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ORCIDBMC Systems Biology, Volume 8 - Supplements
Volume 8, Number S-1, January 2014
- Sherine Awad, Jin Chen:
Inferring transcription factor collaborations in gene regulatory networks. S1 - Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang
:
Prioritizing protein complexes implicated in human diseases by network optimization. S2 - Haijun Gong, Tong Tong Wu, Edmund M. Clarke:
Pathway-gene identification for pancreatic cancer survival via doubly regularized Cox regression. S3 - Ryoichi Kinoshita, Mitsuo Iwadate, Hideaki Umeyama, Y-h. Taguchi:
Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets. S4 - Hui 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. S5 - Yu Qian, Søren Besenbacher, Thomas Mailund, Mikkel Heide Schierup:
Identifying disease associated genes by network propagation. S6 - Yushan Qiu, Takeyuki Tamura, Wai-Ki Ching, Tatsuya Akutsu:
On control of singleton attractors in multiple Boolean networks: integer programming-based method. S7 - Tianhai Tian, Kate Smith-Miles:
Mathematical modeling of GATA-switching for regulating the differentiation of hematopoietic stem cell. S8 - Yijie Wang, Xiaoning Qian:
Joint clustering of protein interaction networks through Markov random walk. S9 - Yanping Xi, Yue Zhao, Li Wang, Fei Wang:
Comparison on extreme pathways reveals nature of different biological processes. S10
Volume 8, Number S-2, March 2014
- David 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. I1 - Ana Conesa, Ali Mortazavi:
The common ground of genomics and systems biology. S1 - Polina 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. S2 - Andreas Schmidt, Ignasi Forne, Axel Imhof:
Bioinformatic analysis of proteomics data. S3 - Oana A. Tomescu, Diethard Mattanovich, Gerhard G. Thallinger:
Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data. S4 - Lisette 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. S5 - Ferran Reverter, Esteban Vegas, Josep M. Oller:
Kernel-PCA data integration with enhanced interpretability. S6 - Ignacio Ponzoni, María José Nueda, Sonia Tarazona, Stefan Götz, David Montaner, Julieta Sol Dussaut, Joaquín Dopazo, Ana Conesa:
Pathway network inference from gene expression data. S7 - Jörg 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. S8 - Rafael 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. S9
Volume 8, Number S-3, October 2014
- Li-Zhi Liu, Fang-Xiang Wu, Wen-Jun Zhang:
A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets. S1 - Shuhao Sun, Fima C. Klebaner, Tianhai Tian:
A new model of time scheme for progression of colorectal cancer. S2 - Gamage Upeksha Ganegoda, Jianxin Wang, Fang-Xiang Wu, Min Li:
Prediction of disease genes using tissue-specified gene-gene network. S3 - Feng Yu, Zhi-Hao Yang, Nan Tang, Hong Lin, Jian Wang, Zhiwei Yang:
Predicting protein complex in protein interaction network - a supervised learning based method. S4 - Sheng Liu, Shamitha Dissanayake, Sanjay Patel, Xin Dang, Todd Mlsna, Yixin Chen, Dawn Wilkins:
Learning accurate and interpretable models based on regularized random forests regression. S5 - Jieyue He, Chunyan Wang, Kunpu Qiu, Wei Zhong:
An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks. S6
Volume 8, Number S-4, December 2014
- Shoba Ranganathan, Tin Wee Tan, Christian Schönbach:
InCoB2014: Systems Biology update from the Asia-Pacific. I1 - Sriganesh 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. S1 - Ashwini Patil, Kenta Nakai:
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles. S2 - Haijun Gong, Lu Feng:
Computational analysis of the roles of ER-Golgi network in the cell cycle. S3 - Takefumi Moriya, Masayuki Yamamura, Daisuke Kiga:
Effects of downstream genes on synthetic genetic circuits. S4 - Rebecca L. Barter, Sarah-Jane Schramm, Graham J. Mann, Yee Hwa Yang:
Network-based biomarkers enhance classical approaches to prognostic gene expression signatures. S5 - Haifen Chen, Piyushkumar A. Mundra, Li Na Zhao, Feng Lin, Jie Zheng:
Highly sensitive inference of time-delayed gene regulation by network deconvolution. S6 - Peng Yang, Xiaoquan Su, Le Ou-Yang, Hon Nian Chua, Xiaoli Li, Kang Ning:
Microbial community pattern detection in human body habitats via ensemble clustering framework. S7 - Tzu-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. S8 - Fu-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. S9 - Changhui Yan, Yingfeng Wang:
A graph kernel method for DNA-binding site prediction. S10 - Chia-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. S11
Volume 8, Number S-5, December 2014
- Kazuhiro Maeda, Hiroyuki Kurata:
Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity. S1 - Fu-Jou Lai, Mei-Huei Jhu, Chia-Chun Chiu, Yueh-Min Huang, Wei-Sheng Wu:
Identifying cooperative transcription factors in yeast using multiple data sources. S2 - Chern Han Yong, Osamu Maruyama, Limsoon Wong:
Discovery of small protein complexes from PPI networks with size-specific supervised weighting. S3 - Kansuporn 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. S4 - Xiaolei Wang, Hiroyuki Kuwahara, Xin Gao:
Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels. S5 - Che 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. S6 - Chih-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. S7 - Jiajie Peng, Hongxiang Li, Qinghua Jiang, Yadong Wang, Jin Chen:
An integrative approach for measuring semantic similarities using gene ontology. S8 - Wei-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. S9
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