hersh006's no-tag [3 articles]

Abstract

Learning regulatory networks from genomics data is an important problem with applications spanning all of biology and biomedicine. Functional genomics projects offer a cost-effective means of greatly expanding the completeness of our regulatory models, and for some prokaryotic organisms they offer a means of learning accurate models that incorporate the majority of the genome. There are, however, several reasons to believe that regulatory network inference is beyond our current reach, such as (i) the combinatorics of the problem, (ii) factors we ...

Abstract

BACKGROUND:The analysis of gene sets has become a popular topic in recent times, with researchers attempting to improve the interpretability and reproducibility of their microarray analyses through the inclusion of supplementary biological information. While a number of options for gene set analysis exist, no consensus has yet been reached regarding which methodology performs best, and under what conditions. The goal of this work was to examine the performance characteristics of a collection of existing gene set analysis methods, on both simulated ...

Abstract

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 ...