16969 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.
	18. 16504 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
	19. 15902 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.
	20. 15232 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.
	21. 14899 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.
	22. 14604 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 \| Cited on BioMed Central
	23. 14098 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
	24. 13763 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
	25. 13760 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 \| 1 comment
	26. 13311 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 \| Cited on BioMed Central \| 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.
	27. 12394 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
	28. 12319 Accesses	Research The origins of phagocytosis and eukaryogenesis Natalya Yutin, Maxim Y Wolf, Yuri I Wolf, Eugene V Koonin Biology Direct 2009, 4:9 (26 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Archaeal ancestors of eukaryotes might have possessed a primitive, actin-based cytoskeleton that would facilitate engulfment of bacteria, in particular, the proto-mitochondrial endosymbiont.
	29. 12063 Accesses	Research 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 Biology Direct 2009, 4:27 (24 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The relatively high zinc content of living cells and its role as cofactor in many key enzymes and RNA structures might reflect the origin of life in zinc-rich environments.
	30. 11983 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
	31. 11800 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
	32. 11237 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 \| Cited on BioMed Central
	33. 11052 Accesses	Research Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:33 (27 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	34. 11009 Accesses	Research Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens Dimitris Papamichail, Nicholas Delihas Biology Direct 2006, 1:12 (22 May 2006) Abstract \| Full text \| PDF \| PubMed
	35. 10950 Accesses	Hypothesis Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases Eugene V Koonin Biology Direct 2006, 1:39 (18 December 2006) Abstract \| Full text \| PDF \| PubMed
	36. 10578 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
	37. 10560 Accesses	Research The immune-body cytokine network defines a social architecture of cell interactions Ziv Frankenstein, Uri Alon, Irun R Cohen Biology Direct 2006, 1:32 (24 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	38. 10479 Accesses	Research Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation Fyodor A Kondrashov, Eugene V Koonin, Igor G Morgunov, Tatiana V Finogenova, Marie N Kondrashova Biology Direct 2006, 1:31 (23 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	39. 10386 Accesses	Research pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model Georg Neuberger, Georg Schneider, Frank Eisenhaber Biology Direct 2007, 2:1 (12 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	40. 10342 Accesses	Research Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin, Eugene V Koonin, Matthew B Stott, Bruce W Mountain, Michelle A Crowe, Angela V Smirnova, Peter F Dunfield, Lu Feng, Lei Wang, Maqsudul Alam Biology Direct 2008, 3:26 (1 July 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Genome sequence of a methanotrophic member of the bacterial phylum Verrucomicrobia reveals adaptations to the methane utilization under acidic conditions and supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a superphylum
	41. 10289 Accesses	Research Method of predicting Splice Sites based on signal interactions Alexander Churbanov, Igor B Rogozin, Jitender S Deogun, Hesham Ali Biology Direct 2006, 1:10 (3 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	42. 10041 Accesses	Review Molecular chaperones and selection against mutations Katarzyna Tomala, Ryszard Korona Biology Direct 2008, 3:5 (26 February 2008) Abstract \| Full text \| PDF \| PubMed
	43. 9823 Accesses	Research The control of CD4⁺CD25⁺Foxp3⁺regulatory T cell survival Pushpa Pandiyan, Michael J Lenardo Biology Direct 2008, 3:6 (27 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	44. 9215 Accesses	Research The origin and evolution of the ribosome Temple F Smith, Jung C Lee, Robin R Gutell, Hyman Hartman Biology Direct 2008, 3:16 (22 April 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	45. 9164 Accesses	Editorial A community experiment with fully open and published peer review Eugene V Koonin, Laura F Landweber, David J Lipman Biology Direct 2006, 1:1 (31 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
	46. 8894 Accesses	Research Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape Artem S Novozhilov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:24 (23 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	47. 8886 Accesses	Research Refuting phylogenetic relationships James Bucknam, Yan Boucher, Eric Bapteste Biology Direct 2006, 1:26 (6 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	48. 8779 Accesses	Research Mathematical modeling of tumor therapy with oncolytic viruses: Regimes with complete tumor elimination within the framework of deterministic models Artem S Novozhilov, Faina S Berezovskaya, Eugene V Koonin, Georgy P Karev Biology Direct 2006, 1:6 (17 February 2006) Abstract \| Full text \| PDF \| PubMed
	49. 8441 Accesses	Hypothesis Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms Arnold J Bendich Biology Direct 2010, 5:42 (29 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Development is traced to the advent of a germ cell lineage in which oxidative stress and organellar DNA damage could be avoided.
	50. 8421 Accesses	Hypothesis Occurrence of cancer at multiple sites: Towards distinguishing multigenesis from metastasis Wei-Kang Zhang, Chun Zhang, Jing J Zhang, Shi V Liu Biology Direct 2008, 3:14 (11 April 2008) Abstract \| Full text \| PDF \| PubMed