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	51. 2666 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. 2642 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
	53. 2616 Accesses	Research Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes Sergei A Filichkin, Todd C Mockler Biology Direct 2012, 7:20 (2 July 2012) Abstract \| Full text \| PDF \| PubMed
	54. 2579 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
	55. 2556 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.
	56. 2547 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 \| Full text \| 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.
	57. 2526 Accesses	Research Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions Jinzhuang Dou, Xiqiang Zhao, Xiaoteng Fu, Wenqian Jiao, Nannan Wang, Lingling Zhang, Xiaoli Hu, Shi Wang, Zhenmin Bao Biology Direct 2012, 7:17 (8 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A de novo SNP calling algorithm called iML which incorporates the mixed Poisson/normal model to exclude incorrect SNP calls resulting from repetitive genomic regions.
	58. 2520 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.
	59. 2450 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
	60. 2448 Accesses	Review How stands the Tree of Life a century and a half after The Origin? Maureen A O'Malley, Eugene V Koonin Biology Direct 2011, 6:32 (30 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	61. 2441 Accesses	Discovery notes On the complexity of miRNA-mediated regulation in plants: novel insights into the genomic organization of plant miRNAs Moreno Colaiacovo, Antonella Lamontanara, Letizia Bernardo, Renzo Alberici, Cristina Crosatti, Lorenzo Giusti, Luigi Cattivelli, Primetta Faccioli Biology Direct 2012, 7:15 (8 May 2012) Abstract \| Full text \| PDF \| PubMed
	62. 2390 Accesses	Research Massive comparative genomic analysis reveals convergent evolution of specialized bacteria Vicky Merhej, Manuela Royer-Carenzi, Pierre Pontarotti, Didier Raoult Biology Direct 2009, 4:13 (10 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	63. 2388 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
	64. 2386 Accesses	Research Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes Kira S Makarova, Yuri I Wolf, Eugene V Koonin Biology Direct 2009, 4:19 (3 June 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	65. 2335 Accesses	Research MicroRNA expression in multiple myeloma is associated with genetic subtype, isotype and survival Jianxiang Chi, Erica Ballabio, Xiao-He Chen, Rajko Kušec, Steve Taylor, Deborah Hay, Daniela Tramonti, Nigel J Saunders, Timothy Littlewood, Francesco Pezzella, Jacqueline Boultwood, James S Wainscoat, Christian SR Hatton, Charles H Lawrie Biology Direct 2011, 6:23 (18 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary By looking at the expression pattern of microRNAs in tumor cells derived from mutiple myeloma (and pre-malignant MGUS) patients as well as counterpart normal cells (CD138+ plasma B cells), microRNAs associated with diagnosis, chromosomal abnormality type and survival are identified.
	66. 2334 Accesses	Comment Endosymbiont or host: who drove mitochondrial and plastid evolution? Jeferson Gross, Debashish Bhattacharya Biology Direct 2011, 6:12 (19 February 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An unresolved question in mitochondrial and plastid evolution is whether the establishment of protein topogenesis into the organelles developed primarily under the control of the host or the endosymbiont genome.
	67. 2326 Accesses	Discovery notes Archaeal origin of tubulin Natalya Yutin, Eugene V Koonin Biology Direct 2012, 7:10 (29 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Probable ancestors of eukaryotic tubulins, denoted artubulins, were discovered in two genomes of thaumarchaeota of the genus Nitrosoarchaeum.
	68. 2303 Accesses	Research Thousands of missed genes found in bacterial genomes and their analysis with COMBREX Derrick E Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P Anton, Lais Osmani, Martin Steffen, Simon Kasif, Steven L Salzberg Biology Direct 2012, 7:37 (30 October 2012) Abstract \| Full text \| PDF \| PubMed
	69. 2265 Accesses	Discovery notes Proteorhodopsin genes in giant viruses Natalya Yutin, Eugene V Koonin Biology Direct 2012, 7:34 (4 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Some giant viruses encode previously unknown proteorhodopsins that are predicted to affect signal transduction in infected protists and might have substantial ecological impact.
	70. 2257 Accesses	Hypothesis Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes Kira S Makarova, Vivek Anantharaman, L Aravind, Eugene V Koonin Biology Direct 2012, 7:40 (14 November 2012) Abstract \| Full text \| PDF \| PubMed
	71. 2251 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
	72. 2251 Accesses	Research Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes Dapeng Wang, Fei Liu, Lei Wang, Shi Huang, Jun Yu Biology Direct 2011, 6:13 (22 February 2011) Abstract \| Full text \| PDF \| PubMed
	73. 2235 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
	74. 2208 Accesses	Research Telling the whole story in a 10,000-genome world Robert G Beiko Biology Direct 2011, 6:34 (30 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	75. 2207 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