BMC Systems Biology - Suplements, Volume 12

Volume 12, Number 1, April 2018

Selected articles from the 16th Asia Pacific Bioinformatics Conference (APBC 2018): systems biology

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  Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci:
  Counting motifs in dynamic networks. 1-12
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  Petronela Buiga, Ari Elson, Lydia Tabernero, Jean-Marc Schwartz:
  Regulation of dual specificity phosphatases in breast cancer during initial treatment with Herceptin: a Boolean model analysis. 13-24
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  Shunsuke Teraguchi, Yutaro Kumagai:
  Estimation of diffusion constants from single molecular measurement without explicit tracking. 25-39
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  Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher:
  ncRNA-disease association prediction based on sequence information and tripartite network. 41-51
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  Yushan Qiu, Hao Jiang, Wai-Ki Ching, Xiaoqing Cheng:
  Discovery of Boolean metabolic networks: integer linear programming based approach. 53-60
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  Bobby Ranjan, Ket Hing Chong, Jie Zheng:
  Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease. 61-74
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  Shuqin Zhang:
  Comparisons of gene coexpression network modules in breast cancer and ovarian cancer. 75-87
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  Mengxuan Lyu, Jiaxing Chen, Yiqi Jiang, Wei Dong, Zhou Fang, Shuai Cheng Li:
  KDiamend: a package for detecting key drivers in a molecular ecological network of disease. 89-99
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  Hui Yu, Kui-Tao Mao, Jian-Yu Shi, Hua Huang, Zhi Chen, Kai Dong, Siu-Ming Yiu:
  Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization. 101-110
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  Soorin Yim, Hasun Yu, Dongjin Jang, Doheon Lee:
  Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations. 111-122

Volume 12, Number S-2, 2018

Proceedings of the 28th International Conference on Genome Informatics: systems biology

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  Yourae Hong, Choa Park, Nayoung Kim, Juyeon Cho, Sung Ung Moon, Jongmin Kim, Euna Jeong, Sukjoon Yoon:
  QSurface: fast identification of surface expression markers in cancers. 1-8
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  Pranjul Mishra, Na-Rae Lee, Meiyappan Lakshmanan, Minsuk Kim, Byung-Gee Kim, Dong-Yup Lee:
  Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica. 9-20
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  Min-Seok Kwon, Sangseob Leem, Joon Yoon, Taesung Park:
  GxGrare: gene-gene interaction analysis method for rare variants from high-throughput sequencing data. 21-31
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  Fang-Yu Liu, Te-Cheng Hsu, Patrick Choong, Min-Hsuan Lin, Yung-Jen Chuang, Bor-Sen Chen, Che Lin:
  Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration. 33-46
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  Hiroshi Mori, Takayuki Maruyama, Masahiro Yano, Takuji Yamada, Ken Kurokawa:
  VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. 47-58
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  Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Jaewoo Kang:
  In silico drug combination discovery for personalized cancer therapy. 59-67
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  Sungjoon Park, Jung Min Kim, Won-Ho Shin, Sung Won Han, Minji Jeon, Hyun Jin Jang, Ik-Soon Jang, Jaewoo Kang:
  BTNET : boosted tree based gene regulatory network inference algorithm using time-course measurement data. 69-77
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  Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yu-Yao Tseng, Jinn-Moon Yang:
  A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. 79-91
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  Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong:
  SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data. 93-108
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  Jiajie Peng, Xuanshuo Zhang, Weiwei Hui, Junya Lu, Qianqian Li, Shuhui Liu, Xuequn Shang:
  Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. 109-116
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  Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung:
  The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. 117-130

Volume 12, Number 3, March 2018

Selected original research articles from the Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2017): systems biology

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  (Withdrawn) Detangling PPI networks to uncover functionally meaningful clusters. 11-23
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  Bertrand Miannay, Stéphane Minvielle, Florence Magrangeas, Carito Guziolowski:
  Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data. 25-37

Volume 12, Number 4, April 2018

Selected papers from the 11th International Conference on Systems Biology (ISB 2017)

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  Abbas Khan, Arif Ali, Muhammad Junaid, Chang Liu, Aman Chandra Kaushik, William C. S. Cho, Dong-Qing Wei:
  Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. 5-16
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  Wentao Dai, Quanxue Li, Bing-Ya Liu, Yi-Xue Li, Yuan-Yuan Li:
  Differential networking meta-analysis of gastric cancer across Asian and American racial groups. 17-28
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  Zehua Zhang, Jian Song, Jijun Tang, Xinying Xu, Fei Guo:
  Detecting complexes from edge-weighted PPI networks via genes expression analysis. 29-40
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  Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Integrating data- and model-driven strategies in systems biology. 38:1-38:3
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  Jialu Hu, Yiqun Gao, Yan Zheng, Xuequn Shang:
  KF-finder: identification of key factors from host-microbial networks in cervical cancer. 41-48
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  Xudong Zou, Ke An, Yun-Dong Wu, Zhi-Qiang Ye:
  PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions. 49-62
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  Fei Liu, Siyuan Chen, Monika Heiner, Hengjie Song:
  Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets. 63-74
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  Jianfeng Jiao, Min Luo, Ruiqi Wang:
  Feedback regulation in a stem cell model with acute myeloid leukaemia. 75-83
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  Limin Li, Xiao He, Karsten M. Borgwardt:
  Multi-target drug repositioning by bipartite block-wise sparse multi-task learning. 85-97
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  Wenying He, Cangzhi Jia, Yucong Duan, Quan Zou:
  70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features. 99-107
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  Kuo-Sheng Hung, Chung-Chi Hsiao, Tun-Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou, Wen-Der Wang, Yet-Ran Chen:
  Functional enrichment analysis based on long noncoding RNA associations. 109-118
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  Min Fu, Wenming Wu, Xiafei Hong, Qiuhua Liu, Jialin Jiang, Yaobin Ou, Yupei Zhao, Xinqi Gong:
  Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images. 119-127
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  Xiujuan Lei, Ming Fang, Fang-Xiang Wu, Luonan Chen:
  Improved flower pollination algorithm for identifying essential proteins. 129-140
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  Fangzhou Shen, Xueting Wu, Luoxi Shi, Hang Zhang, Yangmin Chen, Xiaoquan Qi, Zhuo Wang, Xuan Li:
  Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development. 141-156
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  Fangshu Cui, Bo Yuan:
  Fixation probability of a beneficial mutation conferring decreased generation time in changing environments. 157-166

Volume 12, Number 5, November 2018

Selected articles from the 5th International Work-Conference on Bioinformatics and Biomedical Engineering: systems biology

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  Daniel Urda, Francisco Aragón, Rocío Bautista, Leonardo Franco, Francisco J. Veredas, Manuel Gonzalo Claros, José Manuel Jerez:
  BLASSO: integration of biological knowledge into a regularized linear model. 13-26
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  Marc Legeay, Sébastien Aubourg, Jean-Pierre Renou, Béatrice Duval:
  Large scale study of anti-sense regulation by differential network analysis. 27-41
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  Enzo Rucci, Carlos García, Guillermo Botella, Armando De Giusti, Marcelo R. Naiouf, Manuel Prieto:
  SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences. 43-53
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  María Gabriela Valdés, Iván Galván-Femenía, Vicent J. Ribas Ripoll, Xavier Duran, Jun Yokota, Ricard Gavaldà, Xavier Rafael-Palou, Rafael de Cid:
  Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data. 55-74
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  Antonio Messina, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Alfonso Urso:
  BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. 75-89
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  Víctor González-Menéndez, Germán Martínez, Rachel Serrano, Francisca Muñoz, Jesús Martín, Olga Genilloud, José R. Tormo:
  Ultraviolet (IUV) and mass spectrometry (IMS) imaging for the deconvolution of microbial interactions. 91-97
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  Stepán Papácek, Jiri Jablonsky, Karel Petera:
  Advanced integration of fluid dynamics and photosynthetic reaction kinetics for microalgae culture systems. 93:1-93:12
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  Christophe Guyeux, Bashar Al-Nuaimi, Bassam AlKindy, Jean-François Couchot, Michel Salomon:
  On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella. 99-121
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  José F. Hidalgo, Jose A. Egea, Francisco De Asís Guil Asensio, José M. García:
  Improving the EFMs quality by augmenting their representativeness in LP methods. 123-131

Volume 12, Number 7, December 2018

From Genomics to Systems Biology

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  Mengjie Guo, Sicheng Lu, Hongming Huang, Yaohui Wang, Mary Qu Yang, Ye Yang, Zhimin Fan, Bin Jiang, Youping Deng:
  Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer. 11-17
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  Bei Yang, Yaohui Xu, Andrew S. Maxwell, Wonryull Koh, Ping Gong, Chaoyang Zhang:
  MICRAT: a novel algorithm for inferring gene regulatory networks using time series gene expression data. 19-29
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  Ping Gong, Keri B. Donohue, Anne M. Mayo, Yuping Wang, Huixiao Hong, Mitchell S. Wilbanks, Natalie D. Barker, Xin Guan, Kurt A. Gust:
  Comparative toxicogenomics of three insensitive munitions constituents 2, 4-dinitroanisole, nitroguanidine and nitrotriazolone in the soil nematode Caenorhabditis elegans. 31-46
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  Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang:
  Systems biology analysis reveals new insights into invasive lung cancer. 47-53
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  Mary Qu Yang, Sherman Morton Weissman, William Yang, Jialing Zhang, Allon Canaan, Renchu Guan:
  MISC: missing imputation for single-cell RNA sequencing data. 55-63
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  Steven B. Cogill, Anand K. Srivastava, Mary Qu Yang, Liangjiang Wang:
  Co-expression of long non-coding RNAs and autism risk genes in the developing human brain. 65-73
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  Guannan He, Yanchun Liang, Yan Chen, William Yang, Jun S. Liu, Mary Qu Yang, Renchu Guan:
  A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity. 75-85
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  Ling Hu, Rong Zhang, Qiong Yuan, Yinping Gao, Mary Qu Yang, Chunxiang Zhang, Jiankun Huang, Yufei Sun, William Yang, Jack Y. Yang, Zhen-li Min, Jing Cheng, Youping Deng, Xiamin Hu:
  The emerging role of microRNA-4487/6845-3p in Alzheimer's disease pathologies is induced by Aβ25-35 triggered in SH-SY5Y cell. 119:1-119:10

Volume 12, Number 8, December 2018

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2018: systems biology

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  Yan-Bin Wang, Zhu-Hong You, Xiao Li, Tong-Hai Jiang, Li Cheng, Zhan-Heng Chen:
  Prediction of protein self-interactions using stacked long short-term memory from protein sequences information. 129

Volume 12, Number 9, December 2018

Proceedings of the 29th International Conference on Genome Informatics (GIW 2018): systems biology

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  Quanya Liu, Peng Chen, Bing Wang, Jun Zhang, Jinyan Li:
  Hot spot prediction in protein-protein interactions by an ensemble system. 132
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  Zhen Tian, Zhixia Teng, Shuang Cheng, Maozu Guo:
  Computational drug repositioning using meta-path-based semantic network analysis. 134
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  Ke Zhang, Wei Geng, Shuqin Zhang:
  Network-based logistic regression integration method for biomarker identification. 135