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	1. 1381 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
	2. 667 Accesses	Discovery notes Lateral transfer of tetrahymenol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen Kiyotaka Takishita, Yoshito Chikaraishi, Michelle M Leger, Eunsoo Kim, Akinori Yabuki, Naohiko Ohkouchi, Andrew J Roger Biology Direct 2012, 7:5 (1 February 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Tetrahymanol functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments, and genes encoding the tetrahymanol synthesizing enzyme have been laterally transferred among several phylogenetically diverged eukaryotes.
	3. 649 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
	4. 588 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 \| Provisional PDF \| PubMed \| 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.
	5. 565 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 \| Provisional PDF \| PubMed
	6. 558 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.
	7. 515 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. 501 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.
	9. 478 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. 462 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
	11. 459 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
	12. 454 Accesses	Research The archaeal CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes Kira S Makarova, Eugene V Koonin, Zvi Kelman Biology Direct 2012, 7:7 (13 February 2012) Abstract \| Provisional PDF \| Editor’s summary Comparative genomic analysis reveals diverged orthologs of eukaryotic CDC45 protein and bacterial RecJ nuclease in nearly all archaeal genomes; the CMG complex is conserved in both archaea and eukaryotes, and appears to be an essential component of the ancestral DNA replication machinery.
	13. 408 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.
	14. 405 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
	15. 373 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
	16. 372 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
	17. 369 Accesses	Hypothesis Uniting sex and eukaryote origins in an emerging oxygenic world Jeferson Gross, Debashish Bhattacharya Biology Direct 2010, 5:53 (23 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Accumulation of oxygen during the Archaen might have driven the origin of eukaryotes with evolution of the endomembrane system, mitochondria, sex (meiosis), and the nucleus as responses to oxygen toxicity.
	18. 365 Accesses	Research On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence Douglas L Theobald Biology Direct 2011, 6:60 (24 November 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Douglas Theobald, in response to recent criticisms, provides evidence to further support his claim that Darwin's hypothesis that all life on earth has a universal common ancestor has been formally confirmed by a homology independent statistic test.
	19. 360 Accesses	Research Accurate State Estimation from Uncertain Data and Models: An Application of Data Assimilation to Mathematical Models of Human Brain Tumors Eric J Kostelich, Yang Kuang, Joshua M McDaniel, Nina Z Moore, Nikolay L Martirosyan, Mark C Preul Biology Direct 2011, 6:64 (21 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary State estimation schemes, employed operationally for weather forecasting, can be applied in principle to make useful short-term predictions of the growth and spread of malignant tumors in individual patient cases.
	20. 335 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
	21. 334 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.
	22. 333 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
	23. 330 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.
	24. 318 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.
	25. 313 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.