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Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell lines, tissues, and(More)
Recursive splicing is a process in which large introns are removed in multiple steps by re-splicing at ratchet points--5' splice sites recreated after splicing. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing. Here(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)
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)
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)
Protein sequence data is being generated at a tremendous rate; however, functional annotation of these proteins is proceeding at a much slower pace. Biologists rely on computational biology and pattern recognition to predict the functionality of proteins. This is based on the fact that proteins that share a similar function often exhibit conserved sequence(More)
After the publication of this work [1] it was noticed that there were typographical errors in the following equations: equation 5 in column 2, equation 7 in column 2, equation 8 in column 1. The bracket was placed incorrectly, so it should read: \log_2 (Y_{gij} + 0.5) rather thank (\log_2 Y_{gij} + 0.5) The publisher apologizes for this error.
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