Learn More
Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray(More)
In a recent report, [Zhang et al. (2003) N. Engl. J. Med. 348, 203-213], the presence of CD3+ tumor-infiltrating lymphocytes (TILs) was found to correlate with improved survival in epithelial ovarian cancer. We performed immunohistochemical analysis for TILs and cancer testis antigens in 117 cases of epithelial ovarian cancer. The interrelationship between(More)
This paper reports on a new approach to solving a subset-based points-to analysis for Java using Binary Decision Diagrams (BDDs). In the model checking community, BDDs have been shown very effective for representing large sets and solving very large verification problems. Our work shows that BDDs can also be very effective for developing a points-to(More)
Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung(More)
Modern virtual machines often maintain multiple compiled versions of a method. An on-stack replacement (OSR) mechanism enables a virtual machine to transfer execution between compiled versions, even while a method runs. Relying on this mechanism, the system can exploit powerful techniques to reduce compile time and code space, dynamically de-optimize code,(More)
West Nile virus (WNV), and related flaviviruses such as tick-borne encephalitis, Japanese encephalitis, yellow fever and dengue viruses, constitute a significant global human health problem. However, our understanding of the molecular interaction of such flaviviruses with mammalian host cells is limited. WNV encodes only 10 proteins, implying that it may(More)
This paper reports on a new approach to solving a subset-based points-to analysis for Java using Binary Decision Diagrams (BDDs). In the model checking community, BDDs have been shown very effective for representing large sets and solving very large verification problems. Our work shows that BDDs can also be very effective for developing a points-to(More)
The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320(More)
A robust bioinformatics capability is widely acknowledged as central to realizing the promises of toxicogenomics. Successful application of toxicogenomic approaches, such as DNA microarrays, inextricably relies on appropriate data management, the ability to extract knowledge from massive amounts of data, and the availability of functional information for(More)
Thispaperproposesamethodology for automatically extractingT–S fuzzymodels fromdatausingparticle swarmoptimization (PSO). In theproposedmethod, the structures andparametersof the fuzzymodels are encoded into a particle and evolve together so that the optimal structure and parameters can be achieved simultaneously. An improved version of the original PSO(More)