Journal: BMC Systems Biology

Volume 8, Issue S-5

0 -- 0Fu-Jou Lai, Mei-Huei Jhu, Chia-Chun Chiu, Yueh-Min Huang, Wei-Sheng Wu. Identifying cooperative transcription factors in yeast using multiple data sources
0 -- 0Che Lin, Chin-Nan Lin, Yu-Chao Wang, Fang-Yu Liu, Yu-Wen Chien, Yung-Jen Chuang, Chung-Yu Lan, Wen-Ping Hsieh, Bor-Sen Chen. Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection
0 -- 0Wei-Sheng Wu, Ming-Liang Wei, Chia-Ming Yeh, Darby Tien-Hao Chang. A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae
0 -- 0Chih-Yuan Hsu, Tsu-Chun Yu, Ling-Jiun Lin, Rei-Hsing Hu, Bor-Sen Chen. Systematic approach to Escherichia coli cell population control using a genetic lysis circuit
0 -- 0Kazuhiro Maeda, Hiroyuki Kurata. Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity
0 -- 0Xiaolei Wang, Hiroyuki Kuwahara, Xin Gao. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels
0 -- 0Jiajie Peng, Hongxiang Li, Qinghua Jiang, Yadong Wang, Jin Chen. An integrative approach for measuring semantic similarities using gene ontology
0 -- 0Kansuporn Sriyudthsak, Yuji Sawada, Yukako Chiba, Yui Yamashita, Shigehiko Kanaya, Hitoshi Onouchi, Toru Fujiwara, Satoshi Naito, Eberhard O. Voit, Fumihide Shiraishi, Masami Y. Hirai. A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network
0 -- 0Chern Han Yong, Osamu Maruyama, Limsoon Wong. Discovery of small protein complexes from PPI networks with size-specific supervised weighting

Volume 8, Issue S-4

0 -- 0Fu-Jou Lai, Hong-Tsun Chang, Yueh-Min Huang, Wei-Sheng Wu. A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms
0 -- 0Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin. cytoHubba: identifying hub objects and sub-networks from complex interactome
0 -- 0Ashwini Patil, Kenta Nakai. TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
0 -- 0Rebecca L. Barter, Sarah-Jane Schramm, Graham J. Mann, Yee Hwa Yang. Network-based biomarkers enhance classical approaches to prognostic gene expression signatures
0 -- 0Tzu-Hsien Yang, Chung-Ching Wang, Po-Cheng Hung, Wei-Sheng Wu. cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila
0 -- 0Sriganesh Srihari, Piyush B. Madhamshettiwar, Sarah Song, Chao Liu, Peter T. Simpson, Kum Khanna, Mark A. Ragan. Complex-based analysis of dysregulated cellular processes in cancer
0 -- 0Haifen Chen, Piyushkumar A. Mundra, Li-Na Zhao, Feng Lin, Jie Zheng. Highly sensitive inference of time-delayed gene regulation by network deconvolution
0 -- 0Haijun Gong, Lu Feng. Computational analysis of the roles of ER-Golgi network in the cell cycle
0 -- 0Takefumi Moriya, Masayuki Yamamura, Daisuke Kiga. Effects of downstream genes on synthetic genetic circuits
0 -- 0Changhui Yan, Yingfeng Wang. A graph kernel method for DNA-binding site prediction
0 -- 0Shoba Ranganathan, Tin Wee Tan, Christian Schönbach. InCoB2014: Systems Biology update from the Asia-Pacific
0 -- 0Peng Yang, Xiaoquan Su, Le Ou-Yang, Hon Nian Chua, Xiao-Li Li, Kang Ning. Microbial community pattern detection in human body habitats via ensemble clustering framework

Volume 8, Issue S-3

0 -- 0Jieyue He, Chunyan Wang, Kunpu Qiu, Wei Zhong. An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks
0 -- 0Gamage Upeksha Ganegoda, Jianxin Wang, Fang-Xiang Wu, Min Li. Prediction of disease genes using tissue-specified gene-gene network
0 -- 0Sheng Liu, Shamitha Dissanayake, Sanjay Patel, Xin Dang, Todd Mlsna, Yixin Chen, Dawn Wilkins. Learning accurate and interpretable models based on regularized random forests regression
0 -- 0Li-Zhi Liu, Fang-Xiang Wu, Wen-Jun Zhang. A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets
0 -- 0Feng Yu, Zhi Yang, Nan Tang 0002, Hong Lin, Jian Wang, Zhi Yang. Predicting protein complex in protein interaction network - a supervised learning based method
0 -- 0Shuhao Sun, Fima C. Klebaner, Tianhai Tian. A new model of time scheme for progression of colorectal cancer

Volume 8, Issue S-2

0 -- 0Jörg Menche, Amitabh Sharma, Michael H. Cho, Ruth J. Mayer, Stephen I. Rennard, Bartolome Celli, Bruce E. Miller, Nick Locantore, Ruth Tal-Singer, Soumitra Ghosh, Chris Larminie, Glyn Bradley, John H. Riley, Alvar Agusti, Edwin K. Silverman, Albert-László Barabási. A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary Disease
0 -- 0Lisette J. A. Kogelman, Haja N. Kadarmideen. Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data
0 -- 0Oana A. Tomescu, Diethard Mattanovich, Gerhard G. Thallinger. Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data
0 -- 0Andreas Schmidt, Ignasi Forne, Axel Imhof. Bioinformatic analysis of proteomics data
0 -- 0Ana Conesa, Ali Mortazavi. The common ground of genomics and systems biology
0 -- 0Rafael Hernández-de-Diego, Noemi Boix-Chova, David Gomez-Cabrero, Jesper Tegnér, Imad Abugessaisa, Ana Conesa. STATegra EMS: an Experiment Management System for complex next-generation omics experiments
0 -- 0Polina Reshetova, Age K. Smilde, Antoine H. C. van Kampen, Johan A. Westerhuis. Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data
0 -- 0David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew E. Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam-Rudloff, Ana Conesa, Jesper Tegnér. Data integration in the era of omics: current and future challenges
0 -- 0Ferran Reverter, Esteban Vegas, Josep M. Oller. Kernel-PCA data integration with enhanced interpretability
0 -- 0Ignacio Ponzoni, María José Nueda, Sonia Tarazona, Stefan Götz, David Montaner, Julieta Sol Dussaut, Joaquín Dopazo, Ana Conesa. Pathway network inference from gene expression data

Volume 8, Issue S-1

0 -- 0Haijun Gong, Tong Tong Wu, Edmund M. Clarke. Pathway-gene identification for pancreatic cancer survival via doubly regularized Cox regression
0 -- 0Ryoichi Kinoshita, Mitsuo Iwadate, Hideaki Umeyama, Y-h. Taguchi. Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets
0 -- 0Hui Liu, Tongtong Wang, Hongbo Liu, Yanjun Wei, Guofeng Zhao, Jianzhong Su, Qiong Wu, Hong Qiao, Yan Zhang. Detection of type 2 diabetes related modules and genes based on epigenetic networks
0 -- 0Yanping Xi, Yue Zhao, Li Wang, Fei Wang. Comparison on extreme pathways reveals nature of different biological processes
0 -- 0Yijie Wang, Xiaoning Qian. Joint clustering of protein interaction networks through Markov random walk
0 -- 0Tianhai Tian, Kate Smith-Miles. Mathematical modeling of GATA-switching for regulating the differentiation of hematopoietic stem cell
0 -- 0Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang. Prioritizing protein complexes implicated in human diseases by network optimization
0 -- 0Yu Qian, Søren Besenbacher, Thomas Mailund, Mikkel Heide Schierup. Identifying disease associated genes by network propagation
0 -- 0Sherine Awad, Jin Chen. Inferring transcription factor collaborations in gene regulatory networks
0 -- 0Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu. On control of singleton attractors in multiple Boolean networks: integer programming-based method

Volume 8, Issue 1

0 -- 0Edouard Pauwels, Christian Lajaunie, Jean-Philippe Vert. A Bayesian active learning strategy for sequential experimental design in systems biology