Identification of differentially expressed genes (DEGs) in time course studies is very useful for understanding gene function, and can help determine key genes during specific stages of plant development. A few existing methods focus on the detection of DEGs within a single biological group, enabling to study temporal changes in gene expression. To utilize a rapidly increasing amount of single-group time-series expression data, we propose a two-step method that integrates the temporal characteristics of time-series data to obtain a B-spline curve fit. Firstly, a flat gene filter based on the Ljung–Box test is used to filter out flat genes. Then, a B-spline model is used to identify DEGs. For use in biological experiments, these DEGs should be screened, to determine their biological importance. To identify high-confidence promising DEGs for specific biological processes, we propose a novel gene prioritization approach based on the partner evaluation principle. This novel gene prioritization approach utilizes existing co-expression information to rank DEGs that are likely to be involved in a specific biological process/condition. The proposed method is validated on the Arabidopsis thaliana seed germination dataset and on the rice anther development expression dataset.

Subcellular localization of proteins can provide key hints to infer their functions and structures in cells. With the breakthrough of recent molecule imaging techniques, the usage of 2D bioimages has become increasingly popular in automatically analyzing the protein subcellular location patterns. Compared with the widely used protein 1D amino acid sequence data, the images of protein distribution are more intuitive and interpretable, making the images a better choice at many applications for revealing the dynamic characteristics of proteins, such as detecting protein translocation and quantification of proteins. In this paper, we systematically reviewed the recent progresses in the field of automated image-based protein subcellular location prediction, and classified them into four categories including growing of bioimage databases, description of subcellular location distribution patterns, classification methods, and applications of the prediction systems. Besides, we also discussed some potential directions in this field.

Interaction detection in large-scale genetic association studies has attracted intensive research interest, since many diseases have complex traits. Various approaches have been developed for finding significant genetic interactions. In this article, we propose a novel framework SRMiner to detect interacting susceptible and protective genotype patterns. SRMiner can discover not only probable combination of single nucleotide polymorphisms (SNPs) causing diseases but also the corresponding SNPs suppressing their pathogenic functions, which provides a better prospective to uncover the underlying relevance between genetic variants and complex diseases. We have performed extensive experiments on several real Wellcome Trust Case Control Consortium (WTCCC) datasets. We use the pathway-based and the protein-protein interaction (PPI) network-based evaluation methods to verify the discovered patterns. The results show that SRMiner successfully identifies many disease-related genes verified by the existing work. Furthermore, SRMiner can also infer some uncomfirmed but highly possible disease-related genes.

In the past decade, the remarkable development of high-throughput sequencing technology accelerates the generation of large amount of multiple dimensional data such as genomic, epigenomic, transcriptomic and proteomic data. The comprehensive data make it possible to understand the underlying mechanisms of biology and disease such as cancer systematically. It also provides great challenges for computational cancer genomics due to the complexity, scale and noise of data. In this article, we aim to review the recent developments and progresses of computational models, algorithms and analysis of complex data in cancer genomics. These topics of this paper include the identification of driver mutations, the genetic heterogeneity analysis, genomic markers discovery of drug response, pan-cancer scale analysis and so on.

3D printing has become a promising technique for industry production. This paper presents a research on the manufacturability optimization of discrete products under the influence of 3D printing technology. For this, we first model the problem using a tree structure, and then formulate it as a linear integer programming, where the total production time is to be minimized with the production cost constraint. To solve the problem, a differential evolution (DE) algorithm is developed, which automatically determines whether traditional manufacturing methods or 3D printing technology should be used for each part of the production. The algorithm is further quantitatively evaluated on a synthetic dataset, compared with the exhaustive search and alternating optimization solutions. Simulation results show that the proposed algorithm can well combine the traditional manufacturing methods and 3D printing technology in production, which is helpful to attain optimized product design and process planning concerning manufacture time. Therefore, it is beneficial to provide reference of the widely application and further industrialization of the 3D printing technology.