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  1. 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

    Content type: Research

    Published on:

  2. 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

    Content type: Research

    Published on:

  3. 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

    Content type: Research

    Published on:

  4. 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

    Content type: Research

    Published on:

  5. There are three isoforms of glutamate dehydrogenase. The isoform EC 1.4.1.4 (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

    Content type: Research

    Published on:

  6. 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

    Content type: Research

    Published on:

  7. 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

    Content type: Research

    Published on:

  8. 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

    Content type: Research

    Published on:

  9. 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

    Content type: Research

    Published on:

  10. 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

    Content type: Hypothesis

    Published on:

  11. 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

    Content type: Hypothesis

    Published on:

  12. 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

    Content type: Research

    Published on:

  13. 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

    Content type: Research

    Published on:

  14. 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

    Content type: Research

    Published on:

  15. 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

    Content type: Research

    Published on:

  16. 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

    Content type: Research

    Published on:

  17. 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

    Content type: Review

    Published on:

  18. 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

    Content type: Research

    Published on:

  19. 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

    Content type: Research

    Published on:

  20. 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

    Content type: Research

    Published on:

  21. Microscopic examination of living cells often reveals that cells from some cell strains appear to be in a permanent state of disarray without obvious reason. In all probability such a disorderly state affects ...

    Authors: Johannes WIM Simons

    Citation: Biology Direct 2006 1:9

    Content type: Research

    Published on:

  22. Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis syst...

    Authors: Toni Gabaldón, Berend Snel, Frank van Zimmeren, Wieger Hemrika, Henk Tabak and Martijn A Huynen

    Citation: Biology Direct 2006 1:8

    Content type: Research

    Published on:

  23. All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated (cas) genes that have been previously implicated in a...

    Authors: Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf and Eugene V Koonin

    Citation: Biology Direct 2006 1:7

    Content type: Research

    Published on:

  24. Oncolytic viruses that specifically target tumor cells are promising anti-cancer therapeutic agents. The interaction between an oncolytic virus and tumor cells is amenable to mathematical modeling using adapta...

    Authors: Artem S Novozhilov, Faina S Berezovskaya, Eugene V Koonin and Georgy P Karev

    Citation: Biology Direct 2006 1:6

    Content type: Research

    Published on:

  25. For the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics. The vast majority of these methods ...

    Authors: Srdan V Stankov

    Citation: Biology Direct 2006 1:5

    Content type: Research

    Published on:

  26. The mutation spectra of the TP53 gene and other tumor suppressors contain multiple hotspots, i.e., sites of non-random, frequent mutation in tumors and/or the germline. The origin of the hotspots remains unclear,...

    Authors: Galina V Glazko, Vladimir N Babenko, Eugene V Koonin and Igor B Rogozin

    Citation: Biology Direct 2006 1:4

    Content type: Research

    Published on:

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