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Page 8 of 15

  1. A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.

    Authors: Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin and Anna-Louise Reysenbach
    Citation: Biology Direct 2013 8:9
  2. Invasive cell growth and migration is usually considered a specifically metazoan phenomenon. However, common features and mechanisms of cytoskeletal rearrangements, membrane trafficking and signalling processe...

    Authors: Katarína Vaškovičová, Viktor Žárský, Daniel Rösel, Margaret Nikolič, Roberto Buccione, Fatima Cvrčková and Jan Brábek
    Citation: Biology Direct 2013 8:8
  3. The Michaelis-Menten equation, proposed a century ago, describes the kinetics of enzyme-catalyzed biochemical reactions. Since then, this equation has been used in countless, increasingly complex models of cel...

    Authors: Ed Reznik, Stefan Yohe and Daniel Segrè
    Citation: Biology Direct 2013 8:7
  4. tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequenci...

    Authors: Guilherme Loss-Morais, Peter M Waterhouse and Rogerio Margis
    Citation: Biology Direct 2013 8:6
  5. Twintrons represent a special intronic arrangement in which introns of two different types occupy the same gene position. Consequently, alternative splicing of these introns requires two different spliceosomes...

    Authors: Jessin Janice, Marcin Jąkalski and Wojciech Makałowski
    Citation: Biology Direct 2013 8:4
  6. Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimagin...

    Authors: Cheong Xin Chan and Mark A Ragan
    Citation: Biology Direct 2013 8:3
  7. Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions,...

    Authors: Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely and Fulvia Bono
    Citation: Biology Direct 2013 8:2
  8. Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm), are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC pr...

    Authors: Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano, Aleksandr A Rubel, Igor B Rogozin and Youri I Pavlov
    Citation: Biology Direct 2012 7:47
  9. Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made...

    Authors: Yuri I Wolf, Kira S Makarova, Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2012 7:46
  10. Ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. Previous studies have revealed the presence of eutBC gen...

    Authors: Neelam Khatri, Indu Khatri, Srikrishna Subramanian and Saumya Raychaudhuri
    Citation: Biology Direct 2012 7:45
  11. High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reaso...

    Authors: Frank Emmert-Streib, Shailesh Tripathi and Ricardo de Matos Simoes
    Citation: Biology Direct 2012 7:44
  12. As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computin...

    Authors: Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao and Zhang Zhang
    Citation: Biology Direct 2012 7:43
  13. It has been recently discovered that transposable elements show high activity in the brain of mammals, however, the magnitude of their influence on its functioning is unclear so far. In this paper, I use flux ...

    Authors: György Abrusán
    Citation: Biology Direct 2012 7:41
  14. The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune system...

    Authors: Kira S Makarova, Vivek Anantharaman, L Aravind and Eugene V Koonin
    Citation: Biology Direct 2012 7:40
  15. Members of the Arabidopsis LSH1 and Oryza G1 (ALOG) family of proteins have been shown to function as key developmental regulators in land plants. However, their precise mode of action remains unclear. Using sens...

    Authors: Lakshminarayan M Iyer and L Aravind
    Citation: Biology Direct 2012 7:39
  16. Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specifici...

    Authors: András Szilágyi, Ádám Kun and Eörs Szathmáry
    Citation: Biology Direct 2012 7:38
  17. The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identi...

    Authors: Derrick E Wood, Henry Lin, Ami Levy-Moonshine, Rajiswari Swaminathan, Yi-Chien Chang, Brian P Anton, Lais Osmani, Martin Steffen, Simon Kasif and Steven L Salzberg
    Citation: Biology Direct 2012 7:37
  18. Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive fam...

    Authors: Jerzy Jurka, Weidong Bao, Kenji K Kojima, Oleksiy Kohany and Matthew G Yurka
    Citation: Biology Direct 2012 7:36
  19. Viruses with large genomes encode numerous proteins that do not directly participate in virus biogenesis but rather modify key functional systems of infected cells. We report that a distinct group of giant vir...

    Authors: Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2012 7:34
  20. The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with functi...

    Authors: Valérie de Crécy-Lagard, Farhad Forouhar, Céline Brochier-Armanet, Liang Tong and John F Hunt
    Citation: Biology Direct 2012 7:32
  21. The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of st...

    Authors: Inna S Povolotskaya, Fyodor A Kondrashov, Alice Ledda and Peter K Vlasov
    Citation: Biology Direct 2012 7:30
  22. Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-...

    Authors: François Delavat, Marie-Claire Lett and Didier Lièvremont
    Citation: Biology Direct 2012 7:28
  23. Prions are agents of analog, protein conformation-based inheritance that can confer beneficial phenotypes to cells, especially under stress. Combined with genetic variation, prion-mediated inheritance can be c...

    Authors: Eugene V Koonin
    Citation: Biology Direct 2012 7:27
  24. In previous work, we introduced a concept, a mathematical model and its computer realization that describe the interaction between bacterial and phage type RNA polymerases, protein factors, DNA and RNA seconda...

    Authors: Vassily A Lyubetsky, Oleg A Zverkov, Sergey A Pirogov, Lev I Rubanov and Alexandr V Seliverstov
    Citation: Biology Direct 2012 7:26
  25. Molecular markers based on gene expression profiles have been used in experimental and clinical settings to distinguish cancerous tumors in stage, grade, survival time, metastasis, and drug sensitivity. Howeve...

    Authors: Shinuk Kim, Mark Kon and Charles DeLisi
    Citation: Biology Direct 2012 7:21
  26. Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflic...

    Authors: Dapeng Zhang, Robson F de Souza, Vivek Anantharaman, Lakshminarayan M Iyer and L Aravind
    Citation: Biology Direct 2012 7:18
  27. Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is ...

    Authors: Geoffrey S Diemer and Kenneth M Stedman
    Citation: Biology Direct 2012 7:13
  28. Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in eukaryotic genomes and have recently become the marker of choice in a wide variety of ecological and evolutionary studi...

    Authors: Jinzhuang Dou, Xiqiang Zhao, Xiaoteng Fu, Wenqian Jiao, Nannan Wang, Lingling Zhang, Xiaoli Hu, Shi Wang and Zhenmin Bao
    Citation: Biology Direct 2012 7:17
  29. MicroRNAs (miRNAs) are endogenous small non-coding RNAs of about 20–24 nt, known to play key roles in post-transcriptional gene regulation, that can be coded either by intergenic or intragenic loci. Intragenic...

    Authors: Moreno Colaiacovo, Antonella Lamontanara, Letizia Bernardo, Renzo Alberici, Cristina Crosatti, Lorenzo Giusti, Luigi Cattivelli and Primetta Faccioli
    Citation: Biology Direct 2012 7:15
  30. mtRF1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtRF1a. To elucidate the function of mtRF1, we determined the positions th...

    Authors: Martijn A Huynen, Isabel Duarte, Zofia M A Chrzanowska-Lightowlers and Sander B Nabuurs
    Citation: Biology Direct 2012 7:14
  31. BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively...

    Authors: Grzegorz M Boratyn, Alejandro A Schäffer, Richa Agarwala, Stephen F Altschul, David J Lipman and Thomas L Madden
    Citation: Biology Direct 2012 7:12
  32. Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were inter...

    Authors: Igor B Rogozin, Liran Carmel, Miklos Csuros and Eugene V Koonin
    Citation: Biology Direct 2012 7:11
  33. Tubulins are a family of GTPases that are key components of the cytoskeleton in all eukaryotes and are distantly related to the FtsZ GTPase that is involved in cell division in most bacteria and many archaea. ...

    Authors: Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2012 7:10
  34. Injuries to articular cartilage result in the development of lesions that form on the surface of the cartilage. Such lesions are associated with articular cartilage degeneration and osteoarthritis. The typical...

    Authors: Jason M Graham, Bruce P Ayati, Lei Ding, Prem S Ramakrishnan and James A Martin
    Citation: Biology Direct 2012 7:9

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