http://www.blast2go.de -> Evaluation.

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

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Purpose: To adapt the so-called nonlocal means filter to deal with magnetic resonance (MR) images with spatially varying noise levels (for both Gaussian and Rician distributed noise). Materials and Methods:Most filtering techniques assume an equal noise distribution across the image. When this assumption is not met, the resulting filtering becomes suboptimal. This is the case of MR images with spatially varying noise levels, such as those obtained by parallel imaging (sensitivity-encoded), intensity inhomogeneity-corrected images, or surface coil-based acquisitions. We propose a new method where information regarding the local image noise level is used to adjust the amount of denoising strength of the filter. Such information is automatically obtained from the images using a new local noise estimation method.Results: The proposed method was validated and compared with the standard nonlocal means filter on simulated and real MRI data showing an improved performance in all cases. Conclusion:The new noise-adaptive method was demonstrated to outperform the standard filter when spatially varying noise is present in the images.

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Diffusion Weighted Images (DWI) normally shows a low Signal to Noise Ratio (SNR) due to the presence of noise from the measurement process that complicates and biases the estimation of quantitative diffusion parameters. In this paper, a new denoising methodology is proposed that takes into consideration the multicomponent nature of multi-directional DWI datasets such as those employed in diffusion imaging. This new filter reduces random noise in multicomponent DWI by locally shrinking less significant Principal Components using an overcomplete approach. The proposed method is compared with state-of-the-art methods using synthetic and real clinical MR images, showing improved performance in terms of denoising quality and estimation of diffusion parameters.

In Magnetic Resonance Imaging image resolution comes limited by several factors such as hardware or time limitations. In many cases, the acquired images has to be upsampled to match on any specific resolution, in such cases, image interpolation techniques has been traditionally applied. However, traditional interpolation techniques are not able to recover high frequency information of the underlying high resolution data. In this paper, a new reconstruction method is proposed to recover some of this high frequency information by using a data adaptive patch-based regularization in combination with a subsampling coherence constraint. The proposed method has been evaluated on synthetic and real clinical cases and compared with traditional interpolation methods. The proposed method has shown to outperform classical interpolation methods compared.

This paper proposes two new methods for the three-dimensional denoising of magnetic resonance images that exploit the sparseness and self-similarity properties of the images. The proposed methods are based on a three-dimensional moving-window discrete cosine transform hard thresholding and a three-dimensional rotationally invariant version of the well-known nonlocal means filter. The proposed approaches were compared with related state-of-the-art methods and produced very competitive results. Both methods run in less than a minute, making them usable in most clinical and research settings.