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HIV can evolve drug resistance rapidly in response to new drug treatments, often through a combination of multiple mutations [1–3]. It would be useful to develop automated analyses of HIV sequence polymorphism th...
Citation: Biology Direct 2006 1:14
Evolution at a protein site can be characterized from two different perspectives, by its rate and by the breadth of the set of acceptable amino acids.
Citation: Biology Direct 2012 7:8
The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent spe...
Citation: Biology Direct 2006 1:17
While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplica...
Citation: Biology Direct 2009 4:28
In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is la...
Citation: Biology Direct 2010 5:4
All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importanc...
Citation: Biology Direct 2014 9:32
The origin of the nucleus is a central problem about the origin of eukaryotes. The common ancestry of nuclear pore complexes (NPC) and vesicle coating complexes indicates that the nucleus evolved via the modif...
Citation: Biology Direct 2008 3:31
Compactness of highly/broadly expressed genes in human has been explained as selection for efficiency, regional mutation biases or genomic design. However, highly expressed genes in flowering plants were shown...
Citation: Biology Direct 2009 4:45
Cernunnos-XLF is a nonhomologous end-joining factor that is mutated in patients with a rare immunodeficiency with microcephaly. Several other microcephaly-associated genes such as ASPM and microcephalin experienc...
Citation: Biology Direct 2006 1:15
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. ...
Citation: Biology Direct 2006 1:26
The origin of eukaryotic cells was one of the most dramatic evolutionary transitions in the history of life. It is generally assumed that eukaryotes evolved later then prokaryotes by the transformation or fusi...
Citation: Biology Direct 2007 2:3
There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed. Computational motif discovery has been used with some success...
Citation: Biology Direct 2006 1:11
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...
Citation: Biology Direct 2006 1:18
The transcription machineries of Archaea and eukaryotes are similar in many aspects, but little is understood about archaeal chromatin and its role in transcription. Here, we describe the identification in hyp...
Citation: Biology Direct 2009 4:24
Quorum sensing (QS) is a form of gene regulation based on cell-density that depends on inter-cellular communication. While there are a variety of models for bacterial colony morphology, there is little work li...
Citation: Biology Direct 2009 4:6
For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have per...
Citation: Biology Direct 2016 11:39
It is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems...
Citation: Biology Direct 2010 5:65
Genome-wide studies of intron dynamics in mammalian orthologous genes have found convincing evidence for loss of introns but very little for intron turnover. Similarly, large-scale analysis of intron dynamics ...
Citation: Biology Direct 2011 6:59
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...
Citation: Biology Direct 2011 6:36
It is known that crustaceans and insects can persistently carry one or more viral pathogens at low levels, without signs of disease. They may transmit them to their offspring or to naïve individuals, often wit...
Citation: Biology Direct 2009 4:32