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- 1From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key...
- 2From: Biology Direct. (Vol. 6) Peer-ReviewedBackground The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed...
- 3From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Data assimilation refers to methods for updating the state vector (initial condition) of a complex spatiotemporal model (such as a numerical weather model) by combining new observations with one or more...
- 4From: Biology Direct. (Vol. 6) Peer-ReviewedBackground 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...
- 5From: Biology Direct. (Vol. 6) Peer-ReviewedBackground 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...
- 6From: Biology Direct. (Vol. 6) Peer-ReviewedBackground 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...
- 7From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using...
- 8From: Biology Direct. (Vol. 6) Peer-ReviewedBackground The p53 tumor suppressor protein is involved in a complicated regulatory network, mediating expression of ~1000 human genes. Recent studies have shown that many p53 in vivo binding sites (BSs) reside in...
- 9From: Biology Direct. (Vol. 6) Peer-ReviewedBackground The universal common ancestry (UCA) of all known life is a fundamental component of modern evolutionary theory, supported by a wide range of qualitative molecular evidence. Nevertheless, recently both the...
- 10From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could...
- 11From: Biology Direct. (Vol. 6) Peer-ReviewedBackground 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...
- 12From: Biology Direct. (Vol. 6) Peer-ReviewedBackground More and more antiretroviral therapies are being developed for treatment of HIV infection. The in-vivo efficacy of these drugs is commonly predicted based on in-vitro measures of antiviral effect. One...
- 13From: Biology Direct. (Vol. 6) Peer-ReviewedLife 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 in the form...
- 14From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. In this study, we investigated the phenomenon of chimerism...
- 15From: Biology Direct. (Vol. 6) Peer-ReviewedTransposable 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 scientists....
- 16From: Biology Direct. (Vol. 6) Peer-ReviewedBackground 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...
- 17From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Eukaryotic genomes harbor diverse families of repetitive DNA derived from transposable elements (TEs) that are able to replicate and insert into genomic DNA. The biological role of TEs remains unclear,...
- 18From: Biology Direct. (Vol. 6) Peer-ReviewedBackground We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how...
- 19From: Biology Direct. (Vol. 6) Peer-ReviewedBackground Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA...
- 20From: Biology Direct. (Vol. 6) Peer-ReviewedUnderstanding 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 and...