Journal: BMC Systems Biology

Volume 12, Issue 9

132 -- 0Quanya Liu, Peng Chen 0001, Bing Wang 0004, Jun Zhang, Jinyan Li. Hot spot prediction in protein-protein interactions by an ensemble system
134 -- 0Zhen Tian, Zhixia Teng, Shuang Cheng, Maozu Guo. Computational drug repositioning using meta-path-based semantic network analysis
135 -- 0Ke Zhang, Wei Geng, Shuqin Zhang. Network-based logistic regression integration method for biomarker identification

Volume 12, Issue 8

129 -- 0Yan-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

Volume 12, Issue 7

0 -- 0Ling 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
11 -- 17Mengjie 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
19 -- 29Bei 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
31 -- 46Ping 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
47 -- 53Dan Li, William Yang, Carolyn Arthur, Jun S. Liu, Carolina Cruz-Niera, Mary Qu Yang. Systems biology analysis reveals new insights into invasive lung cancer
55 -- 63Mary Qu Yang, Sherman Morton Weissman, William Yang, Jialing Zhang, Allon Canaan, Renchu Guan. MISC: missing imputation for single-cell RNA sequencing data
65 -- 73Steven 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
75 -- 85Guannan 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

Volume 12, Issue 5

0 -- 0Stepán Papácek, Jiri Jablonsky, Karel Petera. Advanced integration of fluid dynamics and photosynthetic reaction kinetics for microalgae culture systems
13 -- 26Daniel 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
27 -- 41Marc Legeay, Sébastien Aubourg, Jean-Pierre Renou, Béatrice Duval. Large scale study of anti-sense regulation by differential network analysis
43 -- 53Enzo Rucci, Carlos García 0001, Guillermo Botella, Armando De Giusti, Marcelo R. Naiouf, Manuel Prieto 0001. SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
55 -- 74María Gabriela Valdés, Iván Galván-Femenía, Vicent 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
75 -- 89Antonio 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
91 -- 97Víctor 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
99 -- 121Christophe Guyeux, Bashar Al-Nuaimi, Bassam AlKindy, Jean-François Couchot, Michel Salomon. On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella
123 -- 131José F. Hidalgo, Jose A. Egea, Francisco De Asís Guil Asensio, José M. García 0001. Improving the EFMs quality by augmenting their representativeness in LP methods

Volume 12, Issue 4

0 -- 0Yong Wang, Xiang-Sun Zhang, Luonan Chen. Integrating data- and model-driven strategies in systems biology
5 -- 16Abbas 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
17 -- 28Wentao 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
29 -- 40Zehua Zhang, Jian Song, Jijun Tang, Xinying Xu, Fei Guo. Detecting complexes from edge-weighted PPI networks via genes expression analysis
41 -- 48Jialu Hu, Yiqun Gao, Yan Zheng, Xuequn Shang. KF-finder: identification of key factors from host-microbial networks in cervical cancer
49 -- 62Xu-Dong 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
63 -- 74Fei Liu, Siyuan Chen, Monika Heiner, Hengjie Song. Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets
75 -- 83Jianfeng Jiao, Min Luo, Ruiqi Wang. Feedback regulation in a stem cell model with acute myeloid leukaemia
85 -- 97Limin Li, Xiao He, Karsten M. Borgwardt. Multi-target drug repositioning by bipartite block-wise sparse multi-task learning
99 -- 107Wenying He, Cangzhi Jia, Yucong Duan, Quan Zou. 70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features
109 -- 118Kuo-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
119 -- 127Min 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
129 -- 140Xiujuan Lei, Ming Fang, Fang-Xiang Wu, Luonan Chen. Improved flower pollination algorithm for identifying essential proteins
141 -- 156Fangzhou 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
157 -- 166Fangshu Cui, Bo Yuan. Fixation probability of a beneficial mutation conferring decreased generation time in changing environments

Volume 12, Issue 3

11 -- 23Sarah Hall-Swan, Jake Crawford, Rebecca Newman, Lenore J. Cowen. Detangling PPI networks to uncover functionally meaningful clusters
25 -- 37Bertrand Miannay, Stéphane Minvielle, Florence Magrangeas, Carito Guziolowski. Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data

Volume 12, Issue 2

1 -- 8Yourae 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
9 -- 20Pranjul 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
21 -- 31Min-Seok Kwon, Sangseob Leem, Joon Yoon, Taesung Park. GxGrare: gene-gene interaction analysis method for rare variants from high-throughput sequencing data
33 -- 46Fang-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
47 -- 58Hiroshi 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
59 -- 67Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Jaewoo Kang. In silico drug combination discovery for personalized cancer therapy
69 -- 77Sungjoon 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
79 -- 91Sing-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
93 -- 108Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong. SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data
109 -- 116Jiajie 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
117 -- 130Inuk 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

Volume 12, Issue 1

0 -- 0Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Bernhard O. Palsson, Jonathan M. Monk. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
0 -- 0Michael A. Rowland, Hannah Wear, Karen H. Watanabe, Kurt A. Gust, Michael L. Mayo. Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures
0 -- 0Mohamed Shahen, Zihu Guo, Akhtar Hussain Shar, Reham Ebaid, Qin Tao, Wenjuan Zhang, Ziyin Wu, Yaofei Bai, Yingxue Fu, Chunli Zheng, He Wang, Piar Ali Shar, Jianling Liu, Zhenzhong Wang, Wei Xiao, Yonghua Wang. Dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs
0 -- 0Robert W. Smith 0003, Rik P. van Rosmalen, Vítor A. P. Martins dos Santos, Christian Fleck. DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems
0 -- 0Håvard G. Frøysa, Shirin Fallahi, Nello Blaser. Evaluating model reduction under parameter uncertainty
0 -- 0Hooman Sedghamiz, Matthew Morris, Travis J. A. Craddock, Darrell Whitley, Gordon Broderick. High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology
0 -- 0Gabriela I. Guzmán, Connor A. Olson, Ying Hefner, Patrick V. Phaneuf, Edward Catoiu, Lais B. Crepaldi, Lucas Goldschmidt Micas, Bernhard O. Palsson, Adam M. Feist. Reframing gene essentiality in terms of adaptive flexibility
0 -- 0Kimberly C. Olney, David B. Nyer, Daniel A. Vargas, Melissa A. Wilson Sayres, Karmella A. Haynes. The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells
0 -- 0Carlos Vazquez-Hernandez, Antonio Loza, Esteban Peguero-Sanchez, Lorenzo Segovia, Rosa-Maria Gutierrez-Rios. Identification of reaction organization patterns that naturally cluster enzymatic transformations
0 -- 0Peijia Yu, Qing Nie, Chao Tang, Lei Zhang. Nanog induced intermediate state in regulating stem cell differentiation and reprogramming
0 -- 0Alessandra Ordinelli, Nicola Bernabò, Massimiliano Orsini, Mauro Mattioli, Barbara Barboni. Putative human sperm Interactome: a networks study
0 -- 0Bruno Pereira, Joana Miguel, Paulo Vilaça, Simão Soares, Isabel Rocha, Sónia Carneiro. Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z
0 -- 0Qingyang Zhang. A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
0 -- 0Min Song, Stacey D. Finley. Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors
0 -- 0Colin P. McNally, Elhanan Borenstein. Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss
0 -- 0Bo Zhang, Hua Ye, Aidong Yang. Mathematical modelling of interacting mechanisms for hypoxia mediated cell cycle commitment for mesenchymal stromal cells
0 -- 0Rajat Anand, Dipanka Sarmah, Samrat Chatterjee. Extracting proteins involved in disease progression using temporally connected networks
0 -- 0Andreas Kremling, Johannes Geiselmann, Delphine Ropers, Hidde de Jong. An ensemble of mathematical models showing diauxic growth behaviour
0 -- 0Ian R. Vernon, Junli Liu, Michael Goldstein, James Rowe, Jen Topping, Keith Lindsey. Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions
0 -- 0Marcus Thomas, Russell Schwartz. A method for efficient Bayesian optimization of self-assembly systems from scattering data
0 -- 0Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath. Evolution of computational models in BioModels Database and the Physiome Model Repository
0 -- 0Fang Yang, Meng Wang, Baoyun Zhang, Wei Xiang, Ke Zhang, Mingxin Chu, Pingqing Wang. Identification of new progestogen-associated networks in mammalian ovulation using bioinformatics
0 -- 0James T. Yurkovich, Aarash Bordbar, Ólafur E. Sigurjónsson, Bernhard O. Palsson. Systems biology as an emerging paradigm in transfusion medicine
0 -- 0Juan A. Martínez, Alberto Rodriguez, Fabian Moreno, Noemí Flores, Alvaro R. Lara, Octavio T. Ramírez, Guillermo Gosset, Francisco Bolivar. Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production
0 -- 0Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach, Josch Pauling, Aamir Shafi, Rehan Zafar Paracha, Asad Hayat, Amjad Ali. Parameter estimation of qualitative biological regulatory networks on high performance computing hardware
0 -- 0Sang-Mok Choo, Byunghyun Ban, Jae Il Joo, Kwang-Hyun Cho. The phenotype control kernel of a biomolecular regulatory network
0 -- 0Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger, Berthold Göttgens, Jasmin Fisher. SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data
0 -- 0Sarah Hall-Swan, Jake Crawford, Rebecca Newman, Lenore J. Cowen. Retraction Note: detangling PPI networks to uncover functionally meaningful clusters
0 -- 0Helma Zecena, Daniel Tveit, Zi Wang, Ahmed Farhat, Parvita Panchal, Jing Liu, Simar J. Singh, Amandeep Sanghera, Ajay Bainiwal, Shuan Y. Teo, Frank L. Meyskens Jr, Feng Liu-Smith, Fabian V. Filipp. Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma
0 -- 0Chunhe Li, Lei Zhang, Qing Nie. Landscape reveals critical network structures for sharpening gene expression boundaries
0 -- 0Adithya Sagar, Rachel LeCover, Christine Shoemaker, Jeffrey D. Varner. Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models
0 -- 0Xinyue Luo, Ruijie Song, Murat Acar. Multi-component gene network design as a survival strategy in diverse environments
0 -- 0Zhang Wang, Seda Arat, Michal Magid-Slav, James R. Brown. Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets
0 -- 0Brian C. Ross, Mayla Boguslav, Holly Weeks, James C. Costello. Simulating heterogeneous populations using Boolean models
0 -- 0Stefano Casagranda, Suzanne Touzeau, Delphine Ropers, Jean-Luc Gouzé. Principal process analysis of biological models
0 -- 0Günter Neumann, Rebecca Wall, Ignacio Rangel, Tatiana M. Marques, Dirk Repsilber. Qualitative modelling of the interplay of inflammatory status and butyrate in the human gut: a hypotheses about robust bi-stability
0 -- 0Bertrand De Meulder, Diane Lefaudeux, Aruna T. Bansal, Alexander Mazein, Amphun Chaiboonchoe, Hassan Ahmed, Irina Balaur, Mansoor Saqi, Johann Pellet, Stéphane Ballereau, Nathanaël Lemonnier, Kai Sun, Ioannis Pandis, Xian Yang, Manohara Batuwitage, Kosmas Kretsos, Jonathan van Eyll, Alun Bedding, Timothy Davison, Paul Dodson, Christopher Larminie, Anthony Postle, Julie Corfield, Ratko Djukanovic, Kian Fan Chung, Ian M. Adcock, Yike Guo, Peter J. Sterk, Alexander Manta, Anthony Rowe, Frédéric Baribaud, Charles Auffray. A computational framework for complex disease stratification from multiple large-scale datasets
0 -- 0Jinmyung Jung, Mijin Kwon, Sunghwa Bae, Soorin Yim, Doheon Lee. Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy
0 -- 0Minoo Ashtiani, Ali Salehzadeh-Yazdi, Zahra Razaghi-Moghadam, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie, Mohieddin Jafari. A systematic survey of centrality measures for protein-protein interaction networks
0 -- 0Claudia C. Preston, Saranya Wyles, Santiago Reyes, Emily C. Storm, Bruce W. Eckloff, Randolph Faustino. NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module
0 -- 0Daniel Cook, Sirisha Achanta, Jan B. Hoek, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli. Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics
0 -- 0Abel Folch-Fortuny, Bas Teusink, Huub C. J. Hoefsloot, Age K. Smilde, Alberto Ferrer 0001. Dynamic elementary mode modelling of non-steady state flux data
0 -- 0Elena S. Dimitrova, Leslie A. Caromile, Reinhard C. Laubenbacher, Linda H. Shapiro. The innate immune response to ischemic injury: a multiscale modeling perspective
0 -- 0Guan-Sheng Liu, Richard Ballweg, Alan Ashbaugh, Yin Zhang, Joseph Facciolo, Melanie T. Cushion, Tongli Zhang. A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice
0 -- 0Yan-feng Cao, Shi-feng Wang, Xi Li, Yan-ling Zhang, Yanjiang Qiao. The anticancer mechanism investigation of Tanshinone IIA by pharmacological clustering in protein network
0 -- 0T. Conrad, Olaf Kniemeyer, Sebastian Henkel, T. Krüger, D. J. Mattern, V. Valiante, R. Guthke, I. D. Jacobsen, A. A. Brakhage, S. Vlaic, J. Linde. Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
0 -- 0Bob Strome, Ian Shenyen Hsu, Mitchell Li Cheong Man, Taraneh Zarin, Alex N. Nguyen Ba, Alan M. Moses. Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity
0 -- 0Peter D. Karp, Daniel S. Weaver, Mario Latendresse. How accurate is automated gap filling of metabolic models?
0 -- 0Farrah Sadre-Marandi, Thabat Dahdoul, Michael C. Reed, H. Frederik Nijhout. Sex differences in hepatic one-carbon metabolism
0 -- 0Mohamed Shahen, Zihu Guo, Akhtar Hussain Shar, Reham Ebaid, Qin Tao, Wenjuan Zhang, Ziyin Wu, Yaofei Bai, Yingxue Fu, Chunli Zheng, He Wang, Piar Ali Shar, Jianling Liu, Zhenzhong Wang, Wei Xiao, Yonghua Wang. Correction to: dengue virus causes changes of MicroRNA-genes regulatory network revealing potential targets for antiviral drugs
0 -- 0Parvathi Haridas, Alexander P. Browning, Jacqui A. McGovern, D. L. Sean McElwain, Matthew J. Simpson. Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue
0 -- 0Rosa D. Hernansaiz-Ballesteros, Luca Cardelli, Attila Csikász-Nagy. Single molecules can operate as primitive biological sensors, switches and oscillators
0 -- 0Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand Sastry, Erol S. Kavvas, Yara Seif, Larry Smarr, Bernhard O. Palsson. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
0 -- 0Frank Kramer, Steffen Just, Tanja Zeller. New perspectives: systems medicine in cardiovascular disease
0 -- 0Elliot Rowe, Bernhard O. Palsson, Zachary A. King. Escher-FBA: a web application for interactive flux balance analysis
0 -- 0Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic, Mingyang Lu. RACIPE: a computational tool for modeling gene regulatory circuits using randomization
1 -- 12Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher, Tamer Kahveci. Counting motifs in dynamic networks
13 -- 24Petronela 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
25 -- 39Shunsuke Teraguchi, Yutaro Kumagai. Estimation of diffusion constants from single molecular measurement without explicit tracking
41 -- 51Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher. ncRNA-disease association prediction based on sequence information and tripartite network
53 -- 60Yushan Qiu, Hao Jiang, Wai-Ki Ching, Xiaoqing Cheng. Discovery of Boolean metabolic networks: integer linear programming based approach
61 -- 74Bobby Ranjan, Ket Hing Chong, Jie Zheng. Composite mathematical modeling of calcium signaling behind neuronal cell death in Alzheimer's disease
75 -- 87Shuqin Zhang. Comparisons of gene coexpression network modules in breast cancer and ovarian cancer
89 -- 99Mengxuan 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
101 -- 110Hui 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
111 -- 122Soorin Yim, Hasun Yu, Dongjin Jang, Doheon Lee. Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations