Robustness and modular design of the Drosophila segment polarity network

Biomolecular networks have to perform their functions robustly. A robust function may have preferences in the topological structures of the underlying network. We carried out an exhaustive computational analysis on network topologies in relation to a patterning function in Drosophila embryogenesis. We found that while the vast majority of topologies can either not perform the required function or only do so very fragilely, a small fraction of topologies emerges as particularly robust for the function. The topology adopted by Drosophila, that of the segment polarity network, is a top ranking one among all topologies with no direct autoregulation. Furthermore, we found that all robust topologies are modular--each being a combination of three kinds of modules. These modules can be traced back to three sub-functions of the patterning function and their combinations provide a combinatorial variability for the robust topologies. Our results suggest that the requirement of functional robustness drastically reduces the choices of viable topology to a limited set of modular combinations among which nature optimizes its choice under evolutionary and other biological constraints.Comment: Supplementary Information and Synopsis available at http://www.ucsf.edu/tanglab

A Model of Trade with Ricardian Comparative Advantage and Intra-sectoral Firm Heterogeneity

In this paper, we merge the heterogenous firm trade model of Melitz (2003) with the Ricardian model of Dornbusch, Fisher and Samuelson (DFS 1977) to explain how the pattern of international specialization and trade is determined by the interaction of comparative advantage, economies of scale, country sizes and trade barriers. The model is able to capture the existence of inter-industry trade and intra-industry trade in a single unified framework. It explains how trade openness affects the pattern of international specialization and trade. It generalizes Melitz’s firm selection effect in the face of trade liberalization to a setting where the patterns of inter-industry trade and intra-industry are endogenous. Although opening to trade is unambiguously welfare-improving in both countries, trade liberalization can lead to an counter-Melitz effect in the larger country if it is insufficiently competitive in the sectors where it has the strongest comparative disadvantage but still produces. In this case, the operating productivity cutoff is lowered while the exporting cutoff increases in the face of trade liberalization. This is because the intersectoral resource allocation (IRA) effect dominates the Melitz effect in these sectors. Consequently, the larger country can lose from trade liberalization. Some hypotheses related to firms’ exporting behavior across sectors upon opening up to trade and upon trade liberalization are also derived. Analyses of firm-level data of Chinese manufacturing sectors confirm these hypotheses.inter-industry trade, intra-industry trade, heterogeneous firms, trade liberalization

Universal flux-fluctuation law in small systems

We thank Dr. DeMenezes for providing the microchip data. This work was partially supported by the NSF of China under Grant Nos. 11135001, 11275003. Y.C.L. was supported by ARO under Grant No. W911NF-14-1-0504.Peer reviewedPublisher PD

Research on the Service Model of Higher Vocational E-Commercialized Curriculum Based on Value Network

In the environment of internet and e-commerce, the service of e-commercialized curriculum has gradually begun to develop. This paper introduces the theory of value network to support the service model of e-commercialized curriculum. Firstly, it analyzes the value network theory and its relationship with electronic commerce, and then discusses the existing problems and advantages of higher vocational e-commercialized curriculum. On the basis of these, it takes an analysis on the relationship between the members of value network, constructs the service model of higher vocational e-commercialized curriculum based on value network, and analyzes the value source, organizer, key factors and the integration process of the service model of higher vocational e-commercialized curriculum

Optimization and resilience of complex supply-demand networks

Acknowledgments This work was supported by NSF under Grant No. 1441352. SPZ and ZGH were supported by NSF of China under Grants No. 11135001 and No. 11275003. ZGH thanks Prof Liang Huang and Xin-Jian Xu for helpful discussions.Peer reviewedPublisher PD

TGCnA: temporal gene coexpression network analysis using a low-rank plus sparse framework

Various gene network models with distinct physical nature have been widely used in biological studies. For temporal transcriptomic studies, the current dynamic models either ignore the temporal variation in the network structure or fail to scale up to a large number of genes due to severe computational bottlenecks and sample size limitation. Although the correlation-based gene networks are computationally affordable, they have limitations after being applied to gene expression time-course data. We proposed Temporal Gene Coexpression Network Analysis (TGCnA) framework for the transcriptomic time-course data. The mathematical nature of TGCnA is the joint modeling of multiple covariance matrices across time points using a ‘low-rank plus sparse’ framework, in which the network similarity across time points is explicitly modeled in the low-rank component. We demonstrated the advantage of TGCnA in covariance matrix estimation and gene module discovery using both simulation data and real transcriptomic data. The code is available at https://github.com/QiZhangStat/TGCnA