Volume 2, issue 1, December 2007
39 articles in this issue
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Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota"
Authors
- Eugene V Koonin
- Kira S Makarova
- James G Elkins
- Content type: Discovery notes
- Open Access
- Published: 14 December 2007
- Article: 38
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Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla
Authors
- Joseph F Ryan
- Andreas D Baxevanis
- Content type: Review
- Open Access
- Published: 13 December 2007
- Article: 37
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Evolutionary history of bacteriophages with double-stranded DNA genomes
Authors (first, second and last of 4)
- Galina Glazko
- Vladimir Makarenkov
- Arcady Mushegian
- Content type: Research
- Open Access
- Published: 06 December 2007
- Article: 36
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Exosomal transfer of proteins and RNAs at synapses in the nervous system
Authors
- Neil R Smalheiser
- Content type: Review
- Open Access
- Published: 30 November 2007
- Article: 35
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Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach
Authors (first, second and last of 9)
- Flavia Frabetti
- Raffaella Casadei
- Pierluigi Strippoli
- Content type: Research
- Open Access
- Published: 27 November 2007
- Article: 34
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Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
Authors (first, second and last of 5)
- Kira S Makarova
- Alexander V Sorokin
- Eugene V Koonin
- Content type: Research
- Open Access
- Published: 27 November 2007
- Article: 33
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Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins
Authors
- Jacob Bock Axelsen
- Koon-Kiu Yan
- Sergei Maslov
- Content type: Research
- Open Access
- Published: 26 November 2007
- Article: 32
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Evaluating the protein coding potential of exonized transposable element sequences
Authors (first, second and last of 5)
- Jittima Piriyapongsa
- Mark T Rutledge
- I King Jordan
- Content type: Research
- Open Access
- Published: 26 November 2007
- Article: 31
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The new biology: beyond the Modern Synthesis
Authors
- Michael R Rose
- Todd H Oakley
- Content type: Review
- Open Access
- Published: 24 November 2007
- Article: 30
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Opening Pandora's Box: making biological discoveries through computational data exploration
Authors
- L Aravind
- Content type: Editorial
- Open Access
- Published: 20 November 2007
- Article: 29
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Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?
Authors
- Lev Klebanov
- Linlin Chen
- Andrei Yakovlev
- Content type: Research
- Open Access
- Published: 07 November 2007
- Article: 28
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Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data
Authors (first, second and last of 5)
- Larry J Wilhelm
- H James Tripp
- Stephen J Giovannoni
- Content type: Research
- Open Access
- Published: 07 November 2007
- Article: 27
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Calibrating E-values for MS2 database search methods
Authors (first, second and last of 6)
- Gelio Alves
- Aleksey Y Ogurtsov
- Yi-Kuo Yu
- Content type: Research
- Open Access
- Published: 05 November 2007
- Article: 26
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RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics
Authors
- Gelio Alves
- Aleksey Y Ogurtsov
- Yi-Kuo Yu
- Content type: Research
- Open Access
- Published: 25 October 2007
- Article: 25
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Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape
Authors
- Artem S Novozhilov
- Yuri I Wolf
- Eugene V Koonin
- Content type: Research
- Open Access
- Published: 23 October 2007
- Article: 24
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Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?
Authors (first, second and last of 5)
- Nicolas Martin
- Elizabeth A Ruedi
- Gustavo Caetano-Anollés
- Content type: Research
- Open Access
- Published: 25 September 2007
- Article: 23
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A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes
Authors
- Fabrizio Lillo
- David C Krakauer
- Content type: Research
- Open Access
- Published: 18 September 2007
- Article: 22
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The Biological Big Bang model for the major transitions in evolution
Authors
- Eugene V Koonin
- Content type: Hypothesis
- Open Access
- Published: 20 August 2007
- Article: 21
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Extensive parallelism in protein evolution
Authors (first, second and last of 6)
- Georgii A Bazykin
- Fyodor A Kondrashov
- Alexey S Kondrashov
- Content type: Research
- Open Access
- Published: 16 August 2007
- Article: 20
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The intracellular region of Notch ligands: does the tail make the difference?
Authors (first, second and last of 4)
- Alessandro Pintar
- Alfredo De Biasio
- Neli Ivanova
- Content type: Review
- Open Access
- Published: 10 July 2007
- Article: 19
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Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold
Authors (first, second and last of 4)
- A Maxwell Burroughs
- S Balaji
- L Aravind
- Content type: Research
- Open Access
- Published: 02 July 2007
- Article: 18
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Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution
Authors (first, second and last of 4)
- Jesse D Bloom
- Philip A Romero
- Frances H Arnold
- Content type: Research
- Open Access
- Published: 28 June 2007
- Article: 17
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nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays
Authors
- Pan Du
- Warren A Kibbe
- Simon M Lin
- Content type: Research
- Open Access
- Published: 31 May 2007
- Article: 16
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The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
Authors
- Eugene V Koonin
- Content type: Hypothesis
- Open Access
- Published: 31 May 2007
- Article: 15
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On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
Authors
- Yuri I Wolf
- Eugene V Koonin
- Content type: Hypothesis
- Open Access
- Published: 31 May 2007
- Article: 14
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The stochastic behavior of a molecular switching circuit with feedback
Authors (first, second and last of 4)
- Supriya Krishnamurthy
- Eric Smith
- Walter Fontana
- Content type: Research
- Open Access
- Published: 31 May 2007
- Article: 13
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Modelling evolution on design-by-contract predicts an origin of Life through an abiotic double-stranded RNA world
Authors
- Albert DG de Roos
- Content type: Hypothesis
- Open Access
- Published: 27 April 2007
- Article: 12
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Protecting exons from deleterious R-loops: a potential advantage of having introns
Authors
- Deng-Ke Niu
- Content type: Hypothesis
- Open Access
- Published: 25 April 2007
- Article: 11
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The ability of natural tolerance to be applied to allogeneic tissue: determinants and limits
Authors (first, second and last of 4)
- William FN Chan
- Ainhoa Perez-Diez
- Colin C Anderson
- Content type: Research
- Open Access
- Published: 16 April 2007
- Article: 10
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How high is the level of technical noise in microarray data?
Authors
- Lev Klebanov
- Andrei Yakovlev
- Content type: Research
- Open Access
- Published: 11 April 2007
- Article: 9
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Retrospective analysis of protein kinase C-beta (PKC-β) expression in lymphoid malignancies and its association with survival in diffuse large B-cell lymphomas
Authors (first, second and last of 8)
- Shuyu Li
- Mark Phong
- Birong Liao
- Content type: Research
- Open Access
- Published: 21 February 2007
- Article: 8
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Conserved intron positions in ancient protein modules
Authors
- Albert DG de Roos
- Content type: Research
- Open Access
- Published: 08 February 2007
- Article: 7
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Intron Evolution and Information processing in the DNA polymerase α gene in spirotrichous ciliates: A hypothesis for interconversion between DNA and RNA deletion
Authors (first, second and last of 6)
- Wei-Jen Chang
- Victoria M Addis
- Laura F Landweber
- Content type: Research
- Open Access
- Published: 01 February 2007
- Article: 6
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Resistance of the target islet tissue to autoimmune destruction contributes to genetic susceptibility in Type 1 diabetes
Authors (first, second and last of 6)
- Natasha J Hill
- Aleksandr Stotland
- Nora Sarvetnick
- Content type: Research
- Open Access
- Published: 25 January 2007
- Article: 5
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A novel superfamily containing the β-grasp fold involved in binding diverse soluble ligands
Authors (first, second and last of 4)
- A Maxwell Burroughs
- S Balaji
- L Aravind
- Content type: Research
- Open Access
- Published: 24 January 2007
- Article: 4
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Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms
Authors
- Gáspár Jékely
- Content type: Hypothesis
- Open Access
- Published: 19 January 2007
- Article: 3
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Component retention in principal component analysis with application to cDNA microarray data
Authors
- Richard Cangelosi
- Alain Goriely
- Content type: Research
- Open Access
- Published: 17 January 2007
- Article: 2
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pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model
Authors
- Georg Neuberger
- Georg Schneider
- Frank Eisenhaber
- Content type: Research
- Open Access
- Published: 12 January 2007
- Article: 1