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Computational Systems Biology

Regular Papers

Optimizing analytical depth and cost efficiency of IEF-LC/MS proteomics (Page 99)
Ilona Kifer, Rui M. Branca, Amir Ben-Dor, Ping Xu, Janne Lehtio, and Zohar Yakhini

Heavy Path Mining Reveals Novel Protein-Protein Associations in the Malaria Parasite Plasmodium falciparum (Page 107)
Xinran Yu, Turgay Korkmaz, Timothy Lilburn, Hong Cai, Jianying Gu, and Yufeng Wang

Integrative analysis of chemo-transcriptomic profiles for drug-feature specific gene expression signatures (Page 113)
Chang Sik Kim, Qing Wen, and Shu-Dong Zhang

Efficient Updates of network motif instances in the extended protein-protein interaction network (Page 119)
Wooyoung Kim and Sheil Kurmar

Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering (Page 125)
En-Shiun Annie Lee, Ho-Yin Sze-To, Man-Hon Wong, Kwong-Sak Leung, Terrence Chi-Kong Lau, and Andrew K. C. Wong

A scale-free structure prior for Bayesian inference of Gaussian Graphical models (Page 131)
Osamu Maruyama and Shota Shikita

RMA with quantile normalization mixes biological signals between different sample groups in microarray data analysis (Page 139)
Chang Sik Kim, Seungwoo Hwang, and Shu-Dong Zhang

Data Integration and Supervised Learning Based Protein Complex Detection Method (Page 144)
Fengying Yu, Zhihao Yang, Xiaohua Hu, Yuanyuan Sun, Hongfei Lin, and Jian Wang

NovoPair: de novo peptide sequencing for complementary spectra pair (Page 150)
Yan Yan, Anthony J. Kusalik, and Fang-Xiang Wu

Drug sensitivity prediction for cancer cell lines based on pairwise kernels and miRNA profiles (Page 156)
Mehmet Tan

Functional module-centric interpretation of transcriptomic change between human and chimpanzee cerebral cortex (Page 162)
Kimin Oh, Taeho Hwang, Kihoon Cha, and Gwan-Su Yi

CSF protein dynamic driver network: at the crossroads of brain tumorigenesis (Page 168)
Changlin Fu, Zhou Tan, Rui Liu, Shiying Hao, Zhen Li, Pei Chen, Taichang Jang, Milton Merchant, John Whitin, Oxford Wang, Minyi Guo, Harvey Cohen, Lawrence Recht, and Xuefeng Ling

TAMeBS: a sensitive bisulfite-sequencing read mapping tool for DNA methylation analysis (Page 176)
Ruimin Sun, Ye Tian, and Xin Chen

Probabilistic Verification of ER Stress-induced Signaling Pathways (Page 182)
Haijun Gong and Lu Feng

Short Papers

Budgeted Transcript Discovery: A Framework For Joint Exploration And Validation Studies (Page 188)
Sheehan Khan and Russell Greiner

Exploring the relation between the characteristics of protein interaction networks and the performances of computational complex detection methods (Page 192)
Xiaoxia liu, Zhihao Yang, Ziwei Zhou, Yuanyuan Sun, Hongfei Lin, and Jian Wang

Identifying differentially expressed genes for ordinal phenotypes (Page 193)
Yongkang Kim and Taesung Park

A logistic regression based algorithm for identifying human disease genes (Page 197)
Bolin chen, Min Li, Jianxin Wang, and Fang-Xiang Wu

Discovering Phenotype Specific Gene Module using a Novel Biclustering Algorithm in Colorectal Cancer (Page 201)
Jungrim Kim, Jeagyoon Ahn, Youngmi Yoon, Yunku Yeu, and Sanghyun Park

ESclassifier: a Random Forest classifier for detection of exon skipping events from RNA-Seq data (Page 205)
Yang Bai, Shufan Ji, and Yadong Wang

Different Cancer Cell Lines Resistant to the Same Drug Exhibit Differences in Folate Pathway Dynamics (Page 209)
Amrisha Bhosle and Nagasuma Chandra

A New Approach for Multi-omic Data Integration (Page 214)
Yiming Zuo, Guoqiang Yu, Chi Zhang, and Habtom Ressom