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  1. The CRISPR-Cas adaptive immunity systems that are present in most Archaea and many Bacteria function by incorporating fragments of alien genomes into specific genomic loci, transcribing the inserts and using t...

    Authors: Kira S Makarova, L Aravind, Yuri I Wolf and Eugene V Koonin
    Citation: Biology Direct 2011 6:38
    Content type: Research Published on:

  3. Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably i...

    Authors: William F Martin
    Citation: Biology Direct 2011 6:36
    Content type: Review Published on:

  5. Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to ...

    Authors: Robert G Beiko
    Citation: Biology Direct 2011 6:34
    Content type: Research Published on:

  9. Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the ex...

    Authors: Zané Lombard, Chungoo Park, Kateryna D Makova and Michèle Ramsay
    Citation: Biology Direct 2011 6:30
    Content type: Research Published on:

  10. The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the co...

    Authors: Lin Sen, Mario A Fares, Bo Liang, Lei Gao, Bo Wang, Ting Wang and Ying-Juan Su
    Citation: Biology Direct 2011 6:29
    Content type: Research Published on:

  12. False discovery rate (FDR) control is commonly accepted as the most appropriate error control in multiple hypothesis testing problems. The accuracy of FDR estimation depends on the accuracy of the estimation o...

    Authors: Juntao Li, Puteri Paramita, Kwok Pui Choi and R Krishna Murthy Karuturi
    Citation: Biology Direct 2011 6:27
    Content type: Research Published on:

  13. Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary ...

    Authors: Diana Chernikova, Sam Motamedi, Miklós Csürös, Eugene V Koonin and Igor B Rogozin
    Citation: Biology Direct 2011 6:26
    Content type: Research Published on:

  14. GWAS owe their popularity to the expectation that they will make a major impact on diagnosis, prognosis and management of disease by uncovering genetics underlying clinical phenotypes. The dominant paradigm in...

    Authors: Alexander V Alekseyenko, Nikita I Lytkin, Jizhou Ai, Bo Ding, Leonid Padyukov, Constantin F Aliferis and Alexander Statnikov
    Citation: Biology Direct 2011 6:25
    Content type: Research Published on:

  15. The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating s...

    Authors: Deng-Ke Niu and Yu-Fei Yang
    Citation: Biology Direct 2011 6:24
    Content type: Hypothesis Published on:

  16. MicroRNAs are small RNA species that regulate gene expression post-transcriptionally and are aberrantly expressed in many cancers including hematological malignancies. However, the role of microRNAs in the pat...

    Authors: Jianxiang Chi, Erica Ballabio, Xiao-He Chen, Rajko Kušec, Steve Taylor, Deborah Hay, Daniela Tramonti, Nigel J Saunders, Timothy Littlewood, Francesco Pezzella, Jacqueline Boultwood, James S Wainscoat, Christian SR Hatton and Charles H Lawrie
    Citation: Biology Direct 2011 6:23
    Content type: Research Published on:

  17. Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the e...

    Authors: Rodrigo JS Dalmolin, Mauro AA Castro, José L Rybarczyk Filho, Luis HT Souza, Rita MC de Almeida and José CF Moreira
    Citation: Biology Direct 2011 6:22
    Content type: Research Published on:

  20. Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research sci...

    Authors: Aurélie Hua-Van, Arnaud Le Rouzic, Thibaud S Boutin, Jonathan Filée and Pierre Capy
    Citation: Biology Direct 2011 6:19
    Content type: Review Published on:

  24. Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. However, little is known about the quality and completeness of pathways stor...

    Authors: Evgeny Shmelkov, Zuojian Tang, Iannis Aifantis and Alexander Statnikov
    Citation: Biology Direct 2011 6:15
    Content type: Research Published on:

  25. Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "ke...

    Authors: Andrei S Rodin, Eörs Szathmáry and Sergei N Rodin
    Citation: Biology Direct 2011 6:14
    Content type: Research Published on:

  26. Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what ...

    Authors: Dapeng Wang, Fei Liu, Lei Wang, Shi Huang and Jun Yu
    Citation: Biology Direct 2011 6:13
    Content type: Research Published on:

  28. Understanding the evolutionary plasticity of the genome requires a global, comparative approach in which genetic events are considered both in a phylogenetic framework and with regard to population genetics an...

    Authors: Anthony Levasseur and Pierre Pontarotti
    Citation: Biology Direct 2011 6:11
    Content type: Review Published on:

  30. B lymphocyte stimulator (BLyS) is a member of the tumor necrosis factor superfamily of ligands that mediates its action through three known receptors. BLyS has been shown to enhance the production of antibodie...

    Authors: Dennis O Gor, Xuedong Ding, Qing Li, Dilara Sultana, Salamatu S Mambula, Richard J Bram and Neil S Greenspan
    Citation: Biology Direct 2011 6:9
    Content type: Research Published on:

  31. Posttranslationally modified amino acids are chemically distinct types of amino acids and in terms of evolution they might behave differently from their non-modified counterparts. In order to check this possib...

    Authors: Yerbol Z Kurmangaliyev, Alexander Goland and Mikhail S Gelfand
    Citation: Biology Direct 2011 6:8
    Content type: Discovery notes Published on:

  32. In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two ter...

    Authors: Reed A Cartwright and Dan Graur
    Citation: Biology Direct 2011 6:7
    Content type: Opinion Published on:

  33. Genome degradation is an ongoing process in all members of the Rickettsiales order, which makes these bacterial species an excellent model for studying reductive evolution through interspecies variation in genome...

    Authors: Kalliopi Georgiades, Vicky Merhej, Khalid El Karkouri, Didier Raoult and Pierre Pontarotti
    Citation: Biology Direct 2011 6:6
    Content type: Research Published on:

  34. Cancer is a proliferation disease affecting a genetically unstable cell population, in which molecular alterations can be somatically inherited by genetic, epigenetic or extragenetic transmission processes, le...

    Authors: Jennifer Pasquier, Pierre Magal, Céline Boulangé-Lecomte, Glenn Webb and Frank Le Foll
    Citation: Biology Direct 2011 6:5
    Content type: Research Published on:

  36. Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases...

    Authors: Vassily A Lyubetsky, Oleg A Zverkov, Lev I Rubanov and Alexandr V Seliverstov
    Citation: Biology Direct 2011 6:3
    Content type: Research Published on:

  39. Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the pre...

    Authors: Michael S Breen and Fyodor A Kondrashov
    Citation: Biology Direct 2010 5:68
    Content type: Research Published on:

  43. It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly tho...

    Authors: Eugene V Koonin and Yuri I Wolf
    Citation: Biology Direct 2010 5:64
    Content type: Comment Published on:

  48. It is difficult to measure precisely the phenotypic complexity of living organisms. Here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective infor...

    Authors: Yun Jiang and Cunshuan Xu
    Citation: Biology Direct 2010 5:59
    Content type: Research Published on:
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Biology Direct

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