Conclusions:
The data show that inflammation and angiogenesis are important processes in the pathogenesis of vascular tumors, but a definitive ontogeny of the cells that give rise to these tumors remains to be established. The data do not yet distinguish whether functional or ontogenetic plasticity creates this phenotype, although they suggest that cells which give rise to hemangiosarcoma modulate their microenvironment to promote tumor growth and survival. We propose that the frequent occurrence of canine hemangiosarcoma in defined dog breeds, as well as its similarity to homologous tumors in humans, offers unique models to solve the dilemma of stem cell plasticity and whether angiogenic endothelial cells and hematopoietic cells originate from a single cell or from distinct progenitor cel…

In this report, we applied both bioinformatics and functional genomic approaches to scrutinize the unusually large promoter of the IME1 gene in budding yeast. Using a recently described fluorescent protein-based reporter screen, reporter-synthetic genetic array (R-SGA), we assessed the effect of viable deletion mutants on transcription of various IME1 promoter–reporter genes. We discovered potential transcription factors, many of which have no perfect consensus site within the IME1 promoter. Moreover, most of the cis-regulatory sequences with perfect homology to known transcription factor (TF) consensus were found to be nonfunctional in the R-SGA analysis. In addition, our results suggest that lack of conservation may not discriminate against a TF regulatory role at a specific promot…

Conclusions:
Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the “true” number of factors is unknown; in our simulations the proposed methods accurately infer the number of factors used to synthesize the data. We have also identified a “panviral” factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data. (Source: BMC Bioinformatics – Latest articles)

IEEE/ACM Transactions on Computational Biology and Bioinformatics (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)

A team of Universite Laval and Danisco researchers has just unlocked the secret of bacteria’s immune system. The details of the discovery, which may eventually make it possible to prevent certain bacteria from developing resistance to antibiotics, are presented in the scientific journal Nature. The team led by Professor Sylvain Moineau of Université Laval’s Department of Biochemistry, Microbiology, and Bioinformatics showed that this mechanism, called CRISPR/Cas, works by selecting foreign DNA segments and inserting them into very specific locations in a bacterium’s genome… (Source: Health News from Medical News Today)

Conclusions:
This study provides a complex overview of the GmGER genes in soybean. Phylogenetic analysis suggested that the germin and germin-like genes of the plant species that had been founded might be evolved by independent gene duplication events. The experiment indicated that germin genes exhibited diverse expression patterns during soybean development. The different time courses of the mRNAs accumulation of GmGER genes in soybean leaves appeared to have a regular photoperiodical reaction in darkness. Also the GmGER genes were proved to response to abiotic stress (such as auxin and salt), suggesting that these paralogous genes were likely involved in complex biological processes in soybean. (Source: BMC Genomics – Latest articles)

Conclusions:
The results show that SC_{intuit} improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SC_{intuit} can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
MWT can provide more precise TP boundaries than STFT and the boundaries can be further refined by bigger scale MWT. Subtraction of 6bp periodicity signals reduces the number of false positives. Experimentally-introduced frame-shift mutations help recover TP signal that have been lost by possible ancient frame-shifts. More importantly, TP signal has the potential to be used to detect the splice junctions in fully spliced mRNA sequence. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
The text-mining based bioassay neighboring analysis is efficient for correlating bioassays and studying different aspects of a biological process, which are otherwise difficult to achieve by existing neighboring procedures due to the lack of specific annotations and structured information. It is suggested that the text-mining based bioassay neighboring analysis can be used as a standalone or as a complementary tool for the PubChem bioassay neighboring process to enable efficient integration of assay results and generate hypotheses for the discovery of bioactivities of the tested reagents. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
We tested HOPE by comparing its output to the results of manually performed projects. In all straightforward cases HOPE performed similar to a trained bioinformatician. The use of 3D structures helps optimize the results in terms of reliability and details. HOPE’s results are easy to understand and are presented in a way that is attractive for researchers without an extensive bioinformatics background. (Source: BMC Bioinformatics – Latest articles)