BMC Systems Biology, Volume 10 - Supplements

Volume 10, Number S-1, January 2016

Selected articles from the Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016): Systems Biology

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  Hsin-Chuan Chang, Tsung-Han Hsieh, Yi-Wei Lee, Cheng-Fong Tsai, Ya-Ni Tsai, Cheng-Chung Cheng, Hsei-Wei Wang:
  c-Myc and viral cofactor Kaposin B co-operate to elicit angiogenesis through modulating miRNome traits of endothelial cells. 1
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  Hasun Yu, Sungji Choo, Junseok Park, Jinmyung Jung, Yeeok Kang, Doheon Lee:
  Prediction of drugs having opposite effects on disease genes in a directed network. 2
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  Kai-Yao Huang, Julia Tzu-Ya Weng, Tzong-Yi Lee, Shun-Long Weng:
  A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. 3
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  Wangshu Zhang, Marcelo P. Coba, Fengzhu Sun:
  Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships. 4
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  Tatiana C. Mangericao, Zhanhao Peng, Xuegong Zhang:
  Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls. 5
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  Chien-Hsun Huang, Min-Gang Su, Hui-Ju Kao, Jhih-Hua Jhong, Shun-Long Weng, Tzong-Yi Lee:
  UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. 6
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  Fan Zhang, Haoting Chen, Li Na Zhao, Hui Liu, Teresa M. Przytycka, Jie Zheng:
  Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. 7
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  Huili Yuan, Zhenye Li, Nelson L. S. Tang, Minghua Deng:
  A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae. 8
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  Wenyi Qin, Cong Liu, Monsheel Sodhi, Hui Lu:
  Meta-analysis of sex differences in gene expression in schizophrenia. 9
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  Daniel E. Platt, Saugata Basu, Pierre A. Zalloua, Laxmi Parida:
  Characterizing redescriptions using persistent homology to isolate genetic pathways contributing to pathogenesis. 10

Volume 10, Number S-2, August 2016

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2015: Systems biology

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  Losiana Nayak, Nitai P. Bhattacharyya, Rajat K. De:
  Wnt signal transduction pathways: modules, development and evolution. 44
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  Lei Huang, Li Liao, Cathy H. Wu:
  Protein-protein interaction prediction based on multiple kernels and partial network with linear programming. 45
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  Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt:
  SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. 47
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  Brittany R. Hoard, Bruna Jacobson, Kasra Manavi, Lydia Tapia:
  Extending rule-based methods to model molecular geometry and 3D model resolution. 48
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  Chinwe Ekenna, Shawna L. Thomas, Nancy M. Amato:
  Adaptive local learning in sampling based motion planning for protein folding. 49
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  Pei Chen, Yongjun Li:
  The decrease of consistence probability: at the crossroad of catastrophic transition of a biological system. 50
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  Juli Petereit, Sebastian Smith, Frederick C. Harris Jr., Karen Schlauch:
  petal: Co-expression network modelling in R. 51
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  Yuanfang Ren, Qiyao Wang, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci:
  Identifying the topology of signaling networks from partial RNAi data. 53
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  Seong Gon Kim, Nawanol Theera-Ampornpunt, Chih-Hao Fang, Mrudul Harwani, Ananth Grama, Somali Chaterji:
  Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions. 54

Volume 10, Number S-3, August 2016

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2015: Systems biology

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  Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan:
  Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. 61
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  Suleyman Vural, Xiaosheng Wang, Chittibabu Guda:
  Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. 62
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  Rong Xu, QuanQiu Wang:
  Towards understanding brain-gut-microbiome connections in Alzheimer's disease. 63
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  Ru-Dong Li, Hui Cheng, Tao Cheng, Lei Liu:
  Digitalization of a non-irradiated acute myeloid leukemia model. 64
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  Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao:
  Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. 65
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  Yu-Ching Hsu, Yu-Chiao Chiu, Yidong Chen, Tzu-Hung Hsiao, Eric Y. Chuang:
  A simple gene set-based method accurately predicts the synergy of drug pairs. 66
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  Yaoyun Zhang, Heng-Yi Wu, Jun Xu, Jingqi Wang, Ergin Soysal, Lang Li, Hua Xu:
  Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. 67
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  Lei Du, Heng Huang, Jingwen Yan, Sungeun Kim, Shannon L. Risacher, Mark Inlow, Jason H. Moore, Andrew J. Saykin, Li Shen:
  Structured sparse CCA for brain imaging genetics via graph OSCAR. 68
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  Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew Anderson, Zhandong Liu:
  XMRF: an R package to fit Markov Networks to high-throughput genetics data. 69
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  Rongjie Liu, Chunjiang Qian, Shuqian Liu, Yufang Jin:
  State feedback control design for Boolean networks. 70
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  Su-Juan Wu, Junyi Li, Mushui Cao, Jing Yang, Yi-Xue Li, Yuan-Yuan Li:
  A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes. 71

Volume 10, Number 4, December 2016

Proceedings of the 27th International Conference on Genome Informatics: systems biology

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  Wentao Dai, Aiping Wu, Liang-Xiao Ma, Yi-Xue Li, Taijiao Jiang, Yuan-Yuan Li:
  A novel index of protein-protein interface propensity improves interface residue recognition. 381-392
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  Qiwen Dong, Kai Wang, Xuan Liu:
  Identifying the missing proteins in human proteome by biological language model. 393-399
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  Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang, Xiangxiang Zeng:
  Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy. 401-412
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  Yin Wang, Tao Huang, Lu Xie, Lei Liu:
  Integrative analysis of methylation and transcriptional profiles to predict aging and construct aging specific cross-tissue networks. 413-421
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  Inuk Jung, Hongryul Ahn, Seon-Ju Shin, Jukon Kim, Hawk-Bin Kwon, Woosuk Jung, Sun Kim:
  Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. 423-432
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  Heejoon Chae, Sangseon Lee, Kenneth P. Nephew, Sun Kim:
  Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. 433-443
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  Shuqin Zhang, Michael K. Ng:
  Gene-microRNA network module analysis for ovarian cancer. 445-455
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  Cong Liu, Jianping Jiang, Jianlei Gu, Zhangsheng Yu, Tao Wang, Hui Lu:
  High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI). 457-464
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  Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu, Zhixia Teng:
  An improved method for functional similarity analysis of genes based on Gene Ontology. 465-484
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  Yu-An Huang, Zhu-Hong You, Xing Chen, Guiying Yan:
  Improved protein-protein interactions prediction via weighted sparse representation model combining continuous wavelet descriptor and PseAA composition. 485-494
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  Guo-Xian Yu, Wei Luo, Guangyuan Fu, Jun Wang:
  Interspecies gene function prediction using semantic similarity. 495-507
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  Hui Liu, Mengmeng Guo, Ting Xue, Jihong Guan, Libo Luo, Ziheng Zhuang:
  Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks. 509-519
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  Cong-Doan Truong, Tien-Dzung Tran, Yung-Keun Kwon:
  MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks. 521-530
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  Liang Yu, Bingbo Wang, Xiaoke Ma, Lin Gao:
  The extraction of drug-disease correlations based on module distance in incomplete human interactome. 531-539
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  Fan Zhang, Runsheng Liu, Jie Zheng:
  Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. 541-548

Volume 10, Number S-5, December 2016

15th International Conference on Bioinformatics (InCoB 2016): Systems biology

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  Yun Zheng, Vandana Hivrale, Xiaotuo Zhang, Babu Valliyodan, Christine Lelandais-Brière, Andrew D. Farmer, Gregory D. May, Martin Crespi, Henry T. Nguyen, Ramanjulu Sunkar:
  Small RNA profiles in soybean primary root tips under water deficit. 1-10
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  Shila Ghazanfar, Adam J. Bisogni, John T. Ormerod, David M. Lin, Jean Yee Hwa Yang:
  Integrated single cell data analysis reveals cell specific networks and novel coactivation markers. 11-24
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  Yahui Sun, Pathima Nusrath Hameed, Karin Verspoor, Saman K. Halgamuge:
  A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning. 25-38
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  Binh P. Nguyen, Hans Heemskerk, Peter T. C. So, Lisa Tucker-Kellogg:
  Superpixel-based segmentation of muscle fibers in multi-channel microscopy. 39-50
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  Min-Su Lee, HyungJune Lee:
  DMirNet: Inferring direct microRNA-mRNA association networks. 51-63