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  1. Although most of the key components of the transcription apparatus, and in particular, RNA polymerase (RNAP) subunits, are conserved between archaea and eukaryotes, no archaeal homologs of the small RPB8 subun...

    Authors: Eugene V Koonin, Kira S Makarova and James G Elkins
    Citation: Biology Direct 2007 2:38
  2. All standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence com...

    Authors: Flavia Frabetti, Raffaella Casadei, Luca Lenzi, Silvia Canaider, Lorenza Vitale, Federica Facchin, Paolo Carinci, Maria Zannotti and Pierluigi Strippoli
    Citation: Biology Direct 2007 2:34
  3. An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple g...

    Authors: Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2007 2:33
  4. Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes....

    Authors: Jittima Piriyapongsa, Mark T Rutledge, Sanil Patel, Mark Borodovsky and I King Jordan
    Citation: Biology Direct 2007 2:31
  5. The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research duri...

    Authors: Michael R Rose and Todd H Oakley
    Citation: Biology Direct 2007 2:30
  6. This work was undertaken in response to a recently published paper by Okoniewski and Miller (BMC Bioinformatics 2006, 7: Article 276). The authors of that paper came to the conclusion that the process of multiple...

    Authors: Lev Klebanov, Linlin Chen and Andrei Yakovlev
    Citation: Biology Direct 2007 2:28
  7. One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium...

    Authors: Larry J Wilhelm, H James Tripp, Scott A Givan, Daniel P Smith and Stephen J Giovannoni
    Citation: Biology Direct 2007 2:27
  8. The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of vario...

    Authors: Gelio Alves, Aleksey Y Ogurtsov, Wells W Wu, Guanghui Wang, Rong-Fong Shen and Yi-Kuo Yu
    Citation: Biology Direct 2007 2:26
  9. The standard genetic code table has a distinctly non-random structure, with similar amino acids often encoded by codons series that differ by a single nucleotide substitution, typically, in the third or the fi...

    Authors: Artem S Novozhilov, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2007 2:24
  10. Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Sacchar...

    Authors: Nicolas Martin, Elizabeth A Ruedi, Richard LeDuc, Feng-Jie Sun and Gustavo Caetano-Anollés
    Citation: Biology Direct 2007 2:23
  11. Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only ...

    Authors: Georgii A Bazykin, Fyodor A Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak and Alexey S Kondrashov
    Citation: Biology Direct 2007 2:20
  12. The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 a...

    Authors: Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2007 2:14
  13. Both mechanistic features and recent correlative findings suggest a potential role for protein kinase C-beta (PKC-β) in tumor pathogenesis, particularly in B-cell malignancies. To evaluate the role of this gen...

    Authors: Shuyu Li, Mark Phong, Michael Lahn, Leslie Brail, Susan Sutton, Boris K Lin, Donald Thornton and Birong Liao
    Citation: Biology Direct 2007 2:8
  14. The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by e...

    Authors: Albert DG de Roos
    Citation: Biology Direct 2007 2:7
  15. The somatic DNA molecules of spirotrichous ciliates are present as linear chromosomes containing mostly single-gene coding sequences with short 5' and 3' flanking regions. Only a few conserved motifs have been...

    Authors: Wei-Jen Chang, Victoria M Addis, Anya J Li, Elin Axelsson, David H Ardell and Laura F Landweber
    Citation: Biology Direct 2007 2:6
  16. Type 1 diabetes occurs when self-reactive T lymphocytes destroy the insulin-producing islet β cells of the pancreas. The defects causing this disease have often been assumed to occur exclusively in the immune ...

    Authors: Natasha J Hill, Aleksandr Stotland, Michelle Solomon, Patrick Secrest, Elizabeth Getzoff and Nora Sarvetnick
    Citation: Biology Direct 2007 2:5
  17. There are three isoforms of glutamate dehydrogenase. The isoform EC (GDH4) catalyses glutamate synthesis from 2-oxoglutarate and ammonium, using NAD(P)H. Ammonium assimilation is critical for plant gro...

    Authors: Emmanuel Jaspard
    Citation: Biology Direct 2006 1:38
  18. The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed...

    Authors: Yuri I Wolf, Cecile Viboud, Edward C Holmes, Eugene V Koonin and David J Lipman
    Citation: Biology Direct 2006 1:34
  19. The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repos...

    Authors: Shuyu Li, Yiqun Helen Li, Tao Wei, Eric Wen Su, Kevin Duffin and Birong Liao
    Citation: Biology Direct 2006 1:33
  20. The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitra...

    Authors: Fyodor A Kondrashov, Eugene V Koonin, Igor G Morgunov, Tatiana V Finogenova and Marie N Kondrashova
    Citation: Biology Direct 2006 1:31
  21. One of the mechanisms that ensure cancer robustness is tumor heterogeneity, and its effects on tumor cells dynamics have to be taken into account when studying cancer progression. There is no unifying theoreti...

    Authors: Georgy P Karev, Artem S Novozhilov and Eugene V Koonin
    Citation: Biology Direct 2006 1:30

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