A statistical normalization method and differential expression analysis for RNA-seq data between different species

Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved transcriptional responses. To remove systematic variation between different species for a fair comparison, the normalization procedure serves as a crucial pre-processing step that adjusts for the varying sample sequencing depths and other confounding technical effects. Results: In this paper, we propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and hypothesis testing framework. Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors. Conclusions: Simulation studies show that the proposed method performs significantly better than the existing competitor in a wide range of settings. An RNA-seq dataset of different species is also analyzed and it coincides with the conclusion that the proposed method outperforms the existing method. For practical applications, we have also developed an R package named "SCBN" and the software is available at http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html

Design and fabrication of robust broadband extreme ultraviolet multilayers

The random layer thickness variations can induce a great deformation of the experimental reflection of broadband extreme ultraviolet multilayer. In order to reduce this influence of random layer thickness fluctuations, the multiobjective genetic algorithm has been improved and used in the robust design of multilayer with a broad angular bandpass. The robust multilayer with a lower sensitivity to random thickness errors have been obtained and the corresponding multilayer mirrors were fabricated. The experimental results of robust Mo/Si multilayer with a wide angular band were presented and analyzed, and the advantage of robust multilayer design was demonstrated

Data-driven Computational Social Science: A Survey

Social science concerns issues on individuals, relationships, and the whole society. The complexity of research topics in social science makes it the amalgamation of multiple disciplines, such as economics, political science, and sociology, etc. For centuries, scientists have conducted many studies to understand the mechanisms of the society. However, due to the limitations of traditional research methods, there exist many critical social issues to be explored. To solve those issues, computational social science emerges due to the rapid advancements of computation technologies and the profound studies on social science. With the aids of the advanced research techniques, various kinds of data from diverse areas can be acquired nowadays, and they can help us look into social problems with a new eye. As a result, utilizing various data to reveal issues derived from computational social science area has attracted more and more attentions. In this paper, to the best of our knowledge, we present a survey on data-driven computational social science for the first time which primarily focuses on reviewing application domains involving human dynamics. The state-of-the-art research on human dynamics is reviewed from three aspects: individuals, relationships, and collectives. Specifically, the research methodologies used to address research challenges in aforementioned application domains are summarized. In addition, some important open challenges with respect to both emerging research topics and research methods are discussed.Comment: 28 pages, 8 figure