Browsing by Author "Zhu, Yun"

Now showing 1 - 5 of 5
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    Acumen: An Environment for Rapid Prototyping of Cyber-physical Systems
    (2009-09-09) Zhu, Yun
    Cyber-Physical Systems (CPS) combine discrete and continuous physical processes. Developing a new cyber-physical system is an iterative process that involves design, simulation, prototyping, and production. Writing simulation code using current techniques is time consuming. My thesis is that a carefully designed, domain-specific language can alleviate this difficulty. To demonstrate this thesis, I designed and implemented a prototype of a novel simulation environment called Acumen. The centerpiece of Acumen is a physical description language called PhyDL, which allows the user to directly describe dynamic equations governing the system being modeled, making the writing of simulation code much easier for engineers. A series of automatic transformations convert the high-level descriptions into a form that is directly machine executable. This thesis presents the design of PhyDL and several case studies of using PhyDL for designing CPS systems, which show that PhyDL is accurate and easy to use for domain experts.
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    Acumen: An environment for rapid prototyping of Cyber-Physical Systems
    (2009) Zhu, Yun; Taha, Walid
    Cyber-Physical Systems (CPS) combine discrete and continuous physical processes. Developing a new cyber-physical system is an iterative process that involves design, simulation, prototyping, and production. Writing simulation code using current techniques is time consuming. My thesis is that a carefully designed, domain-specific language can alleviate this difficulty. To demonstrate this thesis, I designed and implemented a prototype of a novel simulation environment called Acumen. The centerpiece of Acumen is a physical description language called PhyDL, which allows the user to directly describe dynamic equations governing the system being modeled, making the writing of simulation code much easier for engineers. A series of automatic transformations convert the high-level descriptions into a form that is directly machine executable. This thesis presents the design of PhyDL and several case studies of using PhyDL for designing CPS systems, which show that PhyDL is accurate and easy to use for domain experts.
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    Computational Analysis of Gene Duplication and Network Evolution
    (2014-04-25) Zhu, Yun; Nakhleh, Luay K.; Kavraki, Lydia E.; Kohn, Michael H.; Lin, Zhenguo
    Molecular interaction networks have emerged as a powerful data source for answering a plethora of biological questions ranging from how cells make decisions to how species evolve. The availability of such data from multiple organisms allows for their analysis from an evolutionary perspective. Gene duplication plays an important role in the evolution of genomes and interactomes, and elucidating the interplay between how genomes and interactomes evolve in light of gene duplication is of great interest. In order to achieve this goal, it is important to develop models and algorithms for analyzing network evolution, particularly with respect to gene duplication events. The contributions of my thesis are four-fold. First, I developed a new genotype model that combines genomes with regulatory network, and a population genetic framework for simulating the evolution of this genotype. Using the simulator, I established explanations for gene duplicability. Second, I developed novel algorithms for probabilistic inference of ancestral networks from extant taxa, in a phylogenetic setup. Third, I conducted data analyses focusing on whole-genome duplication in yeast, and established a rate of protein-protein interaction networks, and devised a method for generating hypotheses about gene duplicate fates from network data. Fourth, and not least, I investigated the role of networks in defining adaptive models for gene duplication. In summary, my thesis contributes new analytical tools and data analyses that help elucidate and understand the interplay between gene duplication at the genomic and interactomic levels.
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    Evolution After Whole-genome Duplication: A Network Perspective
    (Genetics Society of America, 2013) Zhu, Yun; Lin, Zhenguo; Nakhleh, Luay
    Gene duplication plays an important role in the evolution of genomes and interactomes. Elucidating how evolution after gene duplication interplays at the sequence and network level is of great interest. In this paper, we analyze a data set of gene pairs that arose through whole-genome duplication (WGD) in yeast. All these pairs have the same duplication time, making them ideal for evolutionary investigation. We investigated the interplay between evolution after WGD at the sequence and network levels, and correlated these two levels of divergence with gene expression and tness data. We nd that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences. Further, we nd that divergence of WGD pairs correlates strongly with gene expression and tness data. Owing to the role of gene duplication in determining redundancy in biological systems and particularly at the network level, we investigated the role of interaction networks in elucidating the evolutionary fate of duplicated genes. We nd that gene neighborhoods in interaction networks provide a mechanism for inferring these fates, and we developed an algorithm for achieving this task. Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques. Finally, we nd that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.
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    Gene Duplicability-Connectivity-Complexity across Organisms and a Neutral Evolutionary Explanation
    (Public Library of Science, 2012) Zhu, Yun; Du, Peng; Nakhleh, Luay
    Gene duplication has long been acknowledged by biologists as a major evolutionary force shaping genomic architectures and characteristics across the Tree of Life. Major research has been conducting on elucidating the fate of duplicated genes in a variety of organisms, as well as factors that affect a geneﾒs duplicabilityﾖthat is, the tendency of certain genes to retain more duplicates than others. In particular, two studies have looked at the correlation between gene duplicability and its degree in a protein-protein interaction network in yeast, mouse, and human, and another has looked at the correlation between gene duplicability and its complexity (length, number of domains, etc.) in yeast. In this paper, we extend these studies to six species, and two trends emerge. There is an increase in the duplicability-connectivity correlation that agrees with the increase in the genome size as well as the phylogenetic relationship of the species. Further, the duplicabilitycomplexity correlation seems to be constant across the species. We argue that the observed correlations can be explained by neutral evolutionary forces acting on the genomic regions containing the genes. For the duplicability-connectivity correlation, we show through simulations that an increasing trend can be obtained by adjusting parameters to approximate genomic characteristics of the respective species. Our results call for more research into factors, adaptive and non-adaptive alike, that determine a geneﾒs duplicability.