Browsing by Author "Wu, Meng"

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    Analysis and Enforcement of Properties in Software Systems
    Wu, Meng (Virginia Tech, 2019-07-02)
    Due to the lack of effective techniques for detecting and mitigating property violations, existing approaches to ensure the safety and security of software systems are often labor intensive and error prone. Furthermore, they focus primarily on functional correctness of the software code while ignoring micro-architectural details of the underlying processor, such as cache and speculative execution, which may undermine their soundness guarantees. To fill the gap, I propose a set of new methods and tools for ensuring the safety and security of software systems. Broadly speaking, these methods and tools fall into three categories. The first category is concerned with static program analysis. Specifically, I develop a novel abstract interpretation framework that considers both speculative execution and a cache model, and guarantees to be sound for estimating the execution time of a program and detecting side-channel information leaks. The second category is concerned with static program transformation. The goal is to eliminate side channels by equalizing the number of CPU cycles and the number of cache misses along all program paths for all sensitive variables. The third category is concerned with runtime safety enforcement. Given a property that may be violated by a reactive system, the goal is to synthesize an enforcer, called the shield, to correct the erroneous behaviors of the system instantaneously, so that the property is always satisfied by the combined system. I develop techniques to make the shield practical by handling both burst error and real-valued signals. The proposed techniques have been implemented and evaluated on realistic applications to demonstrate their effectiveness and efficiency.
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    Inferring the Genetic Basis of Sex Determination from the Genome of a Dioecious Nightshade
    Wu, Meng; Haak, David C.; Anderson, Gregory J.; Hahn, Matthew W.; Moyle, Leonie C.; Guerrero, Rafael F. (2021-07)
    Dissecting the genetic mechanisms underlying dioecy (i.e., separate female and male individuals) is critical for understanding the evolution of this pervasive reproductive strategy. Nonetheless, the genetic basis of sex determination remains unclear in many cases, especially in systems where dioecy has arisen recently. Within the economically important plant genus Solanum (similar to 2,000 species), dioecy is thought to have evolved independently at least 4 times across roughly 20 species. Here, we generate the first genome sequence of a dioecious Solanum and use it to ascertain the genetic basis of sex determination in this species. We de novo assembled and annotated the genome of Solanum appendiculatum (assembly size: similar to 750 Mb scaffold N50: 0.92 Mb; similar to 35,000 genes), identified sex-specific sequences and their locations in the genome, and inferred that males in this species are the heterogametic sex. We also analyzed gene expression patterns in floral tissues of males and females, finding approximately 100 genes that are differentially expressed between the sexes. These analyses, together with observed patterns of gene-family evolution specific to S. appendiculatum, consistently implicate a suite of genes from the regulatory network controlling pectin degradation and modification in the expression of sex. Furthermore, the genome of a species with a relatively young sex-determination system provides the foundational resources for future studies on the independent evolution of dioecy in this Glade.