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		Research Increased burst size in multiply infected cells can alter basic virus dynamics Kara W Cummings, David N Levy, Dominik Wodarz Biology Direct 2012, 7:16 (8 May 2012) Abstract \| Provisional PDF \| PubMed
		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 \| Provisional PDF \| PubMed
		Research Structure based hypothesis of a mitochondrial ribosome rescue mechanism Martijn A Huynen, Isabel Duarte, Zofia M. A. Chrzanowska-Lightowlers, Sander B Nabuurs Biology Direct 2012, 7:14 (8 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Modeling the 3D structure of the human protein mtRF1 shows that it likely functions in recognizing and recycling stalled mitochondrial ribosomes.
		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 \| Provisional PDF \| PubMed \| 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.
		Research Domain enhanced lookup time accelerated BLAST Grzegorz M Boratyn, Alejandro A Schaffer, Richa Agarwala, Stephen F Altschul, David J Lipman, Thomas L Madden Biology Direct 2012, 7:12 (17 April 2012) Abstract \| Provisional 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.
		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 \| Provisional PDF \| PubMed
		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.
		Research Reaction-Diffusion-Delay Model for EPO/TNF-α Interaction in articular cartilage lesion abatement Jason M Graham, Bruce P Ayati, Lei Ding, Prem S Ramakrishnan, James A Martin Biology Direct 2012, 7:9 (21 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Graham et al. present a mathematical model that connects the biochemical interactions of cartilage cells with the spatial behavior observed in cartilage injury.
		Research Rate and breadth of protein evolution are only weakly correlated Sergey A Naumenko, Alexey S Kondrashov Biology Direct 2012, 7:8 (15 February 2012) Abstract \| Full text \| PDF \| PubMed
		Research The 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 \| Full text \| PDF \| PubMed \| 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.
		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
		Discovery notes Lateral transfer of tetrahymanol-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 \| Full text \| 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.
		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 \| 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.
		Research IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice Neil S Greenspan, Myro A Lu, Jacob W Shipley, Xuedong Ding, Qing Li, Dilara Sultana, Maria Kollaros, John R Schreiber, Pingfu Fu, Chaim Putterman, Steven N Emancipator Biology Direct 2012, 7:3 (16 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In MRL/lpr mice, which spontaneously develop autoimmune glomerulonephritis like that in systemic lupus erythematosus, genetic elimination of IgG3 antibody production diminishes renal pathology and extends lifespan.
		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.
		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
		Research CRISPR loci reveal networks of gene exchange in archaea Avital Brodt, Mor N Lurie-Weinberger, Uri Gophna Biology Direct 2011, 6:65 (21 December 2011) Abstract \| Full text \| PDF \| PubMed
		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 \| Full text \| 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.
		Research Purine biosynthesis in archaea: variations on a theme Anne M Brown, Samantha L Hoopes, Robert H White, Catherine A Sarisky Biology Direct 2011, 6:63 (14 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations Etienne Joly Biology Direct 2011, 6:62 (9 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A model whereby new species arise by budding from the ancestral stock rather than by splitting into separate populations, with advantageous recessive phenotypes promoting the direct selection of reproductive barriers.
		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
		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.
		Research Extensive intron gain in the ancestor of placental mammals Dušan Kordiš Biology Direct 2011, 6:59 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Phylogenomic analysis of domesticated genes provides evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution.
		Review Molecular musings in microbial ecology and evolution Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011) Abstract \| Full text \| PDF \| PubMed
		Research Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber Biology Direct 2011, 6:57 (25 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transmembrane helices can be either complex (possibly common ancestry) or simple (likely of convergent evolution); the latter should be excluded from similarity searches to avoid false assignments of protein homology.

	All
		Research Increased burst size in multiply infected cells can alter basic virus dynamics Kara W Cummings, David N Levy, Dominik Wodarz Biology Direct 2012, 7:16 (8 May 2012) Abstract \| Provisional PDF \| PubMed
		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 \| Provisional PDF \| PubMed
		Research Structure based hypothesis of a mitochondrial ribosome rescue mechanism Martijn A Huynen, Isabel Duarte, Zofia M. A. Chrzanowska-Lightowlers, Sander B Nabuurs Biology Direct 2012, 7:14 (8 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Modeling the 3D structure of the human protein mtRF1 shows that it likely functions in recognizing and recycling stalled mitochondrial ribosomes.
		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 \| Provisional PDF \| PubMed \| 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.
		Research Domain enhanced lookup time accelerated BLAST Grzegorz M Boratyn, Alejandro A Schaffer, Richa Agarwala, Stephen F Altschul, David J Lipman, Thomas L Madden Biology Direct 2012, 7:12 (17 April 2012) Abstract \| Provisional 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.
		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 \| Provisional PDF \| PubMed
		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.
		Research Reaction-Diffusion-Delay Model for EPO/TNF-α Interaction in articular cartilage lesion abatement Jason M Graham, Bruce P Ayati, Lei Ding, Prem S Ramakrishnan, James A Martin Biology Direct 2012, 7:9 (21 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Graham et al. present a mathematical model that connects the biochemical interactions of cartilage cells with the spatial behavior observed in cartilage injury.
		Research Rate and breadth of protein evolution are only weakly correlated Sergey A Naumenko, Alexey S Kondrashov Biology Direct 2012, 7:8 (15 February 2012) Abstract \| Full text \| PDF \| PubMed
		Research The 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 \| Full text \| PDF \| PubMed \| 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.
		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
		Discovery notes Lateral transfer of tetrahymanol-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 \| Full text \| 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.
		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 \| 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.
		Research IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice Neil S Greenspan, Myro A Lu, Jacob W Shipley, Xuedong Ding, Qing Li, Dilara Sultana, Maria Kollaros, John R Schreiber, Pingfu Fu, Chaim Putterman, Steven N Emancipator Biology Direct 2012, 7:3 (16 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In MRL/lpr mice, which spontaneously develop autoimmune glomerulonephritis like that in systemic lupus erythematosus, genetic elimination of IgG3 antibody production diminishes renal pathology and extends lifespan.
		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.
		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
		Research CRISPR loci reveal networks of gene exchange in archaea Avital Brodt, Mor N Lurie-Weinberger, Uri Gophna Biology Direct 2011, 6:65 (21 December 2011) Abstract \| Full text \| PDF \| PubMed
		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 \| Full text \| 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.
		Research Purine biosynthesis in archaea: variations on a theme Anne M Brown, Samantha L Hoopes, Robert H White, Catherine A Sarisky Biology Direct 2011, 6:63 (14 December 2011) Abstract \| Full text \| PDF \| PubMed
		Research The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations Etienne Joly Biology Direct 2011, 6:62 (9 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A model whereby new species arise by budding from the ancestral stock rather than by splitting into separate populations, with advantageous recessive phenotypes promoting the direct selection of reproductive barriers.
		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
		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.
		Research Extensive intron gain in the ancestor of placental mammals Dušan Kordiš Biology Direct 2011, 6:59 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Phylogenomic analysis of domesticated genes provides evidence for numerous intron gains in the ancestor of placental mammals and demonstrates that adequate taxon sampling is crucial for reconstructing intron evolution.
		Review Molecular musings in microbial ecology and evolution Rebecca J Case, Yan Boucher Biology Direct 2011, 6:58 (10 November 2011) Abstract \| Full text \| PDF \| PubMed
		Research Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber Biology Direct 2011, 6:57 (25 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transmembrane helices can be either complex (possibly common ancestry) or simple (likely of convergent evolution); the latter should be excluded from similarity searches to avoid false assignments of protein homology.