BMC Systems Biology, Volume 11- Supplements

Volume 11, Number S-1, February 2017

Selected articles from BGRS\SB-2016: systems biology

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  Andjela Rodic, Bojana Blagojevic, Evgeny M. Zdobnov, Magdalena Djordjevic, Marko Djordjevic:
  Understanding key features of bacterial restriction-modification systems through quantitative modeling. 1-15
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  Leonid V. Omelyanchuk, Alina F. Munzarova:
  Theoretical model of mitotic spindle microtubule growth for FRAP curve interpretation. 17-26
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  Olga A. Podkolodnaya, Natalya N. Tverdokhleb, Nikolay Podkolodnyy:
  Computational modeling of the cell-autonomous mammalian circadian oscillator. 27-42

Volume 11, Number S-2, March 2017

Selected articles from the 15th Asia Pacific Bioinformatics Conference (APBC 2017)

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  Pavithra K. Balasubramanian, Anand Balupuri, Hee-Young Kang, Seung Joo Cho:
  Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors. 6:1-6:11
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  Qiao Liu, Mingxin Gan, Rui Jiang:
  A sequence-based method to predict the impact of regulatory variants using random forest. 7:1-7:9
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  Weiqi Chen, Jing Liu, Shan He:
  Prior knowledge guided active modules identification: an integrated multi-objective approach. 8:1-8:12
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  Zhanzhan Cheng, Kai Huang, Yang Wang, Hui Liu, Jihong Guan, Shuigeng Zhou:
  Selecting high-quality negative samples for effectively predicting protein-RNA interactions. 9:1-9:11
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  Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo, Sun Kim:
  PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI. 15:1-15:13
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  Daesik Choi, Byungkyu Park, Hanju Chae, Wook Lee, Kyungsook Han:
  Predicting protein-binding regions in RNA using nucleotide profiles and compositions. 16:1-16:12

Volume 11, Number 3, March 2017

Selected original research articles from the Third International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2016): systems biology

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  Amin Zollanvari, Gil Alterovitz:
  SNP by SNP by environment interaction network of alcoholism. 19:1-19:11
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  Hyundoo Jeong, Byung-Jun Yoon:
  SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. 20:1-20:11
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  Minghan Chen, Fei Li, Shuo Wang, Young Cao:
  Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics. 21:1-21:11
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  Yijie Wang, Xiaoning Qian:
  Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. 22:1-22:11
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  Xiaoxia Liu, Zhihao Yang, Hongfei Lin, Michael Simmons, Zhiyong Lu:
  DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. 23:1-23:11

Volume 11, Number S-4, September 2017

Selected papers from the 10th International Conference on Systems Biology (ISB 2016)

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  Mingxin Gan, Wenran Li, Wanwen Zeng, Xiaojian Wang, Rui Jiang:
  Mimvec: a deep learning approach for analyzing the human phenome. 3-16
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  Bo Tian, Can Zhao, Feiyang Gu, Zengyou He:
  A two-step framework for inferring direct protein-protein interaction network from AP-MS data. 17-25
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  Zehua Zhang, Kecheng Guo, Gaofeng Pan, Jijun Tang, Fei Guo:
  Improvement of phylogenetic method to analyze compositional heterogeneity. 27-33
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  Changhe Fu, Su Deng, Guangxu Jin, Xinxin Wang, Zu-Guo Yu:
  Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data. 35-42
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  Fei Liu, Deshun Sun, Ryutaro Murakami, Hiroshi Matsuno:
  Modeling and analysis of the Delta-Notch dependent boundary formation in the Drosophila large intestine. 43-60
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  Duanchen Sun, Yinliang Liu, Xiang-Sun Zhang, Ling-Yun Wu:
  NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis. 61-74
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  Xiaofei Shi, Ruiqi Wang:
  Glioma cell fate decisions mediated by Dll1-Jag1-Fringe in Notch1 signaling pathway. 75-84
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  Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Understanding biological systems through the lens of data. 77:1-77:2
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  Jing He, Zhou Zhou, Michael Reed, Andrea Califano:
  Accelerated parallel algorithm for gene network reverse engineering. 85-97
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  Yuzhen Guo, Fengying Tao, Zikai Wu, Yong Wang:
  Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations. 99-111
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  Jie Gao, Kang Wang, Tao Ding, Shanshan Zhu:
  Forecasting influenza A pandemic outbreak using protein dynamical network biomarkers. 113-119

Volume 11, Number S-5, October 2017

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: systems biology

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  Haoyang Wu, Elise Miller, Denethi Wijegunawardana, Kelly Regan, Philip R. O. Payne, Fuhai Li:
  MD-Miner: a network-based approach for personalized drug repositioning. 86:1-86:8
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  Jingchun Sun, Qiang Wei, Yubo Zhou, Jingqi Wang, Qi Liu, Hua Xu:
  A systematic analysis of FDA-approved anticancer drugs. 87:1-87:17
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  W. Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu:
  The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. 88:1-88:3
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  Jin Li, Yang Wang, Xi Rao, Yue Wang, Weixing Feng, Hong Liang, Yunlong Liu:
  Roles of alternative splicing in modulating transcriptional regulation. 89:1-89:12
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  Biao Li, Amanda Sierra, Juan Jose Deudero, Fatih Semerci, Andrew Laitman, Marek Kimmel, Mirjana Maletic-Savatic:
  Multitype Bellman-Harris branching model provides biological predictors of early stages of adult hippocampal neurogenesis. 90:1-90:16
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  Ru-Dong Li, Yin Wang, Hui Cheng, Gang Liu, Tao Cheng, Yunlong Liu, Lei Liu:
  System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia. 91:1-91:12
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  Xinan Holly Yang, Fangming Tang, Jisu Shin, John M. Cunningham:
  Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma. 92:1-92:17
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  Turki Turki, Zhi Wei:
  A link prediction approach to cancer drug sensitivity prediction. 94:1-94:14

Volume 11, Number 6, December 2017

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  Quan Zou, Shixiang Wan, Xiangxiang Zeng, Zhanshan (Sam) Ma:
  Reconstructing evolutionary trees in parallel for massive sequences. 15-21
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  Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, Xining Zhang:
  A unified frame of predicting side effects of drugs by using linear neighborhood similarity. 23-34
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  Qi Li, Yongyi Gong:
  A geometric method for contour extraction of Drosophila embryos. 35-44
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  Hao Jiang, Wai-Ki Ching, Yushan Qiu, Xiaoqing Cheng:
  Optimal projection method determination by Logdet Divergence and perturbed von-Neumann Divergence. 45-61
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  Jin-Xing Liu, Dong-Qin Wang, Chun-Hou Zheng, Ying-Lian Gao, Sha-Sha Wu, Junliang Shang:
  Identifying drug-pathway association pairs based on L2, 1-integrative penalized matrix decomposition. 63-73
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  Ou Wei, Zonghao Guo, Yun Niu, Wenyuan Liao:
  Model checking optimal finite-horizon control for probabilistic gene regulatory networks. 75-88
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  Morteza Zihayat, Heidar Davoudi, Aijun An:
  Mining significant high utility gene regulation sequential patterns. 109:1-109:14

Volume 11, Number S-7, December 2017

16th International Conference on Bioinformatics (InCoB 2017): Systems Biology

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  Lichun Ma, Jie Zheng:
  A polynomial based model for cell fate prediction in human diseases. 15-27
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  Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai, Tzong-Yi Lee:
  Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas. 29-44
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  Ying Xu, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan:
  CPredictor3.0: detecting protein complexes from PPI networks with expression data and functional annotations. 45-56
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  Cong-Doan Truong, Yung-Keun Kwon:
  Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks. 57-68
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  Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee:
  Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. 69-80
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  Daniel Trejo-Baños, Pauline Trébulle, Mohamed Elati:
  Integrating transcriptional activity in genome-scale models of metabolism. 81-90
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  Huipeng Li, Lakshmi Venkatraman, Balakrishnan Chakrapani Narmada, Jacob K. White, Hanry Yu, Lisa Tucker-Kellogg:
  Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model. 91-99
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  Maulida Mazaya, Hung-Cuong Trinh, Yung-Keun Kwon:
  Construction and analysis of gene-gene dynamics influence networks based on a Boolean model. 101-111
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  Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He:
  Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. 113-125
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  Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi:
  A linear programming computational framework integrates phosphor-proteomics and prior knowledge to predict drug efficacy. 127:1-127:13
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  Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee:
  MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs. 127-140
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  Ben-gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu, Luonan Chen:
  Detecting causality from short time-series data based on prediction of topologically equivalent attractors. 141-150
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  Shun Asami, Daisuke Kiga, Akihiko Konagaya:
  Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model. 151-162
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  Hao Jiang, Wai-Ki Ching, Wai-Shun Cheung, Wenpin Hou, Hong Yin:
  Hadamard Kernel SVM with applications for breast cancer outcome predictions. 163-174