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BMC Systems Biology, Volume 6 - Supplements
Volume 6, Number S-1, July 2012
- Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Modelling biological systems from molecules to dynamical networks. S1 - Guanying 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. S2 - Shuqiang Wang
, Han-Xiong Li
Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge. S3 - Jing Zhao
Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis. S4 - Ke-Jia Xu, Jiangning Song
The drug cocktail network. S5 - Xiaoke Ma, Lin Gao:
Discovering protein complexes in protein interaction networks via exploring the weak ties effect. S6 - Chen Chen, Junfei Zhao, Qiang Huang, Rui-Sheng Wang
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation. S7 - Xi Chen, Hao Jiang, Yushan Qiu, Wai-Ki Ching:
On optimal control policy for probabilistic Boolean network: a state reduction approach. S8 - Canjun Wang, Ming Yi
Time delay induced transition of gene switch and stochastic resonance in a genetic transcriptional regulatory model. S9 - Shuyun Jiao, Ping Ao:
Absorbing phenomena and escaping time for Muller's ratchet in adaptive landscape. S10 - Ru-Dong Li, Lei Liu:
Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example. S11 - Tao Zeng
Tracing dynamic biological processes during phase transition. S12 - Wei Zhang, Xiufen Zou:
Synchronization ability of coupled cell-cycle oscillators in changing environments. S13 - Xianfu 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. S14 - Yong Wang, Qiao-Feng Wu
Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection. S15 - Xiaoquan Su, Jian Xu
Parallel-META: efficient metagenomic data analysis based on high-performance computation. S16 - Chao Dai, Wenyuan Li, Juan Liu, Xianghong Jasmine Zhou:
Integrating many co-splicing networks to reconstruct splicing regulatory modules. S17 - Min Xu, Frank Alber:
High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization. S18 - Hari Krishna Yalamanchili, Quan-Wu Xiao, Junwen Wang:
A novel neural response algorithm for protein function prediction. S19 - Yan Zhang, Jie Lin, Yang Gao:
In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria. S20 - Chao Xu, Jiajia Chen, Bairong Shen
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? S21 - Melvin Zhang, Hon Wai Leong:
BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity. S22 - Tao Zeng, Luonan Chen:
Correction: Tracing dynamic biological processes during phase transition. S23
Volume 6, Number S-2, December 2012
- Ben-Yang Liao
Natural selection drives rapid evolution of mouse embryonic heart enhancers. S1 - Hufeng Zhou, Jingjing Jin, Haojun Zhang, Bo Yi, Michal Wozniak, Limsoon Wong
IntPath-an integrated pathway gene relationship database for model organisms and important pathogens. S2 - Chuan Hock Koh, Limsoon Wong
Embracing noise to improve cross-batch prediction accuracy. S3 - Dianhui Wang, Sarwar Tapan:
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. S4 - Xin Chen, Qiong Wu, Ruimin Sun, Louxin Zhang:
Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry. S5 - Bin Xu, Xiaoming Wei, Lei Deng, Jihong Guan, Shuigeng Zhou:
A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces. S6 - Shingo 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. S7 - Minzhu Xie, Jianxin Wang, Tao Jiang
A fast and accurate algorithm for single individual haplotyping. S8 - Chuanli Wang, Longyun Guo, Yixue Li, Zhuo Wang:
Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis. S9 - Yu-Feng Huang
Palindromic sequence impedes sequencing-by-ligation mechanism. S10 - Dankyu Yoon, Young Jin Kim, Taesung Park:
Phenotype prediction from genome-wide association studies: application to smoking behaviors. S11 - Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada
Computational gene network analysis reveals TNF-induced angiogenesis. S12 - Chern Han Yong, Guimei Liu
Supervised maximum-likelihood weighting of composite protein networks for complex prediction. S13 - Sung-Chou Li, Kuo-Wang Tsai
MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues. S14 - Martin Haubrock
Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks. S15
Volume 6, Number S-3, December 2012
- Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr
Advances in systems biology: computational algorithms and applications. S1 - Ru Shen, Nalin C. W. Goonesekere, Chittibabu Guda:
Mining functional subgraphs from cancer protein-protein interaction networks. S2 - Tingting Qin, Lam C. Tsoi
Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. S3 - Bingjing Cai, Haiying Wang
Detection of protein complexes from affinity purification/mass spectrometry data. S4 - Hong Cai, Changjin Hong, Jianying Gu
Module-based subnetwork alignments reveal novel transcriptional regulators in malaria parasite Plasmodium falciparum. S5 - Yan Fu, Xiaoshan Jiang, Hang Zhang, Jianhua Xing
A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli. S6 - Adam J. Richards, John Schwacke, Bärbel Rohrer, L. Ashley Cowart, Xinghua Lu:
Revealing functionally coherent subsets using a spectral clustering and an information integration approach. S7 - Cheng Zhu, Akash Kushwaha, Kenneth Berman, Anil G. Jegga
A vertex similarity-based framework to discover and rank orphan disease-related genes. S8 - Pengyue 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. S9 - Tianyi Yang, Ying Ann Chiao, Yunji Wang, Andrew Voorhees
Mathematical modeling of left ventricular dimensional changes in mice during aging. S10 - Pei-Fang Su, Xi Chen, Heidi Chen
Statistical aspects of omics data analysis using the random compound covariate. S11 - Yin Wang, Yuhua Zhou, Yixue Li, Zongxin Ling
An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification. S12 - Peilin Jia, Yang Liu, Zhongming Zhao:
Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. S13 - Bing Han, Xue-wen Chen, Zohreh Talebizadeh, Hua Xu:
Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks. S14 - Yu Liu
Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data. S15 - Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. S16 - Meeta Pradhan, Kshithija Nagulapalli, Mathew J. Palakal:
Cliques for the identification of gene signatures for colorectal cancer across population. S17 - Shu-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. S18 - Linlin Yang, Kailin Tang
Potential metabolic mechanism of girls' central precocious puberty: a network analysis on urine metabonomics data. S19 - Catherine P. Jayapandian, Meng Zhao, Rob M. Ewing
A semantic proteomics dashboard (SemPoD) for data management in translational research. S20 - Yajun Wang, Yao Yu, Bohu Pan, Pei Hao
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome. S21
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