Literature DB >> 20844594

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure.

A Annibale1, Acc Coolen, Lp Fernandes, F Fraternali, J Kleinjung.   

Abstract

We study the tailoring of structured random graph ensembles to real networks, with the objective of generating precise and practical mathematical tools for quantifying and comparing network topologies macroscopically, beyond the level of degree statistics. Our family of ensembles can produce graphs with any prescribed degree distribution and any degree-degree correlation function, its control parameters can be calculated fully analytically, and as a result we can calculate (asymptotically) formulae for entropies and complexities, and for information-theoretic distances between networks, expressed directly and explicitly in terms of their measured degree distribution and degree correlations.

Entities:  

Year:  2009        PMID: 20844594      PMCID: PMC2938474          DOI: 10.1088/1751-8113/42/48/485001

Source DB:  PubMed          Journal:  J Phys A Math Gen        ISSN: 0305-4470


  40 in total

1.  Emergence of scaling in random networks

Authors: 
Journal:  Science       Date:  1999-10-15       Impact factor: 47.728

2.  Evidence for dynamically organized modularity in the yeast protein-protein interaction network.

Authors:  Jing-Dong J Han; Nicolas Bertin; Tong Hao; Debra S Goldberg; Gabriel F Berriz; Lan V Zhang; Denis Dupuy; Albertha J M Walhout; Michael E Cusick; Frederick P Roth; Marc Vidal
Journal:  Nature       Date:  2004-06-09       Impact factor: 49.962

3.  Tuning clustering in random networks with arbitrary degree distributions.

Authors:  M Angeles Serrano; Marián Boguñá
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-09-30

4.  Mixture models and exploratory analysis in networks.

Authors:  M E J Newman; E A Leicht
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-24       Impact factor: 11.205

5.  Entropy of network ensembles.

Authors:  Ginestra Bianconi
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-03-27

6.  Functional organization of the yeast proteome by systematic analysis of protein complexes.

Authors:  Anne-Claude Gavin; Markus Bösche; Roland Krause; Paola Grandi; Martina Marzioch; Andreas Bauer; Jörg Schultz; Jens M Rick; Anne-Marie Michon; Cristina-Maria Cruciat; Marita Remor; Christian Höfert; Malgorzata Schelder; Miro Brajenovic; Heinz Ruffner; Alejandro Merino; Karin Klein; Manuela Hudak; David Dickson; Tatjana Rudi; Volker Gnau; Angela Bauch; Sonja Bastuck; Bettina Huhse; Christina Leutwein; Marie-Anne Heurtier; Richard R Copley; Angela Edelmann; Erich Querfurth; Vladimir Rybin; Gerard Drewes; Manfred Raida; Tewis Bouwmeester; Peer Bork; Bertrand Seraphin; Bernhard Kuster; Gitte Neubauer; Giulio Superti-Furga
Journal:  Nature       Date:  2002-01-10       Impact factor: 49.962

7.  A comprehensive two-hybrid analysis to explore the yeast protein interactome.

Authors:  T Ito; T Chiba; R Ozawa; M Yoshida; M Hattori; Y Sakaki
Journal:  Proc Natl Acad Sci U S A       Date:  2001-03-13       Impact factor: 11.205

8.  Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Authors:  Nicolas Simonis; Jean-François Rual; Anne-Ruxandra Carvunis; Murat Tasan; Irma Lemmens; Tomoko Hirozane-Kishikawa; Tong Hao; Julie M Sahalie; Kavitha Venkatesan; Fana Gebreab; Sebiha Cevik; Niels Klitgord; Changyu Fan; Pascal Braun; Ning Li; Nono Ayivi-Guedehoussou; Elizabeth Dann; Nicolas Bertin; David Szeto; Amélie Dricot; Muhammed A Yildirim; Chenwei Lin; Anne-Sophie de Smet; Huey-Ling Kao; Christophe Simon; Alex Smolyar; Jin Sook Ahn; Muneesh Tewari; Mike Boxem; Stuart Milstein; Haiyuan Yu; Matija Dreze; Jean Vandenhaute; Kristin C Gunsalus; Michael E Cusick; David E Hill; Jan Tavernier; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

9.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Authors:  Nevan J Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P Tikuisis; Thanuja Punna; José M Peregrín-Alvarez; Michael Shales; Xin Zhang; Michael Davey; Mark D Robinson; Alberto Paccanaro; James E Bray; Anthony Sheung; Bryan Beattie; Dawn P Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter Wong; Andrei Starostine; Myra M Canete; James Vlasblom; Samuel Wu; Chris Orsi; Sean R Collins; Shamanta Chandran; Robin Haw; Jennifer J Rilstone; Kiran Gandi; Natalie J Thompson; Gabe Musso; Peter St Onge; Shaun Ghanny; Mandy H Y Lam; Gareth Butland; Amin M Altaf-Ul; Shigehiko Kanaya; Ali Shilatifard; Erin O'Shea; Jonathan S Weissman; C James Ingles; Timothy R Hughes; John Parkinson; Mark Gerstein; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2006-03-22       Impact factor: 49.962

10.  BioGRID: a general repository for interaction datasets.

Authors:  Chris Stark; Bobby-Joe Breitkreutz; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

View more
  6 in total

1.  What you see is not what you get: how sampling affects macroscopic features of biological networks.

Authors:  A Annibale; A C C Coolen
Journal:  Interface Focus       Date:  2011-10-05       Impact factor: 3.906

2.  Protein networks reveal detection bias and species consistency when analysed by information-theoretic methods.

Authors:  Luis P Fernandes; Alessia Annibale; Jens Kleinjung; Anthony C C Coolen; Franca Fraternali
Journal:  PLoS One       Date:  2010-08-18       Impact factor: 3.240

3.  Quantifying randomness in real networks.

Authors:  Chiara Orsini; Marija M Dankulov; Pol Colomer-de-Simón; Almerima Jamakovic; Priya Mahadevan; Amin Vahdat; Kevin E Bassler; Zoltán Toroczkai; Marián Boguñá; Guido Caldarelli; Santo Fortunato; Dmitri Krioukov
Journal:  Nat Commun       Date:  2015-10-20       Impact factor: 14.919

4.  Bridging topological and functional information in protein interaction networks by short loops profiling.

Authors:  Sun Sook Chung; Alessandro Pandini; Alessia Annibale; Anthony C C Coolen; N Shaun B Thomas; Franca Fraternali
Journal:  Sci Rep       Date:  2015-02-23       Impact factor: 4.379

5.  Statistical assessment of crosstalk enrichment between gene groups in biological networks.

Authors:  Theodore McCormack; Oliver Frings; Andrey Alexeyenko; Erik L L Sonnhammer
Journal:  PLoS One       Date:  2013-01-23       Impact factor: 3.240

6.  Estimating degree-degree correlation and network cores from the connectivity of high-degree nodes in complex networks.

Authors:  R J Mondragón
Journal:  Sci Rep       Date:  2020-03-27       Impact factor: 4.379

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.