Review of Biological Network Data and Its Applications
Donghyeon Yu, MinSoo Kim, Guanghua Xiao, Tae Hyun Hwang
Genomics Inform. 2013;11(4):200-210.   Published online 2013 Dec 31     DOI:
Citations to this article as recorded by Crossref logo
Network theory reveals principles of spliceosome structure and dynamics
Harpreet Kaur, Clarisse van der Feltz, Yichen Sun, Aaron A. Hoskins
Structure.2022; 30(1): 190.     CrossRef
Learning representation for multiple biological networks via a robust graph regularized integration approach
Xiwen Zhang, Weiwen Wang, Chuan-Xian Ren, Dao-Qing Dai
Briefings in Bioinformatics.2022;[Epub]     CrossRef
Computational analyses of mechanism of action (MoA): data, methods and integration
Maria-Anna Trapotsi, Layla Hosseini-Gerami, Andreas Bender
RSC Chemical Biology.2022; 3(2): 170.     CrossRef
Modulation of RNA splicing associated with Wnt signaling pathway using FD-895 and pladienolide B
Deepak Kumar, Manoj K. Kashyap, Zhe Yu, Ide Spaanderman, Reymundo Villa, Thomas J. Kipps, James J. La Clair, Michael D. Burkart, Januario E. Castro
Aging.2022; 14(5): 2081.     CrossRef
A Class of Koszul Algebra and Some Homological Invariants through Circulant Matrices and Cycles
Muhammed Nadeem, Mohammed M. M. Jaradat, Imran Siddique, Muhammad Arfan Ali, Muhammad Ahsan, Muhammad Sarwar Sindhu, Gul Rahmat
Journal of Mathematics.2022; 2022: 1.     CrossRef
Saddle-ghost induced heteroclinic cycling in five-dimensional positively auto-regulated and mutually repressive gene regulation networks
Lei Yang, Anfan Jia, Weigang Sun, Marc Turcotte
Nonlinear Dynamics.2022; 109(2): 1081.     CrossRef
Basics on network theory to analyze biological systems: a hands-on outlook
Gerardo Ruiz Amores, Agustino Martínez-Antonio
Functional & Integrative Genomics.2022; 22(6): 1433.     CrossRef
Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review
Trishala Das, Harbinder Kaur, Pratibha Gour, Kartikay Prasad, Andrew M Lynn, Amresh Prakash, Vijay Kumar
Briefings in Bioinformatics.2022;[Epub]     CrossRef
On Bipartite Circulant Graph Decompositions Based on Cartesian and Tensor Products with Novel Topologies and Deadlock-Free Routing
Ahmed El-Mesady, Aleksandr Y. Romanov, Aleksandr A. Amerikanov, Alexander D. Ivannikov
Algorithms.2022; 16(1): 10.     CrossRef
An Efficient and Easy-to-Use Network-Based Integrative Method of Multi-Omics Data for Cancer Genes Discovery
Ting Wei, Botao Fa, Chengwen Luo, Luke Johnston, Yue Zhang, Zhangsheng Yu
Frontiers in Genetics.2021;[Epub]     CrossRef
SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays
Samuel Katz, Jian Song, Kyle P. Webb, Nicolas W. Lounsbury, Clare E. Bryant, Iain D.C. Fraser
Cell Systems.2021; 12(4): 338.     CrossRef
Probabilistic model by Bayesian network for the prediction of antibody glycosylation in perfusion and fed‐batch cell cultures
Liang Zhang, MingLiang Wang, Andreas Castan, Håkan Hjalmarsson, Veronique Chotteau
Biotechnology and Bioengineering.2021; 118(9): 3447.     CrossRef
Relationship between gene regulation network structure and prediction accuracy in high dimensional regression
Yuichi Okinaga, Daisuke Kyogoku, Satoshi Kondo, Atsushi J. Nagano, Kei Hirose
Scientific Reports.2021;[Epub]     CrossRef
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations
Vinay Srinivas Bharadhwaj, Mehdi Ali, Colin Birkenbihl, Sarah Mubeen, Jens Lehmann, Martin Hofmann-Apitius, Charles Tapley Hoyt, Daniel Domingo-Fernández, Inanc Birol
Bioinformatics.2021; 37(19): 3311.     CrossRef
CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis
Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson Araújo Silva
BMC Genomics.2021;[Epub]     CrossRef
Phenotype correlations reveal the relationships of physiological systems underlying human ageing
Meng Hao, Hui Zhang, Zixin Hu, Xiaoyan Jiang, Qi Song, Xi Wang, Jiucun Wang, Zuyun Liu, Xiaofeng Wang, Yi Li, Li Jin
Aging Cell.2021;[Epub]     CrossRef
Novel cancer subtyping method based on patient-specific gene regulatory network
Mai Adachi Nakazawa, Yoshinori Tamada, Yoshihisa Tanaka, Marie Ikeguchi, Kako Higashihara, Yasushi Okuno
Scientific Reports.2021;[Epub]     CrossRef
Evaluating new strategies for anticancer molecules from ethnic medicinal plants through in silico and biological approach - A review
B.V. Vibala, P.K. Praseetha, S. Vijayakumar
Gene Reports.2020; 18: 100553.     CrossRef
Acute Inflammation in Traumatic Brain Injury and Polytrauma Patients Using Network Analysis
Bradley Rowland, Jude P.J. Savarraj, Jay Karri, Xu Zhang, Jessica Cardenas, H. Alex Choi, John B. Holcomb, Charles E. Wade
Shock.2020; 53(1): 24.     CrossRef
On applications of bipartite graph associated with algebraic structures
Xiujun Zhang, Muhammed Nadeem, Sarfraz Ahmad, Muhammad Kamran Siddiqui
Open Mathematics.2020; 18(1): 57.     CrossRef
Similarities in biological processes can be used to bridge ecology and molecular biology
Johan Hallin, Angel F. Cisneros, Mathieu Hénault, Anna Fijarczyk, Rohan Dandage, Carla Bautista, Christian R. Landry
Evolutionary Applications.2020; 13(6): 1335.     CrossRef
Molecular networks in Network Medicine: Development and applications
Edwin K. Silverman, Harald H. H. W. Schmidt, Eleni Anastasiadou, Lucia Altucci, Marco Angelini, Lina Badimon, Jean‐Luc Balligand, Giuditta Benincasa, Giovambattista Capasso, Federica Conte, Antonella Di Costanzo, Lorenzo Farina, Giulia Fiscon, Laurent Gat
WIREs Systems Biology and Medicine.2020;[Epub]     CrossRef
Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells
Kowit Hengphasatporn, Kitiporn Plaimas, Apichat Suratanee, Peemapat Wongsriphisant, Jinn-Moon Yang, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
Molecules.2020; 25(8): 1883.     CrossRef
Turning genome-wide association study findings into opportunities for drug repositioning
Alexandria Lau, Hon-Cheong So
Computational and Structural Biotechnology Journal.2020; 18: 1639.     CrossRef
A biochemical network modeling of a whole-cell
Paulo E. P. Burke, Claudia B. de L. Campos, Luciano da F. Costa, Marcos G. Quiles
Scientific Reports.2020;[Epub]     CrossRef
Dynamical network size estimation from local observations
Xiuchuan Tang, Wei Huo, Ye Yuan, Xiuting Li, Ling Shi, Han Ding, Jürgen Kurths
New Journal of Physics.2020; 22(9): 093031.     CrossRef
Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics
Antonino Aparo, Vincenzo Bonnici, Giovanni Micale, Alfredo Ferro, Dennis Shasha, Alfredo Pulvirenti, Rosalba Giugno
Interdisciplinary Sciences: Computational Life Sciences.2019; 11(1): 21.     CrossRef
scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data
Wenbin Ye, Guoli Ji, Pengchao Ye, Yuqi Long, Xuesong Xiao, Shuchao Li, Yaru Su, Xiaohui Wu
BMC Genomics.2019;[Epub]     CrossRef
Systematic Evaluation of Molecular Networks for Discovery of Disease Genes
Justin K. Huang, Daniel E. Carlin, Michael Ku Yu, Wei Zhang, Jason F. Kreisberg, Pablo Tamayo, Trey Ideker
Cell Systems.2018; 6(4): 484.     CrossRef
Bipartite graphs in systems biology and medicine: a survey of methods and applications
Georgios A Pavlopoulos, Panagiota I Kontou, Athanasia Pavlopoulou, Costas Bouyioukos, Evripides Markou, Pantelis G Bagos
GigaScience.2018;[Epub]     CrossRef
Network Structure Inference, A Survey
Ivan Brugere, Brian Gallagher, Tanya Y. Berger-Wolf
ACM Computing Surveys.2018; 51(2): 1.     CrossRef
Construction of a Transcriptome-Driven Network at the Early Stage of Infection with Influenza A H1N1 in Human Lung Alveolar Epithelial Cells
Myungguen Chung, Soo Young Cho, Young Seek Lee
Biomolecules & Therapeutics.2018; 26(3): 290.     CrossRef
A guide to gene regulatory network inference for obtaining predictive solutions: Underlying assumptions and fundamental biological and data constraints
Sara Barbosa, Bastian Niebel, Sebastian Wolf, Klaus Mauch, Ralf Takors
Biosystems.2018; 174: 37.     CrossRef
Comparative Strategy for the Statistical & Network based Analysis of Biological Networks
Nikhila T Suresh, Sreeja Ashok
Procedia Computer Science.2018; 143: 165.     CrossRef
Integrating Multiple Interaction Networks for Gene Function Inference
Jingpu Zhang, Lei Deng
Molecules.2018; 24(1): 30.     CrossRef
Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea
Jinik Hwang, So Yun Park, Mirye Park, Sukchan Lee, Taek-Kyun Lee, Ulrich Melcher
PLOS ONE.2017; 12(1): e0169841.     CrossRef
Graph-theoretical model of global human interactome reveals enhanced long-range communicability in cancer networks
Evgeny Gladilin, Peter Csermely
PLOS ONE.2017; 12(1): e0170953.     CrossRef
NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks
Yang Cao, Wenjian Xu, Chao Niu, Xiaochen Bo, Fei Li
BioMed Research International.2017; 2017: 1.     CrossRef
On the Variable Ordering in Subgraph Isomorphism Algorithms
Vincenzo Bonnici, Rosalba Giugno
IEEE/ACM Transactions on Computational Biology and Bioinformatics.2017; 14(1): 193.     CrossRef
Biological network border detection
Paulo E. P. Burke, Cesar H. Comin, Filipi N. Silva, Luciano da F. Costa
Integrative Biology.2017; 9(12): 947.     CrossRef
APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks
Vincenzo Bonnici, Federico Busato, Giovanni Micale, Nicola Bombieri, Alfredo Pulvirenti, Rosalba Giugno, Alfonso Valencia
Bioinformatics.2016; 32(14): 2159.     CrossRef
Molecular signatures of ovarian diseases: Insights from network medicine perspective
Medi Kori, Esra Gov, Kazim Yalcin Arga
Systems Biology in Reproductive Medicine.2016; 62(4): 266.     CrossRef
CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction
Gianfranco Politano, Francesca Orso, Monica Raimo, Alfredo Benso, Alessandro Savino, Daniela Taverna, Stefano Di Carlo
BMC Bioinformatics.2016;[Epub]     CrossRef
Correlation-Based Network Generation, Visualization, and Analysis as a Powerful Tool in Biological Studies: A Case Study in Cancer Cell Metabolism
Albert Batushansky, David Toubiana, Aaron Fait
BioMed Research International.2016; 2016: 1.     CrossRef
Compact Integration of Multi-Network Topology for Functional Analysis of Genes
Hyunghoon Cho, Bonnie Berger, Jian Peng
Cell Systems.2016; 3(6): 540.     CrossRef
Tumor suppressor genes and their underlying interactions in paclitaxel resistance in cancer therapy
Jia-Hui Xu, Shi-Lian Hu, Guo-Dong Shen, Gan Shen
Cancer Cell International.2016;[Epub]     CrossRef
Systems biology meets -omic technologies: novel approaches to biomarker discovery and companion diagnostic development
Laura Caberlotto, Mario Lauria
Expert Review of Molecular Diagnostics.2015; 15(2): 255.     CrossRef
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms
Mohieddin Jafari, Mehdi Mirzaie, Mehdi Sadeghi
BMC Bioinformatics.2015;[Epub]     CrossRef
Bilevel optimization techniques in computational strain design
Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas
Computers & Chemical Engineering.2015; 72: 363.     CrossRef
Deciphering complex patterns of class‐I HLA–peptide cross‐reactivity via hierarchical grouping
Sumanta Mukherjee, Jim Warwicker, Nagasuma Chandra
Immunology & Cell Biology.2015; 93(6): 522.     CrossRef
A Genetically Modified Protein-Based Hydrogel for 3D Culture of AD293 Cells
Xiao Du, Jingyu Wang, Wentao Diao, Ling Wang, Jiafu Long, Hao Zhou, Bing Xu
PLoS ONE.2014; 9(9): e107949.     CrossRef