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Network analysis methods for studying microbial communities: A mini review

Monica Steffi Matchado, Michael Lauber, Sandra Reitmeier, Tim Kacprowski, Jan Baumbach, Dirk Haller, Markus List
2021 Computational and Structural Biotechnology Journal  
In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns.  ...  Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods.  ...  Systems and network biology approaches have been used to decipher microbial co-occurrence patterns and range from correlation methods to complex graph-based models.  ... 
doi:10.1016/j.csbj.2021.05.001 pmid:34093985 pmcid:PMC8131268 fatcat:ba6wne7jprat3jgnngfbzkebq4

Predicting defects using network analysis on dependency graphs

Thomas Zimmermann, Nachiappan Nagappan
2008 Proceedings of the 13th international conference on Software engineering - ICSE '08  
In our evaluation on Windows Server 2003, we found that the recall for models built from network measures is by 10% points higher than for models built from complexity metrics.  ...  In this paper, we propose to use network analysis on these dependency graphs. This allows managers to identify central program units that are more likely to face defects.  ...  between dependencies and defects.  ... 
doi:10.1145/1368088.1368161 dblp:conf/icse/ZimmermannN08 fatcat:wjsdbofmnve6xgqjv3ryietovm

Complex Networks Models and Spectral Decomposition in the Analysis of Swimming Athletes' Performance at Olympic Games

Vanessa Helena Pereira-Ferrero, Theodore Gyle Lewis, Luciane Graziele Pereira Ferrero, Leonardo Tomazeli Duarte
2019 Frontiers in Physiology  
two types of complex networks (graphs) for each edition, using mathematical correlations, metrics and the spectral decomposition analysis.  ...  This study aims to present complex network models which analyze professional swimmers of 50-m freestyle Olympic competitions, comparing characteristics and variables that are considered performance determinants  ...  FIGURE 1 | 1 The heat map of the Pearson's correlations results among variables for each edition and complex network model.  ... 
doi:10.3389/fphys.2019.01134 pmid:31551810 pmcid:PMC6733958 fatcat:e75wudsbbjaflazhjbf7ku4rmq

Research of Chinese Stock Market' Complex Network Structure

He Nie, Yuan-Biao Zhang, Jun-Ru Chen, Xin-Guang Lv
2015 International Journal of Economics and Finance  
network theory to study the correlation between stocks; Sun (2013) studied stock's price gain and price volatility time series of complex network.  ...  to concluded that there was the correlation between the stock price; Zou (2013) established the undirected network and make use of social network analysis method to study the stock price correlation;  ...  Acknowledgements The authors acknowledge the financial support of this research by the Key Laboratory of Product Packaging and  ... 
doi:10.5539/ijef.v7n5p116 fatcat:or3vji57ubbadauyuxyqocpaa4

Multifractal cross-correlation effects in two-variable time series of complex network vertex observables

Paweł Oświȩcimka, Lorenzo Livi, Stanisław Drożdż
2016 Physical review. E  
Moreover, the analysis of protein contact networks reveals characteristics shared with both scale-free and small-world models.  ...  In particular, it is possible to distinguish between Erdös-Rényi, Barabási-Albert, and Watts-Strogatz networks on the basis of fractal cross-correlation.  ...  We have considered both models and real complex networks (protein contact networks).  ... 
doi:10.1103/physreve.94.042307 pmid:27841489 fatcat:lb4djgyxxfh7hka6xzs3lqzm24

Innovative Spatial-Temporal Network Modeling and Analysis Method of Air Quality

Guyu Zhao, Guoyan Huang, Hongdou He, Qian Wang
2019 IEEE Access  
The time correlation analysis of air quality nodes is conducted by calculating the time correlation matrix to construct the air quality network topology.  ...  INDEX TERMS Air quality system, the complex network, dynamic model, data mining.  ...  ACKNOWLEDGMENT The authors are grateful to valuable comments and suggestions of the reviewers.  ... 
doi:10.1109/access.2019.2900997 fatcat:kark2fcowze7ziqsgdphf37ejy

compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes

Victor Solis-Mezarino, Franz Herzog
2017 Nucleic Acids Research  
In a first step, modeling protein abundances and functional annotations from Gene Ontology (GO) results in a network which, in a second step, is integrated with connectivity data from XL-MS analysis in  ...  order to complement and validate the protein complexes in the network.  ...  There are two different approaches for modeling network topology in the population of interactions: the Spoke model and the Matrix model (6).  ... 
doi:10.1093/nar/gkx411 pmid:28498958 pmcid:PMC5570167 fatcat:nimp3ubjxncyxfjgwjc2dschky

Systematic evaluation of a new combinatorial curvature for complex networks

R.P. Sreejith, Jürgen Jost, Emil Saucan, Areejit Samal
2017 Chaos, Solitons & Fractals  
In this contribution, we perform a comparative analysis of Forman curvature with other edge-based measures such as edge betweenness, embeddedness and dispersion in diverse model and real networks.  ...  In this contribution, we also examine these two possible definitions of Forman curvature of nodes in diverse model and real networks.  ...  Supplementary Information Supplementary Table S1: Association of node-based measures with normalized and unnormalized Forman curvature of nodes in model and real networks.  ... 
doi:10.1016/j.chaos.2017.05.021 fatcat:eancfb4h2nbrhltbw23detucae

Evaluation Indexes and Correlation Analysis of Origination–Destination Travel Time of Nanjing Metro Based on Complex Network Method

Yu, Ye, Chen, Yan, Wang
2020 Sustainability  
Based on the complex network model, this research quantitatively analyzes the Pearson correlation of the indexes of OD travel time.  ...  The complex network index is based on two models: Space P and ride time, including the minimum number of rides, and the shortest ride time.  ...  Wei Y proposed the concept and performance index of the supernetwork model based on the complex network model, and analyzed the performance analysis, combined with the Nanjing metro network [42] .  ... 
doi:10.3390/su12031113 fatcat:xm5cumeg2bce7j7w2snxdd4lk4

Effect of dataset selection on the topological interpretation of protein interaction networks

Luke Hakes, David L Robertson, Stephen G Oliver
2005 BMC Genomics  
Studies of the yeast protein interaction network have revealed distinct correlations between the connectivity of individual proteins within the network and the average connectivity of their neighbours.  ...  We show how the use of different interaction data sets, such as those resulting from high-throughput or small-scale studies, and different modelling methodologies for the derivation pair-wise protein interactions  ...  Simon Lovell and for insights and discussions. LH is supported by a CASE Studentship from the Biotechnology & Biological Sciences Research Council (BBSRC) and AstraZeneca.  ... 
doi:10.1186/1471-2164-6-131 pmid:16174296 pmcid:PMC1249571 fatcat:mrde7vpnibhghixn47vb5lilma

Predicting the Success of NFL Teams using Complex Network Analysis

Matheus de Oliveira Salim, Wladmir Cardoso Brandão
2018 Proceedings of the 20th International Conference on Enterprise Information Systems  
In this article, we model the behavior of NFL players and teams using complex network analysis.  ...  social network and predict team success.  ...  The interactions between NFL teams and coaches were modeled as a complex network (Fast and Jensen, 2006) .  ... 
doi:10.5220/0006697101350142 dblp:conf/iceis/SalimB18 fatcat:xmp4duhbf5bahnlcsr7mgkduk4

Linear relation on the correlation in complex networks

C. W. Ma, K. Y. Szeto
2006 Physical Review E  
Correlation in complex networks follows a linear relation between the degree of a node and the total degrees of its neighbors for six different classes of real networks.  ...  Analytical expression for this linear relation for three standard models of complex networks: the Erdos-Renyi, Watts-Strogatz, and Barabasi-Albert networks is provided.  ...  Our analysis include the Erdos and Renyi random network ͑ER model͒, the Watts and Strogatz small world network model ͑WS model͒, and the scale free network of Barabasi and Albert ͑BA model͒.  ... 
doi:10.1103/physreve.73.047101 pmid:16711951 fatcat:uvfht6crnneoxbru3dnfffoetq

An Analysis of Centrality Measures for Complex and Social Networks

Felipe Grando, Diego Noble, Luis C. Lamb
2016 2016 IEEE Global Communications Conference (GLOBECOM)  
Measures of complex network analysis, such as vertex centrality, have the potential to unveil existing network patterns and behaviors.  ...  Our work thus contributes towards the development of a methodology for principled network analysis and evaluation.  ...  The relation between the real network samples and the complex network models will be important for a complementary analysis of centrality measures behavior in distinct contexts and useful to reinforce  ... 
doi:10.1109/glocom.2016.7841580 dblp:conf/globecom/GrandoNL16 fatcat:3n3acjq2onbybkfin2ep3midoi

Network Modelling and Visualisation Analysis of the Undergraduate Dental Curriculum System in China

Qian Ren, Xiao Peng, Xiaoyu Liu, Qiao Zheng, Ting He, Die Hu, Xuelian Jiang, Linglin Zhang
2021 Journal of Computer and Communications  
Objectives: This study aims to present the characteristics of the undergraduate dental curriculum system using network modelling and visualisation analysis based on complex network theory, thus providing  ...  Methods: The correlation coefficient was used to quantify the intensity of the correlation between courses, and a visualisation complex network of the dental curriculum was built to explore the curriculum  ...  In recent years, network modelling and visualisation analysis of big data using complex networks has been given great importance in various fields [10] [11] .  ... 
doi:10.4236/jcc.2021.96003 fatcat:6kn52q5eebclzbdjsumpnmro5e

Network Analysis: A Novel Approach to Understand Suicidal Behaviour

Derek de Beurs
2017 International Journal of Environmental Research and Public Health  
To understand the complex interaction between the many variables as proposed in complex models such as the IMV model, a new psychometric technique called network analysis has been proposed.  ...  A new approach called network analysis can help us better understand this process as it allows us to visualize and quantify the complex association between many different symptoms or risk factors.  ...  To understand the complex interaction between the many variables as proposed in complex models such as the IMV model, a new psychometric technique called network analysis has been proposed.  ... 
doi:10.3390/ijerph14030219 fatcat:innnlf34svhdtbk5hzysmxofh4
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