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	51. 255 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
	52. 254 Accesses	Discovery notes AID/APOBEC cytosine deaminase induces genome-wide kataegis Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano, Aleksandr A Rubel, Igor B Rogozin, Youri I Pavlov Biology Direct 2012, 7:47 (18 December 2012) Abstract \| Full text \| PDF \| PubMed
	53. 255 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
	54. 249 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
	55. 248 Accesses	Review Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution Jaroslav Flegr Biology Direct 2013, 8:1 (16 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Punctuational theories of evolution, which can be divided into five distinct types, provide explanations for a much broader spectrum of known evolutionary and ecological phenomena than classical gradualistic evolutionary theories.
	56. 246 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.
	57. 242 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
	58. 242 Accesses	Research The look-ahead effect of phenotypic mutations Dion J Whitehead, Claus O Wilke, David Vernazobres, Erich Bornberg-Bauer Biology Direct 2008, 3:18 (14 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	59. 233 Accesses	Research Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer Yuri I Wolf, Kira S Makarova, Natalya Yutin, Eugene V Koonin Biology Direct 2012, 7:46 (14 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Analysis of the updated set of orthologs in 120 archaeal genomes reveals a complex history of gene exchange with no major "highways" of horizontal gene transfer.
	60. 232 Accesses	Hypothesis Genome increase as a clock for the origin and evolution of life Alexei A Sharov Biology Direct 2006, 1:17 (12 June 2006) Abstract \| Full text \| PDF \| PubMed
	61. 231 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.
	62. 223 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.
	63. 212 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
	64. 212 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
	65. 211 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.
	66. 212 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.
	67. 209 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
	68. 208 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.
	69. 208 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
	70. 204 Accesses	Research CAIcal: A combined set of tools to assess codon usage adaptation Pere Puigbò, Ignacio G Bravo, Santiago Garcia-Vallve Biology Direct 2008, 3:38 (16 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The analysis of codon usage has been widely used for estimation of gene expressivity or gene adaptation, and may also be helpful for refining genome annotation.
	71. 203 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
	72. 204 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
	73. 201 Accesses	Research A family of GFP-like proteins with different spectral properties in lancelet Branchiostoma floridae Diana Baumann, Malcolm Cook, Limei Ma, Arcady Mushegian, Erik Sanders, Joel Schwartz, C Ron Yu Biology Direct 2008, 3:28 (3 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	74. 203 Accesses	Opinion The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:33 (29 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A tree is a natural representation of evolution owing to the inherent tree-like character of the replication process but the fundamental units of evolution amenable to tree analysis seem to be individual genetic elements rather than complete genomes.
	75. 201 Accesses	Comment FOXP3 and GARP (LRRC32): the master and its minion Michael Probst-Kepper, Jan Buer Biology Direct 2010, 5:8 (5 February 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent identification of glycoprotein-A repetitions predominant (GARP or LRRC32) as receptors for latent TGFb (which dominantly controls FOXP3 and the regulatory phenotype via a positive feedback loop) provides a missing link in our molecular understanding of FOXP3 in regulatory T cells