Literature DB >> 20018705

Missing and spurious interactions and the reconstruction of complex networks.

Roger Guimerà1, Marta Sales-Pardo.   

Abstract

Network analysis is currently used in a myriad of contexts, from identifying potential drug targets to predicting the spread of epidemics and designing vaccination strategies and from finding friends to uncovering criminal activity. Despite the promise of the network approach, the reliability of network data is a source of great concern in all fields where complex networks are studied. Here, we present a general mathematical and computational framework to deal with the problem of data reliability in complex networks. In particular, we are able to reliably identify both missing and spurious interactions in noisy network observations. Remarkably, our approach also enables us to obtain, from those noisy observations, network reconstructions that yield estimates of the true network properties that are more accurate than those provided by the observations themselves. Our approach has the potential to guide experiments, to better characterize network data sets, and to drive new discoveries.

Mesh:

Year:  2009        PMID: 20018705      PMCID: PMC2799723          DOI: 10.1073/pnas.0908366106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  21 in total

1.  Optimal network topologies for local search with congestion.

Authors:  R Guimerà; A Díaz-Guilera; F Vega-Redondo; A Cabrales; A Arenas
Journal:  Phys Rev Lett       Date:  2002-11-21       Impact factor: 9.161

2.  A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Authors:  Ronald Jansen; Haiyuan Yu; Dov Greenbaum; Yuval Kluger; Nevan J Krogan; Sambath Chung; Andrew Emili; Michael Snyder; Jack F Greenblatt; Mark Gerstein
Journal:  Science       Date:  2003-10-17       Impact factor: 47.728

3.  Mixing patterns in networks.

Authors:  M E J Newman
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-02-27

4.  Epidemic spreading in correlated complex networks.

Authors:  Marián Boguñá; Romualdo Pastor-Satorras
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-10-21

5.  The structure of the nervous system of the nematode Caenorhabditis elegans.

Authors:  J G White; E Southgate; J N Thomson; S Brenner
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1986-11-12       Impact factor: 6.237

6.  Synchronization reveals topological scales in complex networks.

Authors:  Alex Arenas; Albert Díaz-Guilera; Conrad J Pérez-Vicente
Journal:  Phys Rev Lett       Date:  2006-03-22       Impact factor: 9.161

7.  A network-based method for target selection in metabolic networks.

Authors:  R Guimerà; M Sales-Pardo; L A N Amaral
Journal:  Bioinformatics       Date:  2007-04-26       Impact factor: 6.937

8.  A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.

Authors:  Tony Chiang; Denise Scholtens
Journal:  Nat Protoc       Date:  2009-03-26       Impact factor: 13.491

9.  Hierarchical structure and the prediction of missing links in networks.

Authors:  Aaron Clauset; Cristopher Moore; M E J Newman
Journal:  Nature       Date:  2008-05-01       Impact factor: 49.962

10.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).

Authors:  Jennifer L Reed; Thuy D Vo; Christophe H Schilling; Bernhard O Palsson
Journal:  Genome Biol       Date:  2003-08-28       Impact factor: 13.583

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  99 in total

1.  Social network models predict movement and connectivity in ecological landscapes.

Authors:  Robert J Fletcher; Miguel A Acevedo; Brian E Reichert; Kyle E Pias; Wiley M Kitchens
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-14       Impact factor: 11.205

2.  Matching-centrality decomposition and the forecasting of new links in networks.

Authors:  Rudolf P Rohr; Russell E Naisbit; Christian Mazza; Louis-Félix Bersier
Journal:  Proc Biol Sci       Date:  2016-02-10       Impact factor: 5.349

3.  Modular coherence of protein dynamics in yeast cell polarity system.

Authors:  Juntao Tony Gao; Roger Guimerà; Hua Li; Inês Mendes Pinto; Marta Sales-Pardo; Stephanie C Wai; Boris Rubinstein; Rong Li
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-18       Impact factor: 11.205

4.  Leaders in social networks, the Delicious case.

Authors:  Linyuan Lü; Yi-Cheng Zhang; Chi Ho Yeung; Tao Zhou
Journal:  PLoS One       Date:  2011-06-27       Impact factor: 3.240

5.  Toward link predictability of complex networks.

Authors:  Linyuan Lü; Liming Pan; Tao Zhou; Yi-Cheng Zhang; H Eugene Stanley
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-06       Impact factor: 11.205

6.  Accurate and scalable social recommendation using mixed-membership stochastic block models.

Authors:  Antonia Godoy-Lorite; Roger Guimerà; Cristopher Moore; Marta Sales-Pardo
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-23       Impact factor: 11.205

7.  Convex skeletons of complex networks.

Authors:  Lovro Šubelj
Journal:  J R Soc Interface       Date:  2018-08       Impact factor: 4.118

Review 8.  Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Authors:  Peter Csermely; Tamás Korcsmáros; Huba J M Kiss; Gábor London; Ruth Nussinov
Journal:  Pharmacol Ther       Date:  2013-02-04       Impact factor: 12.310

9.  Clustering network layers with the strata multilayer stochastic block model.

Authors:  Natalie Stanley; Saray Shai; Dane Taylor; Peter J Mucha
Journal:  IEEE Trans Netw Sci Eng       Date:  2016-03-25

10.  Modeling Combination Hepatitis C Virus Treatment and Prevention Strategies in a Network of People Who Inject Drugs in the United States.

Authors:  Alexei Zelenev; Jianghong Li; Portia Shea; Robert Hecht; Frederick L Altice
Journal:  Clin Infect Dis       Date:  2021-03-01       Impact factor: 9.079

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