Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be ne...Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing.highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.展开更多
Nearly two decades have passed since the publication of the first study reporting the discovery of microRNAs （miRNAs）. The key role of miRNAs in post-transcriptional gene regulation led to the performance of an incr...Nearly two decades have passed since the publication of the first study reporting the discovery of microRNAs （miRNAs）. The key role of miRNAs in post-transcriptional gene regulation led to the performance of an increasing number of studies focusing on origins, mech- anisms of action and functionality of miRNAs. In order to associate each miRNA to a specific functionality it is essential to unveil the rules that govern miRNA action. Despite the fact that there has been significant improvement exposing structural characteristics of the miRNA-mRNA interaction, the entire physical mechanism is not yet fully understood. In this respect, the development of computa- tional algorithms for miRNA target prediction becomes increasingly important. This manuscript summarizes the research done on miRNA target prediction. It describes the experimental data currently available and used in the field and presents three lines of compu tational approaches for target prediction. Finally, the authors put forward a number of considerations regarding current challenges and future directions.展开更多
基金funded by the Valle d’Aosta Regional Government (http://www.regione.vda.it/) in the frame of the regional law n.84-07/12/1993 (project ParIS-Parkinson Informative System)
文摘Analysis of images obtained from two-dimensional gel electrophoresis （2D-GE） is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing.highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.
文摘Nearly two decades have passed since the publication of the first study reporting the discovery of microRNAs （miRNAs）. The key role of miRNAs in post-transcriptional gene regulation led to the performance of an increasing number of studies focusing on origins, mech- anisms of action and functionality of miRNAs. In order to associate each miRNA to a specific functionality it is essential to unveil the rules that govern miRNA action. Despite the fact that there has been significant improvement exposing structural characteristics of the miRNA-mRNA interaction, the entire physical mechanism is not yet fully understood. In this respect, the development of computa- tional algorithms for miRNA target prediction becomes increasingly important. This manuscript summarizes the research done on miRNA target prediction. It describes the experimental data currently available and used in the field and presents three lines of compu tational approaches for target prediction. Finally, the authors put forward a number of considerations regarding current challenges and future directions.
