Browsing by Author "FARES, MARIO ALI"
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Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects
FARES, MARIO ALI (2009)Comparative genomics has become a real tantalizing challenge in the postgenomic era. This fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. The overwhelming list of new ... -
Describing the structural robustness landscape of bacterial small RNAs
FARES, MARIO ALI (2012)Background: The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory ... -
Evidence from comparative genomics for a complete sexual cycle in the "asexual" pathogenic yeast Candida glabrata
FARES, MARIO ALI; WOLFE, KENNETH (BioMed Central, 2003)BACKGROUND: Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related ... -
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network
FARES, MARIO ALI (2012)Genes show a bewildering variation in their patterns of molecular ev olution, as a result of the action of different levels and types of selective forces. The factors underlying this variation are, however, s till poorly ... -
In silico identification of functional divergence between the multiple groEL gene paralogs in Chlamydiae
FARES, MARIO ALI (2007)Background Heat-shock proteins are specialized molecules performing different and essential roles in the cell including protein degradation, folding and trafficking. GroEL is a 60 Kda heat-shock protein ubiquitous in ... -
Molecular evolution of psbA gene in ferns: Unraveling selective pressure and co-evolutionary pattern
FARES, MARIO ALI (2012)Abstract Background: The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded ... -
Molecular evolution of rbcL in three gymnosperm families: Identifying adaptive and coevolutionary patterns
FARES, MARIO ALI (2011)Background: 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 ... -
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Pivotal Advance: Avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products
FARES, MARIO ALI (2010)Macrophages are involved in many aspects of development, host defense, pathology, and homeostasis. Their normal differentiation, proliferation, and survival are controlled by CSF-1 via the activation of the CSF-1R. A ... -
Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
FARES, MARIO ALI (2012)Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene ... -
The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes
FARES, MARIO ALI (2013)Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) ... -
Structural Calibration of the Rates of Amino Acid Evolution in a Search for Darwin in Drifting Biological Systems.
FARES, MARIO ALI (Oxford University Press, 2010)In the last two decades, many reports of proteins under positive selection have brought the neutral theory into question. However, the methods used to detect selection have ignored the evolvability of amino acids within ... -
Why should we care about molecular coevolution?
FARES, MARIO ALI (2008)Abstract: Non-independent evolution of amino acid sites has become a noticeable limitation of most methods aimed at identifying selective constraints at functionally important amino acid sites or protein regions. The ...