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ORCIDBMC Systems Biology, Volume 5 - Supplements
Volume 5, Number S-1, June 2011
- Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Computational systems biology: integration of sequence, structure, network, and dynamics. S1 - Bingchuan Liu, Jiajia Chen, Bairong Shen
:
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. S2 - Chia-Sheng Chuang, Tun-Wen Pai, Chin-Hua Hu, Wen-Shyong Tzou, Margaret Dah-Tsyr Chang, Hao-Teng Chang, Chih-Chia Chen:
Functional pathway mapping analysis for hypoxia-inducible factors. S3 - Rachita Sharma, Patricia A. Evans, Virendrakumar C. Bhavsar:
Regulatory link mapping between organisms. S4 - Zhenhua Li, Limsoon Wong, Jinyan Li:
DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts. S5 - Yong-Cui Wang, Yong Wang, Zhixia Yang, Nai-Yang Deng:
Support vector machine prediction of enzyme function with conjoint triad feature and hierarchical context. S6 - Jing-Na Si, Zengming Zhang, Biaoyang Lin, Michael Schroeder, Bingding Huang:
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction. S7 - Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Conditional random field approach to prediction of protein-protein interactions using domain information. S8 - Lin Wang, Lin Hou, Minping Qian, Fangting Li, Minghua Deng:
Integrating multiple types of data to predict novel cell cycle-related genes. S9 - Shao Li, Bo Zhang, Ningbo Zhang:
Network target for screening synergistic drug combinations with application to traditional Chinese medicine. S10 - Zhen-Ping Li, Rui-Sheng Wang, Xiang-Sun Zhang:
Two-stage flux balance analysis of metabolic networks for drug target identification. S11 - Ru-Dong Li, Yuan-Yuan Li, Lingyi Lu, Cong Ren, Yi-Xue Li, Lei Liu:
An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis. S12 - Chang Gu, Junjie Zhang, Ying-Yu Chen, Jinzhi Lei:
A trigger model of apoptosis induced by tumor necrosis factor signaling. S13 - Jimmy Omony, Leo H. de Graaff, Gerrit van Straten, Anton J. B. van Boxtel:
Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger. S14 - Hong-Bo Lei, Ji-Feng Zhang, Luonan Chen:
Multi-equilibrium property of metabolic networks: SSI module. S15 - Huarong Zhou, Shigeru Saito, Guanying Piao, Zhi-Ping Liu, Jiguang Wang, Katsuhisa Horimoto, Luonan Chen:
Network screening of Goto-Kakizaki rat liver microarray data during diabetic progression. S16 - Shigeru Saito, Yasuko Onuma, Yuzuru Ito, Hiroaki Tateno, Masashi Toyoda, Akutsu Hidenori, Koichiro Nishino, Emi Chikazawa, Yoshihiro Fukawatase, Yoshitaka Miyagawa, Hajime Okita, Nobutaka Kiyokawa, Yohichi Shimma, Akihiro Umezawa, Jun Hirabayashi, Katsuhisa Horimoto, Makoto Asashima:
Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells. S17
Volume 5, Number S-2, December 2011
- Dukyong Yoon, Hyosil Kim, Haeyoung Suh-Kim, Rae Woong Park, KiYoung Lee:
Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection. S1 - Rui Jiang, Mingxin Gan, Peng He:
Constructing a gene semantic similarity network for the inference of disease genes. S2 - Xi Wang, Xuegong Zhang:
Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite. S3 - Sangwoo Kim, Hojung Nam, Doheon Lee:
Exploring molecular links between lymph node invasion and cancer prognosis in human breast cancer. S4 - Henry Han:
A high performance profile-biomarker diagnosis for mass spectral profiles. S5 - Tomokazu Konishi:
Microarray test results should not be compensated for multiplicity of gene contents. S6 - Mariko Morita, Megumi Nakamura, Michito Hamada, Satoru Takahashi:
Combinatorial motif analysis of regulatory gene expression in Mafb deficient macrophages. S7 - Zhirui Hu, Minping Qian, Michael Q. Zhang:
Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. S8 - Chengxiang Qiu, Juan Wang, Qinghua Cui:
miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators. S9 - Young-Kyu Park, Ok Bang, Min-Ho Cha, Jaeheup Kim, John W. Cole, Doheon Lee, Young Kim:
SigCS base: an integrated genetic information resource for human cerebral stroke. S10 - Jaehoon Lee, Soyeon Ahn, Sohee Oh, Bruce Weir, Taesung Park:
SNP-PRAGE: SNP-based parametric robust analysis of gene set enrichment. S11 - Keunwan Park, Dongsup Kim:
Drug-drug relationship based on target information: application to drug target identification. S12 - Sung Hee Park, Ji Young Lee, Sangsoo Kim:
A methodology for multivariate phenotype-based genome-wide association studies to mine pleiotropic genes. S13 - Hyun Uk Kim, Tae Kim, Sang Lee:
Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network. S14 - Li C. Xia, Joshua A. Steele, Jacob A. Cram, Zoe G. Cardon, Sheri L. Simmons, Joseph J. Vallino, Jed A. Fuhrman, Fengzhu Sun:
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. S15
Volume 5, Number S-3, December 2011
- Ke Zhang, Yunlong Liu, Jack Y. Yang, Hamid R. Arabnia, Andrzej Niemierko, Arif Ghafoor, Weizhong Li, Youping Deng:
From genes to networks: in systematic points of view. I1 - Zhongxue Chen, Jianzhong Liu, Hon Ng, Saralees Nadarajah, Howard L. Kaufman, Jack Y. Yang, Youping Deng:
Statistical methods on detecting differentially expressed genes for RNA-seq data. S1 - Guan Ning Lin, Chao Zhang, Dong Xu:
Polytomy identification in microbial phylogenetic reconstruction. S2 - Xi Wu, Peng Li, Nan Wang, Ping Gong, Edward J. Perkins, Youping Deng, Chaoyang Zhang:
State Space Model with hidden variables for reconstruction of gene regulatory networks. S3 - Linglin Xie, Brent Weichel, Joyce Ohm, Ke Zhang:
An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver. S4 - Wooyoung Kim, Min Li, Jianxin Wang, Yi Pan:
Biological network motif detection and evaluation. S5 - Jun Liu, Jianxun Chen, Xiaoming Liu, Lei Chun, Jinshan Tang, Youping Deng:
Mass segmentation using a combined method for cancer detection. S6 - Jiliang Li, Fan Zhang, Jake Y. Chen:
An integrated proteomics analysis of bone tissues in response to mechanical stimulation. S7 - Jigang Wang, Xiaojie Qiu, Yuhua Li, Youping Deng, Tieliu Shi:
A transcriptional dynamic network during Arabidopsis thaliana pollen development. S8 - Omid Ghasemi, Merry Lindsey, Tianyi Yang, Nguyen T. Nguyen, Yufei Huang, Yufang Jin:
Bayesian parameter estimation for nonlinear modelling of biological pathways. S9 - Jianxin Wang, Gang Chen, Min Li, Yi Pan:
Integration of breast cancer gene signatures based on graph centrality. S10 - Feng Xu, Chen Zhao, Yuhua Li, Jiang Li, Youping Deng, Tieliu Shi:
Exploring virus relationships based on virus-host protein-protein interaction network. S11 - Peilin Jia, Chung-Feng Kao, Po-Hsiu Kuo, Zhongming Zhao:
A comprehensive network and pathway analysis of candidate genes in major depressive disorder. S12 - Walker H. Land Jr., Xingye Qiao, Daniel Margolis, William S. Ford, Christopher T. Paquette, Joseph F. Perez-Rogers, Jeffrey A. Borgia, Jack Y. Yang, Youping Deng:
Kernelized partial least squares for feature reduction and classification of gene microarray data. S13 - Gonzalo Martín, Maria-Cristina V. Marinescu, David E. Singh, Jesús Carretero:
Leveraging social networks for understanding the evolution of epidemics. S14
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