Xintao Wei

Learn More
UNLABELLED Pathway Commons is a resource permitting simultaneous queries of multiple pathway databases. However, there is no standard mechanism for using these data (stored in BioPAX format) to annotate and build quantitative mathematical models. Therefore, we developed a new module within the virtual cell modeling and simulation software. It provides(More)
As the number of sequenced genomes has grown, we have become increasingly aware of the impact of horizontal gene transfer on our understanding of genome evolution. Methods for detecting horizontal gene transfer from sequence abound. Among the most accurate are methods based on phylogenetic tree inference, but even these can perform poorly in some cases,(More)
Gene set analyses have become a standard approach for increasing the sensitivity of transcriptomic studies. However, analytical methods incorporating gene sets require the availability of pre-defined gene sets relevant to the underlying physiology being studied. For novel physiological problems, relevant gene sets may be unavailable or existing gene set(More)
Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance due in part to a lack of sensitive assessment metrics. We present a series of(More)
  • 1