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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven explorati...

    Authors: Eugene V Koonin, Tatiana G Senkevich and Valerian V Dolja
    Citation: Biology Direct 2006 1:29
  13. While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most euk...

    Authors: Pavel V Baranov, Bente Vestergaard, Thomas Hamelryck, Raymond F Gesteland, Jens Nyborg and John F Atkins
    Citation: Biology Direct 2006 1:28
  14. DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inhe...

    Authors: Jaroslav P Novak, Seon-Young Kim, Jun Xu, Olga Modlich, David J Volsky, David Honys, Joan L Slonczewski, Douglas A Bell, Fred R Blattner, Eduardo Blumwald, Marjan Boerma, Manuel Cosio, Zoran Gatalica, Marian Hajduch, Juan Hidalgo, Roderick R McInnes…
    Citation: Biology Direct 2006 1:27
  15. Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. ...

    Authors: James Bucknam, Yan Boucher and Eric Bapteste
    Citation: Biology Direct 2006 1:26
  16. Fitness landscapes, the dependences of fitness on the genotype, are of critical importance for the evolution of living beings. Unfortunately, fitness landscapes that are relevant to the evolution of complex bi...

    Authors: Alex A Neyfakh, Natalya N Baranova and Lev J Mizrokhi
    Citation: Biology Direct 2006 1:23
  17. Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed – the most difficult problems in phylogeny. Protein pa...

    Authors: Thomas Cavalier-Smith
    Citation: Biology Direct 2006 1:19
  18. Gene expression microarray technology continues to evolve and its use has expanded into all areas of biology. However, the high dimensionality of the data makes analysis a difficult challenge. Evaluating measu...

    Authors: Jaroslav P Novak, Merrill C Miller III and Douglas A Bell
    Citation: Biology Direct 2006 1:18
  19. Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygo...

    Authors: James L Weber
    Citation: Biology Direct 2006 1:16
  20. HIV can evolve drug resistance rapidly in response to new drug treatments, often through a combination of multiple mutations [13]. It would be useful to develop automated analyses of HIV sequence polymorphism th...

    Authors: Lamei Chen and Christopher Lee
    Citation: Biology Direct 2006 1:14
  21. We present psi-square, a program for searching the space of gene vectors. The program starts with a gene vector, i.e., the set of measurements associated with a gene, and finds similar vectors, derives a proba...

    Authors: Galina Glazko, Michael Coleman and Arcady Mushegian
    Citation: Biology Direct 2006 1:13
  22. Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of s...

    Authors: Alexander Churbanov, Igor B Rogozin, Jitender S Deogun and Hesham Ali
    Citation: Biology Direct 2006 1:10

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