BioMed Research International Advances in Computational Genomics NeuralGuest Editors: Computation Leng Han, Yan Guo, Zhixi Su, for Siyuan Rehabilitation Zheng, and Zhixiang Lu Advances in Computational Genomics BioMed Research International Advances in Computational Genomics Guest Editors: Leng Han, Yan Guo, Zhixi Su, Siyuan Zheng, and Zhixiang Lu Copyright © 2015 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Advances in Computational Genomics, Leng Han, Yan Guo, Zhixi Su, Siyuan Zheng, and Zhixiang Lu Volume 2015, Article ID 187803, 2 pages Genepleio Software for Effective Estimation of Gene Pleiotropy from Protein Sequences, Wenhai Chen, Dandan Chen, Ming Zhao, Yangyun Zou, Yanwu Zeng, and Xun Gu Volume 2015, Article ID 269150, 6 pages Integration Strategy Is a Key Step in Network-Based Analysis and Dramatically Affects Network Topological Properties and Inferring Outcomes, Nana Jin, Deng Wu, Yonghui Gong, Xiaoman Bi, Hong Jiang, Kongning Li, and Qianghu Wang Volume 2014, Article ID 296349, 13 pages Informative Gene Selection and Direct Classification of Tumor Based on Chi-Square Test of Pairwise Gene Interactions, Hongyan Zhang, Lanzhi Li, Chao Luo, Congwei Sun, Yuan Chen, Zhijun Dai, and Zheming Yuan Volume 2014, Article ID 589290, 9 pages miRNA Signature in Mouse Spermatogonial Stem Cells Revealed by High-Throughput Sequencing, Tao Tan, Yanfeng Zhang, Weizhi Ji, and Ping Zheng Volume 2014, Article ID 154251, 11 pages Advanced Heat Map and Clustering Analysis Using Heatmap3, Shilin Zhao, Yan Guo, Quanhu Sheng, and Yu Shyr Volume 2014, Article ID 986048, 6 pages Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome,Yue-DongGao, Yuqi Zhao, and Jingfei Huang Volume 2014, Article ID 694967, 11 pages Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways,YanLi, Weiguo Li, Xin Chen, Hong Jiang, Jiatong Sun, Huan Chen, and Sali Lv Volume2014,ArticleID931825,10pages Effect of Duplicate Genes on Mouse Genetic Robustness: An Update,ZhixiSu,JunqiangWang, and Xun Gu Volume 2014, Article ID 758672, 13 pages Designing Peptide-Based HIV Vaccine for Chinese, Jiayi Shu, Xiaojuan Fan, Jie Ping, Xia Jin, and Pei Hao Volume 2014, Article ID 272950, 8 pages RNA-Seq Identifies Key Reproductive Gene Expression Alterations in Response to Cadmium Exposure, Hanyang Hu, Xing Lu, Xiang Cen, Xiaohua Chen, Feng Li, and Shan Zhong Volume 2014, Article ID 529271, 11 pages Stratification of Gene Coexpression Patterns and GO Function Mining for a RNA-Seq Data Series, Hui Zhao, Fenglin Cao, Yonghui Gong, Huafeng Xu, Yiping Fei, Longyue Wu, Xiangmei Ye, Dongguang Yang, Xiuhua Liu, Xia Li, and Jin Zhou Volume2014,ArticleID969768,8pages BLAT-Based Comparative Analysis for Transposable Elements: BLATCAT, Sangbum Lee, Sumin Oh, Keunsoo Kang, and Kyudong Han Volume 2014, Article ID 730814, 7 pages A Systematic Analysis of miRNA-mRNA Paired Variations Reveals Widespread miRNA Misregulation in Breast Cancer, Lei Zhong, Kuixi Zhu, Nana Jin, Deng Wu, Jianguo Zhang, Baoliang Guo, Zhaoqi Yan, and Qingyuan Zhang Volume 2014, Article ID 291280, 8 pages O18Quant: A Semiautomatic Strategy for Quantitative Analysis of High-Resolution 16O/18OLabeled Data, Yan Guo, Masaru Miyagi, Rong Zeng, and Quanhu Sheng Volume 2014, Article ID 971857, 7 pages Antioxidant Defense Enzyme Genes and Asthma Susceptibility: Gender-Specific Effects and Heterogeneity in Gene-Gene Interactions between Pathogenetic Variants of the Disease, Alexey V. Polonikov, Vladimir P. Ivanov, Alexey D. Bogomazov, Maxim B. Freidin, Thomas Illig, and Maria A. Solodilova Volume 2014, Article ID 708903, 17 pages Hindawi Publishing Corporation BioMed Research International Volume 2015, Article ID 187803, 2 pages http://dx.doi.org/10.1155/2015/187803 Editorial Advances in Computational Genomics Leng Han,1 Yan Guo,2 Zhixi Su,3 Siyuan Zheng,1 and Zhixiang Lu4 1 Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA 2Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232, USA 3State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China 4Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA Correspondence should be addressed to Leng Han; [email protected] Received 14 September 2014; Accepted 13 October 2014 Copyright © 2015 Leng Han et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. High-throughput technologies, such as microarray and next including highly customizable legends and side annotation, generation sequencing (NGS), have emerged as a powerful a wider range of color selections, and new labeling features. tool less than a decade ago and have produced an avalanche W. Chen et al. developed a newly developed software of genome sequences. Computational genomics, which focus package, Genepleio, to estimate the effective gene pleiotropy on computational analysis from genome sequences to other from phylogenetic analysis of protein sequences. This work postgenomic data, including both DNA and RNA sequences, would facilitate the understanding of how gene pleiotropy protein profiling, and epigenetic profiling, have become one affected the pattern of genotype-phenotype map and the of the most important avenues for biological discovery. consequence of organismal evolution. Transforming genomic information into biomedical and S.Leeatal.developedtheBLAST-likealignmenttool biological knowledge requires creative and innovative new (BLAT) based comparative analysis for transposable elements computational methods for all aspects of genomics. In this (BLATCAT) program and compared specific regions of special issue, we selected fifteen high-quality papers in com- representative primate genome sequences. putational genomics field after in-depth peer review, andwe H. Zhang et al. developed a new method for tumor-gene briefly described these papers below. selection,thechi-squaretest-basedintegratedgenerankand Z. Su et al. performed an extensive analysis of the direct classifier. The informative genes selected significantly mouse knockout phenotype data and corroborated a strong improved the independent test precision of other classifiers. effect of duplicate genes on mouse genetics robustness. The L. Zhong et al. analyzed miRNA-mRNA paired variations study suggested the potential correlation between the effect (MMPVs) comprehensively and demonstrated that the exis- of genetic buffering and sequence conservation as well as tence of MMPVs is general and widespread but that there is a protein-protein interactivity. general unbalance in the distribution of MMPVs among the Y.Guoetal.developedasoftwarepackage,O18Quant, different pathological features. which calculated the peptide/protein relative ratio and pro- N. Jin et al. systematically evaluated frequently used vided a friendly graphical user interface (GUI). The software methods using two types of integration strategies, empirical greatly enhanced user’s visualization and understanding in and machine, and provided an important basis for future quantitative proteomics data analysis. network-based biological research learning methods. S. Zhao et al. developed an R package, “heatmap3,” H. Zhao et al. developed an integrated strategy to identify which significantly improved the original “heatmap” function differential coexpression patterns of genes and probed the by adding several more powerful and convenient features, functional mechanisms of the modules. This approach was 2 BioMed Research International able to robustly detect coexpression patterns in transcrip- tomes and to stratify patterns according to their relative differences. A. V. Polonikov et al. comprehensively analyzed the associations between adult asthma and single nucleotide polymorphisms and found the epistatic interactions between ADE genes underlying asthma susceptibility and the genetic heterogeneity between allergic and nonallergic variants of the disease. J. Shu et al. constructed a database to design vaccine that targeted the Chinese, and predicted 20 potential HIV epitopes. This work will facilitate the development of a CD4+ T cell vaccine especially catered for the Chinese. Y. Li et al. built a link map between small molecules and pathways using gene expression profiles, pathways, and gene expression of cancer cell lines intervened by small molecules and provided a valuable reference for identifying drug candidates and targets in molecularly targeted therapy. Y.-D. Gao et al. investigated the E. coli strains in the human gut microbiome by using deep sequencing data. The authors reconstructed genome-wide metabolic networks forthethreemostcommonE. coli strains and provided a systematic perspective on E. coli strains in the human gut microbiome. T. Tan et al. compared small RNA signatures to address small RNA transition during mouse spermatogenesis and provided insight into the mechanisms involved in the regu- lation of spermatogonial