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BMC Systems Biology, Volume 7 - Supplements

Volume 7, Number S-1, August 2013

Selected articles from the 10th International Workshop on Computational Systems Biology (WCSB) 2013: Systems Biology

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  Antti Ylipää, Olli Yli-Harja, Wei Zhang, Matti Nykter:
  Characterization of aberrant pathways across human cancers. S1
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  Riku Louhimo, Marko Laakso, Tuomas Heikkinen, Susanna Laitinen, Pekka Manninen, Vladimir Rogojin, Minna Miettinen, Carl Blomqvist, Jianjun Liu, Heli Nevanlinna, Sampsa Hautaniemi:
  Identification of genetic markers with synergistic survival effect in cancer. S2
• 
  Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro:
  Effects of multimerization on the temporal variability of protein complex abundance. S3
• 
  Daniella Schittler, Frank Allgöwer, Rob J. De Boer:
  A new model to simulate and analyze proliferating cell populations in BrdU labeling experiments. S4
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  Syeda Hassan, Muhammad Farhan, Rahul Mangayil, Heikki Huttunen, Tommi Aho:
  Bioprocess data mining using regularized regression and random forests. S5

Volume 7, Number S-2, October 2013

Selected articles from the 6th International Conference on Computational Systems Biology (ISB2012)

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  Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Computational systems biology in the big data era. S1
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  Vladimir Trifonov, Laura Pasqualucci, Enrico Tiacci, Brunangelo Falini, Raul Rabadan:
  SAVI: a statistical algorithm for variant frequency identification. S2
• 
  Hao Zhang, Zhi Li, Yanpu Li, Yuanning Liu, Junxin Liu, Xin Li, Tingjie Shen, Yunna Duan, Minggang Hu, Dong Xu:
  A computational method for predicting regulation of human microRNAs on the influenza virus genome. S3
• 
  Junhua Zhang, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang:
  Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. S4
• 
  Zhiyuan Yang, Yan Zhang, Luonan Chen:
  Investigation of anti-cancer mechanisms by comparative analysis of naked mole rat and rat. S5
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  Qiang Huang, Ling-Yun Wu, Xiang-Sun Zhang:
  Corbi: a new R package for biological network alignment and querying. S6
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  Huayong Xu, Hui Yu, Kang Tu, Qianqian Shi, Chaochun Wei, Yuan-Yuan Li, Yi-Xue Li:
  cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. S7
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  Yue Deng, Lin Gao, Bingbo Wang:
  ppiPre: predicting protein-protein interactions by combining heterogeneous features. S8
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  Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen:
  Identifying novel glioma associated pathways based on systems biology level meta-analysis. S9
• 
  Jingde Bu, Xuebin Chi, Zhong Jin:
  HSA: A Heuristic Splice Alignment Tool. S10
• 
  Juan Liu, Xinghuo Ye, Fang-Xiang Wu:
  Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits. S11
• 
  Fuhai Li, Hua Tan, Jaykrishna Singh, Jian Yang, Xiaofeng Xia, Jiguang Bao, Jinwen Ma, Ming Zhan, Stephen T. C. Wong:
  A 3D multiscale model of cancer stem cell in tumor development. S12
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  Limin Li, Hao Jiang, Yushan Qiu, Wai-Ki Ching, Vassilios S. Vassiliadis:
  Discovery of metabolite biomarkers: flux analysis and reaction-reaction network approach. S13
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  Shaoqiang Zhang, Xiguo Zhou, Chuanbin Du, Zhengchang Su:
  SPIC: A novel similarity metric for comparing transcription factor binding site motifs based on information contents. S14
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  Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
  Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. S15

Volume 7, Number S-3, November 2013

Twelfth International Conference on Bioinformatics (InCoB2013): Systems Biology

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  Christian Schönbach, Bairong Shen, Tin Wee Tan, Shoba Ranganathan:
  InCoB2013 introduces Systems Biology as a major conference theme. S1
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  Chengkun Wu, Jean-Marc Schwartz, Goran Nenadic:
  PathNER: a tool for systematic identification of biological pathway mentions in the literature. S2
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  Kenta Yoshida, Kazuya Maeda, Hiroyuki Kusuhara, Akihiko Konagaya:
  Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models. S3
• 
  Minho Lee, Keunwan Park, Dongsup Kim:
  Interaction network among functional drug groups. S4
• 
  Haijun Gong:
  Analysis of intercellular signal transduction in the tumor microenvironment. S5
• 
  Yifei Tang, Wenying Yan, Jiajia Chen, Cheng Luo, Antti Kaipia, Bairong Shen:
  Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. S6
• 
  Pramote Chumnanpuen, Intawat Nookaew, Jens Nielsen:
  Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast. S7
• 
  Dokyoon Kim, Hyunjung Shin, Je-Gun Joung, Su-Yeon Lee, Ju Han Kim:
  Intra-relation reconstruction from inter-relation: miRNA to gene expression. S8
• 
  Zuoshuang Xiang, Tingting Qin, Zhaohui S. Qin, Yongqun He:
  A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. S9
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  Yosvany López, Ashwini Patil, Kenta Nakai:
  Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. S10
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  Arsen O. Batagov, Aliaksandr A. Yarmishyn, Piroon Jenjaroenpun, Jovina Z. Tan, Yuichiro Nishida, Igor Kurochkin:
  Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells. S11

Volume 7, Number S-4, October 2013

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2012: Systems Biology

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  Yuanzhe Bei, Pengyu Hong:
  A novel approach to minimize false discovery rate in genome-wide data analysis. S1
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  Jie Cheng, Joel Greshock, Leming Shi, Shu Zheng, Alan Menius, Kwan Lee:
  Good practice guidelines for biomarker discovery from array data: a case study for breast cancer prognosis. S2
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  Md Mahmudul Hasan, Yusuf Kavurucu, Tamer Kahveci:
  A scalable method for discovering significant subnetworks. S3
• 
  Xingchi Hu, Chuang Ma, Yanhong Zhou:
  A novel two-layer SVM model in miRNA Drosha processing site detection. S4
• 
  Jingyao Li, Dongdong Lin, Hongbao Cao, Yu-Ping Wang:
  An improved sparse representation model with structural information for Multicolour Fluorescence In-Situ Hybridization (M-FISH) image classification. S5
• 
  Yifeng Li, Alioune Ngom:
  Sparse representation approaches for the classification of high-dimensional biological data. S6
• 
  Vance Chiang-Chi Liao, Ming-Syan Chen:
  Efficient mining gapped sequential patterns for motifs in biological sequences. S7
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  Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Catalina O. Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
  A framework for biomedical figure segmentation towards image-based document retrieval. S8
• 
  Ran Qi, Dengyuan Wu, Li Sheng, Donald Henson, Arnold M. Schwartz, Eric Xu, Kai Xing, Dechang Chen:
  On an ensemble algorithm for clustering cancer patient data. S9
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  Rehman Qureshi, Ahmet Sacan:
  Weighted set enrichment of gene expression data. S10
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  Zeehasham Rasheed, Huzefa Rangwala, Daniel Barbará:
  16S rRNA metagenome clustering and diversity estimation using locality sensitive hashing. S11
• 
  Jun Ren, Jianxin Wang, Min Li, Lusheng Wang:
  Identifying protein complexes based on density and modularity in protein-protein interaction network. S12
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  Lei Shang, David P. Gardner, Weijia Xu, Jamie J. Cannone, Daniel P. Miranker, Stuart Ozer, Robin Ray Gutell:
  Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems. S13
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  Qianqian Wu, Kate Smith-Miles, Tianshou Zhou, Tianhai Tian:
  Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model. S14

Volume 7, Number S-5, December 2013

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM 2013): Systems Biology

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  Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander R. Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta:
  Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. S1
• 
  Hui Yu, Chen-Ching Lin, Yuan-Yuan Li, Zhongming Zhao:
  Dynamic protein interaction modules in human hepatocellular carcinoma progression. S2
• 
  William T. Budd, Sarah Seashols, Danielle Weaver, Cyriac Joseph, Zendra E. Zehner:
  A networks method for ranking microRNA dysregulation in cancer. S3
• 
  Xu Shi, Jinghua Gu, Xi Chen, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
  mAPC-GibbsOS: an integrated approach for robust identification of gene regulatory networks. S4
• 
  Chifeng Ma, Hung-I Harry Chen, Mario Flores, Yufei Huang, Yidong Chen:
  BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database. S5
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  Chao Wu, Ranga Chandra Gudivada, Bruce J. Aronow, Anil G. Jegga:
  Computational drug repositioning through heterogeneous network clustering. S6
• 
  Qi Liu, Shilin Zhao, Pei-Fang Su, Shyr Yu:
  Gene and isoform expression signatures associated with tumor stage in kidney renal clear cell carcinoma. S7
• 
  Fan Zhang, Mu Wang, Tran Michael, Renee Drabier:
  Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer. S8
• 
  Jing Wang, Dabing Zhang, Jing Li:
  PREAL: prediction of allergenic protein by maximum Relevance Minimum Redundancy (mRMR) feature selection. S9
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  Vicky Wang, Li Xi, Ahmed Enayetallah, Eric Fauman, Daniel Ziemek:
  GeneTopics - interpretation of gene sets via literature-driven topic models. S10

Volume 7, Number S-6, December 2013

Selected articles from the 24th International Conference on Genome Informatics (GIW2013)

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  Frank Eisenhaber, Wing-Kin Sung, Limsoon Wong:
  International Conference on Genome Informatics (GIW 2013) in Singapore: introduction to the systems biology contributions. I1
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  Zhongyuan Tian, Adrien Fauré, Hirotada Mori, Hiroshi Matsuno:
  Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model. S1
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  Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Yuki Moriya, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto:
  KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. S2
• 
  Yasuo Tabei, Yoshihiro Yamanishi:
  Scalable prediction of compound-protein interactions using minwise hashing. S3
• 
  Masahiko Nakatsui, Michihiro Araki, Akihiko Kondo:
  An approach for dynamical network reconstruction of simple network motifs. S4
• 
  Florian Goebels, Dmitrij Frishman:
  Prediction of protein interaction types based on sequence and network features. S5
• 
  Hufeng Zhou, Javad Rezaei, Hugo Willy, Shangzhi Gao, Jingjing Jin, Mengyuan Fan, Chern Han Yong, Michal Wozniak, Limsoon Wong:
  Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions. S6
• 
  Yi-Min Chen, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu:
  OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly. S7
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  Takahiro Mimori, Naoki Nariai, Kaname Kojima, Mamoru Takahashi, Akira Ono, Yukuto Sato, Yumi Yamaguchi-Kabata, Masao Nagasaki:
  iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. S8
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  Kyung-Ah Sohn, Dokyoon Kim, Jaehyun Lim, Ju Han Kim:
  Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors. S9
• 
  Wan-Shu Cheng, Jung-Hsien Chiang:
  CGPredictor: a systematic integrated analytic tool for mining and examining genome-scale cancer independent prognostic epigenetic marker panels. S10
• 
  Hsiuying Wang, Chia-Chun Chiu, Yi-Ching Wu, Wei-Sheng Wu:
  Shrinkage regression-based methods for microarray missing value imputation. S11
• 
  Chia-Chun Chiu, Shih-Yao Chan, Chung-Ching Wang, Wei-Sheng Wu:
  Missing value imputation for microarray data: a comprehensive comparison study and a web tool. S12
• 
  Tzu-Hsien Yang, Wei-Sheng Wu:
  Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. S13
• 
  Chasanah Kusumastuti Widita, Osamu Maruyama:
  PPSampler2: Predicting protein complexes more accurately and efficiently by sampling. S14
• 
  Jiin Choi, Taesung Park:
  Multivariate generalized multifactor dimensionality reduction to detect gene-gene interactions. S15
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  Agnieszka Podsiadlo, Mariusz Wrzesien, Wieslaw Paja, Witold R. Rudnicki, Bartek Wilczynski:
  Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data. S16
• 
  Oliver L. Tessmer, Yuhua Jiao, Jeffrey A. Cruz, David M. Kramer, Jin Chen:
  Functional approach to high-throughput plant growth analysis. S17
• 
  Hiroaki Iwata, Sayaka Mizutani, Yasuo Tabei, Masaaki Kotera, Susumu Goto, Yoshihiro Yamanishi:
  Inferring protein domains associated with drug side effects based on drug-target interaction network. S18