Journal: BMC Systems Biology

Volume 6, Issue S-3

0 -- 0Yajun Wang, Yao Yu, Bohu Pan, Pei Hao, Yixue Li, Zhifeng Shao, Xiaogang Xu, Xuan Li. Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome
0 -- 0Ru Shen, Nalin C. W. Goonesekere, Chittibabu Guda. Mining functional subgraphs from cancer protein-protein interaction networks
0 -- 0Shu-Hao Yu, Lulu Zheng, Yun Li, Chunyan Li, Chenchen Ma, Yixue Li, Xuan Li, Pei Hao. A cross-species analysis method to analyze animal models' similarity to human's disease state
0 -- 0Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang 0001. Detection of protein complexes from affinity purification/mass spectrometry data
0 -- 0Meeta Pradhan, Kshithija Nagulapalli, Mathew J. Palakal. Cliques for the identification of gene signatures for colorectal cancer across population
0 -- 0Yin Wang, Yuhua Zhou, Yixue Li, Zongxin Ling, Yan Zhu, Xiaokui Guo, Hong Sun. An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification
0 -- 0Yu Liu, Sean Maxwell, Tao Feng, Xiaofeng Zhu, Robert C. Elston, Mehmet Koyutürk, Mark R. Chance. Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data
0 -- 0Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen. Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes
0 -- 0Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang. Advances in systems biology: computational algorithms and applications
0 -- 0Pengyue Zhang, Raphaël Mourad, Yang Xiang, Kun Huang, Tim Hui-Ming Huang, Kenneth P. Nephew, Yunlong Liu, Lang Li. A dynamic time order network for time-series gene expression data analysis
0 -- 0Yan Fu, Xiaoshan Jiang, Hang Zhang, Jianhua Xing. A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli
0 -- 0Linlin Yang, Kailin Tang, Ying Qi, Hao Ye, Wenlian Chen, Yongyu Zhang, Zhiwei Cao. Potential metabolic mechanism of girls' central precocious puberty: a network analysis on urine metabonomics data
0 -- 0Cheng Zhu, Akash Kushwaha, Kenneth Berman, Anil G. Jegga. A vertex similarity-based framework to discover and rank orphan disease-related genes
0 -- 0Adam J. Richards, John Schwacke, Bärbel Rohrer, L. Ashley Cowart, Xinghua Lu. Revealing functionally coherent subsets using a spectral clustering and an information integration approach
0 -- 0Pei-Fang Su, Xi Chen, Heidi Chen, Yu Shyr. Statistical aspects of omics data analysis using the random compound covariate
0 -- 0Bing Han, Xue-wen Chen, Zohreh Talebizadeh, Hua Xu. Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks
0 -- 0Tingting Qin, Lam C. Tsoi, Kellie J. Sims, Xinghua Lu, W. Jim Zheng. Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network
0 -- 0Catherine P. Jayapandian, Meng Zhao, Rob M. Ewing, Guo-Qiang Zhang, Satya Sanket Sahoo. A semantic proteomics dashboard (SemPoD) for data management in translational research
0 -- 0Hong Cai, Changjin Hong, Jianying Gu, Timothy G. Lilburn, Rui Kuang, Yufeng Wang. Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum
0 -- 0Peilin Jia, Yang Liu, Zhongming Zhao. Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer
0 -- 0Tianyi Yang, Ying Ann Chiao, Yunji Wang, Andrew Voorhees, Hai-Chao Han, Merry Lindsey, Yufang Jin. Mathematical modeling of left ventricular dimensional changes in mice during aging

Volume 6, Issue S-2

0 -- 0Martin Haubrock, Jie Li, Edgar Wingender. Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks
0 -- 0Xin Chen, Qiong Wu, Ruimin Sun, Louxin Zhang. Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry
0 -- 0Dianhui Wang, Sarwar Tapan. MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences
0 -- 0Bin Xu, Xiaoming Wei, Lei Deng, Jihong Guan, Shuigeng Zhou. A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces
0 -- 0Sung-Chou Li, Kuo-Wang Tsai, Hung-Wei Pan, Yung-Ming Jeng, Meng-Ru Ho, Wen-Hsiung Li. MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues
0 -- 0Minzhu Xie, Jianxin Wang, Tao Jiang. A fast and accurate algorithm for single individual haplotyping
0 -- 0Chern Han Yong, Guimei Liu, Hon Nian Chua, Limsoon Wong. Supervised maximum-likelihood weighting of composite protein networks for complex prediction
0 -- 0Chuan Hock Koh, Limsoon Wong. Embracing noise to improve cross-batch prediction accuracy
0 -- 0Ben-Yang Liao, Meng-Pin Weng. Natural selection drives rapid evolution of mouse embryonic heart enhancers
0 -- 0Yu-Feng Huang, Sheng-Chung Chen, Yih-Shien Chiang, Tzu-Han Chen, Kuo Ping Chiu. Palindromic sequence impedes sequencing-by-ligation mechanism
0 -- 0Shingo Kikugawa, Kensaku Nishikata, Katsuhiko Murakami, Yoshiharu Sato, Mami Suzuki, Md. Altaf-Ul-Amin, Shigehiko Kanaya, Tadashi Imanishi. PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset
0 -- 0Dankyu Yoon, Young-Jin Kim, Taesung Park. Phenotype prediction from genome-wide association studies: application to smoking behaviors
0 -- 0Chuanli Wang, Longyun Guo, Yixue Li, Zhuo Wang. Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis
0 -- 0Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano. Computational gene network analysis reveals TNF-induced angiogenesis
0 -- 0Hufeng Zhou, Jingjing Jin, Haojun Zhang, Bo Yi, Michal Wozniak, Limsoon Wong. IntPath-an integrated pathway gene relationship database for model organisms and important pathogens

Volume 6, Issue S-1

0 -- 0Tao Zeng, Luonan Chen. Tracing dynamic biological processes during phase transition
0 -- 0Guanying Piao, Shigeru Saito, Yidan Sun, Zhi-Ping Liu, Yong Wang, Xiao Han, Jiarui Wu, Huarong Zhou, Luonan Chen, Katsuhisa Horimoto. A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats
0 -- 0Tao Zeng, Luonan Chen. Correction: Tracing dynamic biological processes during phase transition
0 -- 0Xiaoquan Su, Jian Xu, Kang Ning. Parallel-META: efficient metagenomic data analysis based on high-performance computation
0 -- 0Yong Wang, Xiang-Sun Zhang, Luonan Chen. Modelling biological systems from molecules to dynamical networks
0 -- 0Shu-Qiang Wang, Han-Xiong Li. Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge
0 -- 0Min Xu, Frank Alber. High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization
0 -- 0Chao Xu, Jiajia Chen, Bairong Shen. The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?
0 -- 0Chao Dai, Wenyuan Li, Juan Liu, Xianghong Jasmine Zhou. Integrating many co-splicing networks to reconstruct splicing regulatory modules
0 -- 0Ru-Dong Li, Lei Liu. Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example
0 -- 0Wei Zhang, Xiufen Zou. Synchronization ability of coupled cell-cycle oscillators in changing environments
0 -- 0Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao. The drug cocktail network
0 -- 0Xianfu Gao, Wanjia Chen, Rongxia Li, Minfeng Wang, Chunlei Chen, Rong Zeng, Yueyi Deng. Systematic variations associated with renal disease uncovered by parallel metabolomics of urine and serum
0 -- 0Yan Zhang, Jie Lin, Yang Gao. In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria
0 -- 0Hari Krishna Yalamanchili, Quan-Wu Xiao, Junwen Wang. A novel neural response algorithm for protein function prediction
0 -- 0Jing Zhao, Jie Chen 0008, Tinghong Yang, Petter Holme. Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis
0 -- 0Chen Chen, Junfei Zhao, Qiang Huang, Rui-Sheng Wang, Xiang-Sun Zhang. Inferring domain-domain interactions from protein-protein interactions in the complex network conformation
0 -- 0Canjun Wang, Ming Yi, Keli Yang, Lijian Yang. Time delay induced transition of gene switch and stochastic resonance in a genetic transcriptional regulatory model
0 -- 0Shuyun Jiao, Ping Ao. Absorbing phenomena and escaping time for Muller's ratchet in adaptive landscape
0 -- 0Melvin Zhang, Hon Wai Leong. BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity
0 -- 0Xi Chen, Hao Jiang, Yushan Qiu, Wai-Ki Ching. On optimal control policy for probabilistic Boolean network: a state reduction approach
0 -- 0Yong Wang, Qiao-Feng Wu, Chen Chen, Ling-Yun Wu, Xian-Zhong Yan, ShuGuang Yu, Xiang-Sun Zhang, Fan-Rong Liang. Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection
0 -- 0Xiaoke Ma, Lin Gao. Discovering protein complexes in protein interaction networks via exploring the weak ties effect