A survey of visualization tools for biological network analysis

The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology. Very often the pure amount of data and their heterogeneity provides a challenge for the visualization of the data. There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions. These methods are applicable to a wide range of problems, nevertheless many of them reach a limit in terms of user friendliness when thousands of nodes and connections have to be analyzed and visualized. In this study we are reviewing visualization tools that are currently available for visualization of biological networks mainly invented in the latest past years. We comment on the functionality, the limitations and the specific strengths of these tools, and how these tools could be further developed in the direction of data integration and information sharing

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations

<p>Abstract</p> <p>Background</p> <p>Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations.</p> <p>Results</p> <p>We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations.</p> <p>Conclusion</p> <p>These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.</p

Suppression and azimuthal anisotropy of prompt and nonprompt J/psi production in PbPb collisions at root S-NN=2.76 TeV

The nuclear modification factor RAA and the azimuthal anisotropy coefficient v2 of prompt and nonprompt (i.e. those from decays of b hadrons) J/ψ mesons, measured from PbPb and pp collisions at sNN−−−√=2.76 TeV at the LHC, are reported. The results are presented in several event centrality intervals and several kinematic regions, for transverse momenta pT>6.5 GeV/c and rapidity |y|<2.4 , extending down to pT=3 GeV/c in the 1.6<|y|<2.4 range. The v2 of prompt J/ψ is found to be nonzero, but with no strong dependence on centrality, rapidity, or pT over the full kinematic range studied. The measured v2 of nonprompt J/ψ is consistent with zero. The RAA of prompt J/ψ exhibits a suppression that increases from peripheral to central collisions but does not vary strongly as a function of either y or pT in the fiducial range. The nonprompt J/ψ RAA shows a suppression which becomes stronger as rapidity or pT increases. The v2 and RAA of open and hidden charm, and of open charm and beauty, are compared