Biology Direct | All articles

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

Evolutionary history of bacteriophages with double-stranded DNA genomes

Galina Glazko, Vladimir Makarenkov, Jing Liu, Arcady Mushegian Biology Direct 2007, 2:36 (6 December 2007)

Abstract | Full text | PDF | PubMed

Exosomal transfer of proteins and RNAs at synapses in the nervous system

Neil R Smalheiser Biology Direct 2007, 2:35 (30 November 2007)

Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach

Flavia Frabetti, Raffaella Casadei, Luca Lenzi, Silvia Canaider, Lorenza Vitale, Federica Facchin, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli Biology Direct 2007, 2:34 (27 November 2007)

Abstract | Full text | PDF | PubMed

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

Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

Jacob Axelsen, Koon-Kiu Yan, Sergei Maslov Biology Direct 2007, 2:32 (26 November 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Evaluating the protein coding potential of exonized transposable element sequences

Jittima Piriyapongsa, Mark T Rutledge, Sanil Patel, Mark Borodovsky, I King Jordan Biology Direct 2007, 2:31 (26 November 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

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

Opening Pandora's Box: making biological discoveries through computational data exploration

L Aravind Biology Direct 2007, 2:29 (20 November 2007)

Abstract | Full text | PDF | PubMed

Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?

Lev Klebanov, Linlin Chen, Andrei Yakovlev Biology Direct 2007, 2:28 (7 November 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

Larry J Wilhelm, H James Tripp, Scott A Givan, Daniel P Smith, Stephen J Giovannoni Biology Direct 2007, 2:27 (7 November 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Calibrating E-values for MS²database search methods

Gelio Alves, Aleksey Y Ogurtsov, Wells W Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu Biology Direct 2007, 2:26 (5 November 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics

Gelio Alves, Aleksey Y Ogurtsov, Yi-Kuo Yu Biology Direct 2007, 2:25 (25 October 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

Artem S Novozhilov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:24 (23 October 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?

Nicolas Martin, Elizabeth A Ruedi, Richard LeDuc, Feng-Jie Sun, Gustavo Caetano-Anollés Biology Direct 2007, 2:23 (25 September 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes

Fabrizio Lillo, David C Krakauer Biology Direct 2007, 2:22 (18 September 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

The Biological Big Bang model for the major transitions in evolution

Eugene V Koonin Biology Direct 2007, 2:21 (20 August 2007)

Extensive parallelism in protein evolution

Georgii A Bazykin, Fyodor A Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, Alexey S Kondrashov Biology Direct 2007, 2:20 (16 August 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

The intracellular region of Notch ligands: does the tail make the difference?

Alessandro Pintar, Alfredo De Biasio, Matija Popovic, Neli Ivanova, Sándor Pongor Biology Direct 2007, 2:19 (10 July 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold

A Maxwell Burroughs, S Balaji, Lakshminarayan M Iyer, L Aravind Biology Direct 2007, 2:18 (2 July 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

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)

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

Pan Du, Warren A Kibbe, Simon M Lin Biology Direct 2007, 2:16 (31 May 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

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)

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

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

	All
		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
		Research Evolutionary history of bacteriophages with double-stranded DNA genomes Galina Glazko, Vladimir Makarenkov, Jing Liu, Arcady Mushegian Biology Direct 2007, 2:36 (6 December 2007) Abstract \| Full text \| PDF \| PubMed
		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
		Research Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach Flavia Frabetti, Raffaella Casadei, Luca Lenzi, Silvia Canaider, Lorenza Vitale, Federica Facchin, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli Biology Direct 2007, 2:34 (27 November 2007) Abstract \| Full text \| PDF \| PubMed
		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
		Research Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins Jacob Axelsen, Koon-Kiu Yan, Sergei Maslov Biology Direct 2007, 2:32 (26 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Evaluating the protein coding potential of exonized transposable element sequences Jittima Piriyapongsa, Mark T Rutledge, Sanil Patel, Mark Borodovsky, I King Jordan Biology Direct 2007, 2:31 (26 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		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
		Editorial Opening Pandora's Box: making biological discoveries through computational data exploration L Aravind Biology Direct 2007, 2:29 (20 November 2007) Abstract \| Full text \| PDF \| PubMed
		Research Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis? Lev Klebanov, Linlin Chen, Andrei Yakovlev Biology Direct 2007, 2:28 (7 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data Larry J Wilhelm, H James Tripp, Scott A Givan, Daniel P Smith, Stephen J Giovannoni Biology Direct 2007, 2:27 (7 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Calibrating E-values for MS²database search methods Gelio Alves, Aleksey Y Ogurtsov, Wells W Wu, Guanghui Wang, Rong-Fong Shen, Yi-Kuo Yu Biology Direct 2007, 2:26 (5 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics Gelio Alves, Aleksey Y Ogurtsov, Yi-Kuo Yu Biology Direct 2007, 2:25 (25 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape Artem S Novozhilov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:24 (23 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? Nicolas Martin, Elizabeth A Ruedi, Richard LeDuc, Feng-Jie Sun, Gustavo Caetano-Anollés Biology Direct 2007, 2:23 (25 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes Fabrizio Lillo, David C Krakauer Biology Direct 2007, 2:22 (18 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		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
		Research Extensive parallelism in protein evolution Georgii A Bazykin, Fyodor A Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, Alexey S Kondrashov Biology Direct 2007, 2:20 (16 August 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Review The intracellular region of Notch ligands: does the tail make the difference? Alessandro Pintar, Alfredo De Biasio, Matija Popovic, Neli Ivanova, Sándor Pongor Biology Direct 2007, 2:19 (10 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold A Maxwell Burroughs, S Balaji, Lakshminarayan M Iyer, L Aravind Biology Direct 2007, 2:18 (2 July 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		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
		Research nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays Pan Du, Warren A Kibbe, Simon M Lin Biology Direct 2007, 2:16 (31 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		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
		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
		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

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