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    Journal: BMC Systems Biology

    Volume 10, Issue S-5

    1 -- 10Yun 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
    11 -- 24Shila 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
    25 -- 38Yahui Sun, Pathima Nusrath Hameed, Karin Verspoor, Saman Halgamuge. A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning
    39 -- 50Binh P. Nguyen, Hans Heemskerk, Peter T. C. So, Lisa Tucker-Kellogg. Superpixel-based segmentation of muscle fibers in multi-channel microscopy
    51 -- 63Min Su Lee, HyungJune Lee. DMirNet: Inferring direct microRNA-mRNA association networks

    Volume 10, Issue S-3

    61 -- 0Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan. Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015
    62 -- 0Suleyman Vural, Xiaosheng Wang, Chittibabu Guda. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches
    63 -- 0Rong Xu, QuanQiu Wang. Towards understanding brain-gut-microbiome connections in Alzheimer's disease
    64 -- 0Ru-Dong Li, Hui Cheng, Tao Cheng, Lei Liu. Digitalization of a non-irradiated acute myeloid leukemia model
    65 -- 0Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao. Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach
    66 -- 0Yu-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
    67 -- 0Yaoyun Zhang, Heng-Yi Wu, Jun Xu 0007, Jingqi Wang, Ergin Soysal, Lang Li, Hua Xu. Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature
    68 -- 0Lei 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
    69 -- 0Ying-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
    70 -- 0Rongjie Liu, Chunjiang Qian, Shuqian Liu, Yufang Jin. State feedback control design for Boolean networks
    71 -- 0Su-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

    Volume 10, Issue S-2

    44 -- 0Losiana Nayak, Nitai P. Bhattacharyya, Rajat K. De. Wnt signal transduction pathways: modules, development and evolution
    45 -- 0Lei Huang, Li Liao, Cathy H. Wu. Protein-protein interaction prediction based on multiple kernels and partial network with linear programming
    47 -- 0Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt. SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
    48 -- 0Brittany Hoard, Bruna Jacobson, Kasra Manavi, Lydia Tapia. Extending rule-based methods to model molecular geometry and 3D model resolution
    49 -- 0Chinwe Ekenna, Shawna L. Thomas, Nancy M. Amato. Adaptive local learning in sampling based motion planning for protein folding
    50 -- 0Pei Chen, Yongjun Li. The decrease of consistence probability: at the crossroad of catastrophic transition of a biological system
    51 -- 0Juli Petereit, Sebastian Smith, Frederick C. Harris Jr., Karen Schlauch. petal: Co-expression network modelling in R
    53 -- 0Yuanfang Ren, Qiyao Wang, Md Mahmudul Hasan, Ahmet Ay, Tamer Kahveci. Identifying the topology of signaling networks from partial RNAi data
    54 -- 0Seong-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

    Volume 10, Issue S-1

    1 -- 0Hsin-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
    2 -- 0Hasun Yu, Sungji Choo, Junseok Park, Jinmyung Jung, Yeeok Kang, Doheon Lee. Prediction of drugs having opposite effects on disease genes in a directed network
    3 -- 0Kai-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
    4 -- 0Wangshu Zhang, Marcelo P. Coba, Fengzhu Sun. Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships
    5 -- 0Tatiana C. Mangericao, Zhanhao Peng, Xuegong Zhang. Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls
    6 -- 0Chien-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
    7 -- 0Fan 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
    8 -- 0Huili Yuan, Zhenye Li, Nelson L. S. Tang, Minghua Deng. A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae
    9 -- 0Wenyi Qin, Cong Liu, Monsheel Sodhi, Hui Lu. Meta-analysis of sex differences in gene expression in schizophrenia
    10 -- 0Daniel E. Platt, Saugata Basu, Pierre A. Zalloua, Laxmi Parida. Characterizing redescriptions using persistent homology to isolate genetic pathways contributing to pathogenesis

    Volume 10, Issue 4

    381 -- 392Wentao 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
    393 -- 399Qiwen Dong, Kai Wang, Xuan Liu. Identifying the missing proteins in human proteome by biological language model
    401 -- 412Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang, Xiangxiang Zeng. Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy
    413 -- 421Yin Wang, Tao Huang, Lu Xie, Lei Liu. Integrative analysis of methylation and transcriptional profiles to predict aging and construct aging specific cross-tissue networks
    423 -- 432Inuk 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
    433 -- 443Heejoon Chae, Sangseon Lee, Kenneth P. Nephew, Sun Kim. Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines
    445 -- 455Shuqin Zhang, Michael K. Ng. Gene-microRNA network module analysis for ovarian cancer
    457 -- 464Cong 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)
    465 -- 484Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu, Zhixia Teng. An improved method for functional similarity analysis of genes based on Gene Ontology
    485 -- 494Yu-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
    495 -- 507Guo-Xian Yu, Wei Luo, Guangyuan Fu, Jun Wang. Interspecies gene function prediction using semantic similarity
    509 -- 519Hui 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
    521 -- 530Cong-Doan Truong, Tien-Dzung Tran, Yung-Keun Kwon. MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks
    531 -- 539Liang Yu, Bingbo Wang, Xiaoke Ma, Lin Gao. The extraction of drug-disease correlations based on module distance in incomplete human interactome
    541 -- 548Fan Zhang, Runsheng Liu, Jie Zheng. Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation
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