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Handling Noise in Protein Interaction Networks
Correia, Fernanda; Coelho, Edgar D.; Oliveira, José L.; Arrais, Joel P.Protein-protein interactions (PPIs) can be conveniently represented as networks, allowing the use of graph theory for their study. Network topology studies may reveal patterns associated with specific organisms. Here, we propose a new methodology to denoise PPI networks and predict missing links solely based on the network topology, the organization measurement (OM) method. The OM methodology was applied in the...
Phenotypic heterogeneity promotes adaptive evolution
Bódi, Zoltán; Farkas, Zoltán; Nevozhay, Dmitry; Kalapis, Dorottya; Lázár, Viktória; Csörgő, Bálint; Nyerges, Ákos; Szamecz, Béla; Fekete, GergelyGenetically identical cells frequently display substantial heterogeneity in gene expression, cellular morphology and physiology. It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits, phenotypic heterogeneity (or plasticity) accelerates the rate of adaptive evolution in populations facing extreme environmental challenges. This issue is important as cell-to-cell phenotypic...
Análise de repetições em dados biológicos
Lousado, José P.; Oliveira, José L.A descodificação dos genomas veio criar novos desafios na comunidade científica ligada à área da computação e da informática. Diariamente são alimentadas inúmeras bases de dados com biliões de registos provenientes de equipamentos cada vez mais evoluídos, que auxiliam na descodificação dos genomas. Determinar o quão importante e relevante são esses dados, de forma a retirar valor acrescentado – informação, e ob...
Improving the accuracy of recombinant protein production through integration of...
Ragionieri, Lapo; Vitorino, Rui; Frommlet, Joerg; Oliveira, José L.; Gaspar, Paulo; Ribas de Pouplana, Lluís; Santos, Manuel A. SilvaHeterologous protein production is a key technology for biotechnological, health sciences and many other research fields. Various approaches have been developed for its optimization, but the research emphasis has been on optimization of protein yield rather than protein quality. In this study, we have established a workflow for synthetic gene optimization for heterologous protein expression that combines bioinf...
Computational prediction of the human-microbial oral interactome
Coelho, Edgar D.; Arrais, Joel P.; Matos, Sérgio; Pereira, Carlos; Rosa, Nuno; Correia, Maria J.; Barros, Marlene; Oliveira, José L.Background: The oral cavity is a complex ecosystem where human chemical compounds coexist with a particular microbiota. However, shifts in the normal composition of this microbiota may result in the onset of oral ailments, such as periodontitis and dental caries. In addition, it is known that the microbial colonization of the oral cavity is mediated by protein-protein interactions (PPIs) between the host and mi...
Species-specific codon context rules unveil non-neutrality effects of synonymou...
Moura, Gabriela R.; Pinheiro, Miguel; Freitas, Adelaide; Oliveira, José L.; Frommlet, Jörg C.; Carreto, Laura; Soares, Ana R.; Bezerra, Ana R.Background: Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution. Methodologies/Princi...
Parallel DNA pyrosequencing unveils new zebrafish microRNAs
Soares, Ana R.; Pereira, Patrícia M. R.; Santos, Bruno; Egas, Conceição; Gomes, Ana C.; Arrais, Joel P.; Oliveira, José L.; Moura, Gabriela R.Background: MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biolog...
Parallel DNA pyrosequencing unveils new zebrafish microRNAs
Soares, Ana R.; Pereira, Patrícia M.; Santos, Bruno; Egas, Conceição; Gomes, Ana C.; Arrais, Joel; Oliveira, José L.; Moura, Gabriela R.Background - MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biolo...
Codon-triplet context unveils unique features of the Candida albicans protein c...
Moura, Gabriela R.; Lousado, José P.; Pinheiro, Miguel; Carreto, Laura; Silva, Raquel M.; Oliveira, José L.; Santos, Manuel A. S.Background - The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each d...
Large scale comparative codon-pair context analysis unveils general rules that ...
Moura, Gabriela; Pinheiro, Miguel; Arrais, Joel; Gomes, Ana Cristina; Carreto, Laura; Freitas, Adelaide; Oliveira, José L.; Santos, Manuel A. S.Background. Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. Methodologies/Principal Findings. We have developed mathematical and software...