Literature DB >> 16383786

Generating uniformly distributed random networks.

Yael Artzy-Randrup1, Lewi Stone.   

Abstract

The analysis of real networks taken from the biological, social, and physical sciences often requires a carefully posed statistical null-hypothesis approach. One common method requires comparing real networks to an ensemble of random matrices that satisfy realistic constraints in which each different matrix member is equiprobable. We discuss existing methods for generating uniformly distributed (constrained) random matrices, describe their shortcomings, and present an efficient technique that should have many practical applications.

Year:  2005        PMID: 16383786     DOI: 10.1103/PhysRevE.72.056708

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  17 in total

1.  Network structure of cerebral cortex shapes functional connectivity on multiple time scales.

Authors:  Christopher J Honey; Rolf Kötter; Michael Breakspear; Olaf Sporns
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-04       Impact factor: 11.205

2.  Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution.

Authors:  Tal Dagan; Yael Artzy-Randrup; William Martin
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-16       Impact factor: 11.205

3.  NetMODE: network motif detection without Nauty.

Authors:  Xin Li; Douglas S Stones; Haidong Wang; Hualiang Deng; Xiaoguang Liu; Gang Wang
Journal:  PLoS One       Date:  2012-12-18       Impact factor: 3.240

Review 4.  Graph analysis of functional brain networks: practical issues in translational neuroscience.

Authors:  Fabrizio De Vico Fallani; Jonas Richiardi; Mario Chavez; Sophie Achard
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-10-05       Impact factor: 6.237

5.  Evidence of strain structure in Plasmodium falciparum var gene repertoires in children from Gabon, West Africa.

Authors:  Karen P Day; Yael Artzy-Randrup; Kathryn E Tiedje; Virginie Rougeron; Donald S Chen; Thomas S Rask; Mary M Rorick; Florence Migot-Nabias; Philippe Deloron; Adrian J F Luty; Mercedes Pascual
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-01       Impact factor: 11.205

6.  Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity.

Authors:  Nicholas L Turner; Thomas Macrina; J Alexander Bae; Runzhe Yang; Alyssa M Wilson; Casey Schneider-Mizell; Kisuk Lee; Ran Lu; Jingpeng Wu; Agnes L Bodor; Adam A Bleckert; Derrick Brittain; Emmanouil Froudarakis; Sven Dorkenwald; Forrest Collman; Nico Kemnitz; Dodam Ih; William M Silversmith; Jonathan Zung; Aleksandar Zlateski; Ignacio Tartavull; Szi-Chieh Yu; Sergiy Popovych; Shang Mu; William Wong; Chris S Jordan; Manuel Castro; JoAnn Buchanan; Daniel J Bumbarger; Marc Takeno; Russel Torres; Gayathri Mahalingam; Leila Elabbady; Yang Li; Erick Cobos; Pengcheng Zhou; Shelby Suckow; Lynne Becker; Liam Paninski; Franck Polleux; Jacob Reimer; Andreas S Tolias; R Clay Reid; Nuno Maçarico da Costa; H Sebastian Seung
Journal:  Cell       Date:  2022-02-24       Impact factor: 66.850

7.  Mass-balanced randomization of metabolic networks.

Authors:  Georg Basler; Oliver Ebenhöh; Joachim Selbig; Zoran Nikoloski
Journal:  Bioinformatics       Date:  2011-03-23       Impact factor: 6.937

8.  Unraveling spurious properties of interaction networks with tailored random networks.

Authors:  Stephan Bialonski; Martin Wendler; Klaus Lehnertz
Journal:  PLoS One       Date:  2011-08-05       Impact factor: 3.240

9.  A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.

Authors:  Kai Kruse; Sven Sewitz; M Madan Babu
Journal:  Nucleic Acids Res       Date:  2012-11-21       Impact factor: 16.971

10.  Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum.

Authors:  Yael Artzy-Randrup; Mary M Rorick; Karen Day; Donald Chen; Andrew P Dobson; Mercedes Pascual
Journal:  Elife       Date:  2012-12-18       Impact factor: 8.140

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