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	1. 17938 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.
	2. 11248 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
	3. 9001 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
	4. 8278 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
	5. 8248 Accesses	Comment The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)^a Harold S Bernhardt Biology Direct 2012, 7:23 (13 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary It is argued that the RNA world hypothesis, although far from perfect or complete, is the best model we currently have to understand the backstory to contemporary biology.
	6. 7513 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.
	7. 7098 Accesses	Research Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics Dapeng Zhang, Robson F de Souza, Vivek Anantharaman, Lakshminarayan M Iyer, L Aravind Biology Direct 2012, 7:18 (25 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comprehensive dissection of polymorphic and related secreted toxin systems uncovers nearly 240 toxin and immunity domains with implications for intra-organismal conflict, kin discrimination, pathogenesis and emergence of eukaryotic sub-cellular systems.
	8. 6963 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
	9. 6748 Accesses	Review Bioinformatics clouds for big data manipulation Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao, Zhang Zhang Biology Direct 2012, 7:43 (28 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Bioinformatics clouds are capable of delivering a large variety of computer resources as services via the Internet and thus bear great promise in addressing big data storage and analysis issues.
	10. 6548 Accesses	Review Origin and evolution of spliceosomal introns Igor B Rogozin, Liran Carmel, Miklos Csuros, Eugene V Koonin Biology Direct 2012, 7:11 (16 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	11. 5966 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. 5708 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.
	13. 5683 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
	14. 5668 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.
	15. 5442 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.
	16. 4968 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.
	17. 4948 Accesses	Opinion Does the central dogma still stand? Eugene V Koonin Biology Direct 2012, 7:27 (23 August 2012) Abstract \| Full text \| PDF \| PubMed
	18. 4924 Accesses	Research On the molecular mechanism of GC content variation among eubacterial genomes Hao Wu, Zhang Zhang, Songnian Hu, Jun Yu Biology Direct 2012, 7:2 (10 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New large-scale comparative genome analyses provided further evidences indicating that polymerases involved in either replication or repair pathways underlie the GC content variability in eubacteria.
	19. 4859 Accesses	Research Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely, Fulvia Bono Biology Direct 2013, 8:2 (16 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of a large sequence dataset from the thermotolerant hydrothermal vent annelid Alvinella pompejana identified the CvP-bias as a robust measure of thermostability in eukaryotes.
	20. 4846 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
	21. 4841 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
	22. 4813 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.
	23. 4573 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. 4490 Accesses	Opinion The multiple personalities of Watson and Crick strands Reed A Cartwright, Dan Graur Biology Direct 2011, 6:7 (8 February 2011) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary In genetics and genomics, the terminology of Watson and Crick strands is muddled by divergent and conflicting meanings; it requires standardization.
	25. 4475 Accesses	Research Domain enhanced lookup time accelerated BLAST Grzegorz M Boratyn, Alejandro A Schäffer, Richa Agarwala, Stephen F Altschul, David J Lipman, Thomas L Madden Biology Direct 2012, 7:12 (17 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DELTA-BLAST is a new BLAST alignment tool for sensitive protein searches that uses conserved domain models to construct a position specific scoring matrix.
	26. 4419 Accesses	Research Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs Saakshi Jalali, Gopal Jayaraj, Vinod Scaria Biology Direct 2012, 7:25 (7 August 2012) Abstract \| Full text \| PDF \| PubMed
	27. 4400 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
	28. 3955 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
	29. 3916 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
	30. 3740 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
	31. 3711 Accesses	Comment Next-generation phylogenomics Cheong Xin Chan, Mark A Ragan Biology Direct 2013, 8:3 (22 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Highly scalable phylogenomic approaches are needed to make evolutionary sense of the ongoing deluge of sequence data; these approaches can be free from multiple sequence alignment.
	32. 3629 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 \| Cited on BioMed Central
	33. 3604 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 \| Cited on BioMed Central
	34. 3572 Accesses	Research Pathway-based classification of cancer subtypes Shinuk Kim, Mark Kon, Charles DeLisi Biology Direct 2012, 7:21 (3 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Determining the most significant pathway biomarkers for differentiating cancer subtypes can provide significantly more reproducible discriminatory gene sets under varying experimental/clinical conditions.
	35. 3408 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
	36. 3379 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.
	37. 3231 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.
	38. 3086 Accesses	Research Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns Lin Sen, Mario A Fares, Bo Liang, Lei Gao, Bo Wang, Ting Wang, Ying-Juan Su Biology Direct 2011, 6:29 (3 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	39. 3017 Accesses	Review Constructive neutral evolution: exploring evolutionary theory’s curious disconnect Arlin Stoltzfus Biology Direct 2012, 7:35 (13 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Ideas such as "Constructive Neutral Evolution" expose a curious disconnect: theoreticians routinely invoke formal models that imply mutationism, yet our notions of causation and explanation remain anchored in Darwinism.
	40. 2985 Accesses	Hypothesis Amino acid fermentation at the origin of the genetic code Harold P de Vladar Biology Direct 2012, 7:6 (10 February 2012) Abstract \| Full text \| PDF \| PubMed
	41. 2950 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
	42. 2918 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
	43. 2915 Accesses	Research The origin of life is a spatially localized stochastic transition Meng Wu, Paul G Higgs Biology Direct 2012, 7:42 (24 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Replication in the RNA World originates by a rare chance event involving a small number of molecules, followed by a rapid deterministic spread of an autocatalytic state.
	44. 2873 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
	45. 2868 Accesses	Hypothesis Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? Harold S Bernhardt, Warren P Tate Biology Direct 2012, 7:4 (20 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The greater stability of key RNA bonds at acidic pH, such as link the phosphodiester backbone and between amino acids and tRNA, suggests the RNA world evolved in acidic conditions.
	46. 2841 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.
	47. 2810 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
	48. 2741 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 \| Cited on BioMed Central \| 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.
	49. 2705 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 \| 1 comment \| F1000 Biology
	50. 2688 Accesses	Research Transcription factor binding sites are highly enriched within microRNA precursor sequences Jittima Piriyapongsa, I King Jordan, Andrew B Conley, Tom Ronan, Neil R Smalheiser Biology Direct 2011, 6:61 (2 December 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment