BMC Systems Biology, Volume 6 - Supplements

Volume 6, Number S-1, July 2012

Selected articles from The 5th IEEE International Conference on Systems Biology (ISB 2011)

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  Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Modelling biological systems from molecules to dynamical networks. S1
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  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
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  Shu-Qiang Wang, Han-Xiong Li:
  Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge. S3
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  Jing Zhao, Jie Chen, Tinghong Yang, Petter Holme:
  Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis. S4
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  Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao:
  The drug cocktail network. S5
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  Xiaoke Ma, Lin Gao:
  Discovering protein complexes in protein interaction networks via exploring the weak ties effect. S6
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  Chen Chen, Junfei Zhao, Qiang Huang, Rui-Sheng Wang, Xiang-Sun Zhang:
  Inferring domain-domain interactions from protein-protein interactions in the complex network conformation. S7
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  Xi Chen, Hao Jiang, Yushan Qiu, Wai-Ki Ching:
  On optimal control policy for probabilistic Boolean network: a state reduction approach. S8
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  Canjun Wang, Ming Yi, Keli Yang, Lijian Yang:
  Time delay induced transition of gene switch and stochastic resonance in a genetic transcriptional regulatory model. S9
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  Shuyun Jiao, Ping Ao:
  Absorbing phenomena and escaping time for Muller's ratchet in adaptive landscape. S10
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  Ru-Dong Li, Lei Liu:
  Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example. S11
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  Tao Zeng, Luonan Chen:
  Tracing dynamic biological processes during phase transition. S12
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  Wei Zhang, Xiufen Zou:
  Synchronization ability of coupled cell-cycle oscillators in changing environments. S13
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  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
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  Yong 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. S15
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  Xiaoquan Su, Jian Xu, Kang Ning:
  Parallel-META: efficient metagenomic data analysis based on high-performance computation. S16
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  Chao Dai, Wenyuan Li, Juan Liu, Xianghong Jasmine Zhou:
  Integrating many co-splicing networks to reconstruct splicing regulatory modules. S17
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  Min Xu, Frank Alber:
  High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization. S18
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  Hari Krishna Yalamanchili, Quan-Wu Xiao, Junwen Wang:
  A novel neural response algorithm for protein function prediction. S19
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  Yan Zhang, Jie Lin, Yang Gao:
  In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria. S20
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  Chao Xu, Jiajia Chen, Bairong Shen:
  The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? S21
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  Melvin Zhang, Hon Wai Leong:
  BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity. S22
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  Tao Zeng, Luonan Chen:
  Correction: Tracing dynamic biological processes during phase transition. S23

Volume 6, Number S-2, December 2012

Proceedings of the 23rd International Conference on Genome Informatics (GIW 2012)

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  Ben-Yang Liao, Meng-Pin Weng:
  Natural selection drives rapid evolution of mouse embryonic heart enhancers. S1
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  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
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  Chuan Hock Koh, Limsoon Wong:
  Embracing noise to improve cross-batch prediction accuracy. S3
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  Dianhui Wang, Sarwar Tapan:
  MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. S4
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  Xin Chen, Qiong Wu, Ruimin Sun, Louxin Zhang:
  Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry. S5
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  Bin Xu, Xiaoming Wei, Lei Deng, Jihong Guan, Shuigeng Zhou:
  A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces. S6
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  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
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  Minzhu Xie, Jianxin Wang, Tao Jiang:
  A fast and accurate algorithm for single individual haplotyping. S8
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  Chuanli Wang, Longyun Guo, Yixue Li, Zhuo Wang:
  Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis. S9
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  Yu-Feng Huang, Sheng-Chung Chen, Yih-Shien Chiang, Tzu-Han Chen, Kuo-Ping Chiu:
  Palindromic sequence impedes sequencing-by-ligation mechanism. S10
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  Dankyu Yoon, Young Jin Kim, Taesung Park:
  Phenotype prediction from genome-wide association studies: application to smoking behaviors. S11
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  Kentaro Ogami, Rui Yamaguchi, Seiya Imoto, Yoshinori Tamada, Hiromitsu Araki, Cristin G. Print, Satoru Miyano:
  Computational gene network analysis reveals TNF-induced angiogenesis. S12
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  Chern Han Yong, Guimei Liu, Hon Nian Chua, Limsoon Wong:
  Supervised maximum-likelihood weighting of composite protein networks for complex prediction. S13
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  Sung-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. S14
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  Martin Haubrock, Jie Li, Edgar Wingender:
  Using potential master regulator sites and paralogous expansion to construct tissue-specific transcriptional networks. S15

Volume 6, Number S-3, December 2012

The International Conference on Intelligent Biology and Medicine (ICIBM): Systems Biology

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  Yufei Huang, Zhongming Zhao, Hua Xu, Yu Shyr, Bing Zhang:
  Advances in systems biology: computational algorithms and applications. S1
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  Ru Shen, Nalin C. W. Goonesekere, Chittibabu Guda:
  Mining functional subgraphs from cancer protein-protein interaction networks. S2
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  Tingting Qin, Lam C. Tsoi, Kellie J. Sims, Xinghua Lu, W. Jim Zheng:
  Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. S3
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  Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang:
  Detection of protein complexes from affinity purification/mass spectrometry data. S4
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  Hong 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. S5
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  Yan Fu, Xiaoshan Jiang, Hang Zhang, Jianhua Xing:
  A strategy to study pathway cross-talks of cells under repetitive exposure to stimuli. S6
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  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
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  Cheng Zhu, Akash Kushwaha, Kenneth Berman, Anil G. Jegga:
  A vertex similarity-based framework to discover and rank orphan disease-related genes. S8
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  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
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  Tianyi 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. S10
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  Pei-Fang Su, Xi Chen, Heidi Chen, Yu Shyr:
  Statistical aspects of omics data analysis using the random compound covariate. S11
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  Yin 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. S12
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  Peilin Jia, Yang Liu, Zhongming Zhao:
  Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. S13
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  Bing Han, Xue-wen Chen, Zohreh Talebizadeh, Hua Xu:
  Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks. S14
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  Yu 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. S15
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  Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen:
  Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. S16
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  Meeta Pradhan, Kshithija Nagulapalli, Mathew J. Palakal:
  Cliques for the identification of gene signatures for colorectal cancer across population. S17
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  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
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  Linlin 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. S19
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  Catherine P. Jayapandian, Meng Zhao, Rob M. Ewing, Guo-Qiang Zhang, Satya Sanket Sahoo:
  A semantic proteomics dashboard (SemPoD) for data management in translational research. S20
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  Yajun 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. S21