Literature DB >> 27047991

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.

Koon-Kiu Yan1, Daifeng Wang1, Anurag Sethi1, Paul Muir2, Robert Kitchen1, Chao Cheng3, Mark Gerstein4.   

Abstract

Biological systems are complex. In particular, the interactions between molecular components often form dense networks that, more often than not, are criticized for being inscrutable 'hairballs'. We argue that one way of untangling these hairballs is through cross-disciplinary network comparison-leveraging advances in other disciplines to obtain new biological insights. In some cases, such comparisons enable the direct transfer of mathematical formalism between disciplines, precisely describing the abstract associations between entities and allowing us to apply a variety of sophisticated formalisms to biology. In cases where the detailed structure of the network does not permit the transfer of complete formalisms between disciplines, comparison of mechanistic interactions in systems for which we have significant day-to-day experience can provide analogies for interpreting relatively more abstruse biological networks. Here, we illustrate how these comparisons benefit the field with a few specific examples related to network growth, organizational hierarchies, and the evolution of adaptive systems.

Entities:  

Year:  2016        PMID: 27047991      PMCID: PMC4817108          DOI: 10.1016/j.cels.2016.02.014

Source DB:  PubMed          Journal:  Cell Syst        ISSN: 2405-4712            Impact factor:   10.304


  76 in total

1.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

2.  Community structure in time-dependent, multiscale, and multiplex networks.

Authors:  Peter J Mucha; Thomas Richardson; Kevin Macon; Mason A Porter; Jukka-Pekka Onnela
Journal:  Science       Date:  2010-05-14       Impact factor: 47.728

3.  Network architecture of the long-distance pathways in the macaque brain.

Authors:  Dharmendra S Modha; Raghavendra Singh
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-13       Impact factor: 11.205

4.  Some protein interaction data do not exhibit power law statistics.

Authors:  Reiko Tanaka; Tau-Mu Yi; John Doyle
Journal:  FEBS Lett       Date:  2005-09-26       Impact factor: 4.124

5.  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

6.  Universal distribution of component frequencies in biological and technological systems.

Authors:  Tin Yau Pang; Sergei Maslov
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-25       Impact factor: 11.205

Review 7.  Design principles of regulatory networks: searching for the molecular algorithms of the cell.

Authors:  Wendell A Lim; Connie M Lee; Chao Tang
Journal:  Mol Cell       Date:  2013-01-24       Impact factor: 17.970

8.  Architecture of the human regulatory network derived from ENCODE data.

Authors:  Mark B Gerstein; Anshul Kundaje; Manoj Hariharan; Stephen G Landt; Koon-Kiu Yan; Chao Cheng; Xinmeng Jasmine Mu; Ekta Khurana; Joel Rozowsky; Roger Alexander; Renqiang Min; Pedro Alves; Alexej Abyzov; Nick Addleman; Nitin Bhardwaj; Alan P Boyle; Philip Cayting; Alexandra Charos; David Z Chen; Yong Cheng; Declan Clarke; Catharine Eastman; Ghia Euskirchen; Seth Frietze; Yao Fu; Jason Gertz; Fabian Grubert; Arif Harmanci; Preti Jain; Maya Kasowski; Phil Lacroute; Jing Jane Leng; Jin Lian; Hannah Monahan; Henriette O'Geen; Zhengqing Ouyang; E Christopher Partridge; Dorrelyn Patacsil; Florencia Pauli; Debasish Raha; Lucia Ramirez; Timothy E Reddy; Brian Reed; Minyi Shi; Teri Slifer; Jing Wang; Linfeng Wu; Xinqiong Yang; Kevin Y Yip; Gili Zilberman-Schapira; Serafim Batzoglou; Arend Sidow; Peggy J Farnham; Richard M Myers; Sherman M Weissman; Michael Snyder
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

9.  Phylomemetics--evolutionary analysis beyond the gene.

Authors:  Christopher J Howe; Heather F Windram
Journal:  PLoS Biol       Date:  2011-05-31       Impact factor: 8.029

10.  A simple dependence between protein evolution rate and the number of protein-protein interactions.

Authors:  Hunter B Fraser; Dennis P Wall; Aaron E Hirsh
Journal:  BMC Evol Biol       Date:  2003-05-23       Impact factor: 3.260

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  7 in total

Review 1.  Context-aware synthetic biology by controller design: Engineering the mammalian cell.

Authors:  Nika Shakiba; Ross D Jones; Ron Weiss; Domitilla Del Vecchio
Journal:  Cell Syst       Date:  2021-06-16       Impact factor: 11.091

2.  System-Based Differential Gene Network Analysis for Characterizing a Sample-Specific Subnetwork.

Authors:  Yoshihisa Tanaka; Yoshinori Tamada; Marie Ikeguchi; Fumiyoshi Yamashita; Yasushi Okuno
Journal:  Biomolecules       Date:  2020-02-14

3.  CANTARE: finding and visualizing network-based multi-omic predictive models.

Authors:  Janet C Siebert; Martine Saint-Cyr; Sarah J Borengasser; Brandie D Wagner; Catherine A Lozupone; Carsten Görg
Journal:  BMC Bioinformatics       Date:  2021-02-19       Impact factor: 3.307

4.  A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets.

Authors:  Bharat Mishra; Nilesh Kumar; M Shahid Mukhtar
Journal:  Comput Struct Biotechnol J       Date:  2022-04-21       Impact factor: 6.155

5.  Network biology discovers pathogen contact points in host protein-protein interactomes.

Authors:  Hadia Ahmed; T C Howton; Yali Sun; Natascha Weinberger; Youssef Belkhadir; M Shahid Mukhtar
Journal:  Nat Commun       Date:  2018-06-13       Impact factor: 14.919

6.  ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

Authors:  Nam D Nguyen; Ian K Blaby; Daifeng Wang
Journal:  BMC Genomics       Date:  2019-12-30       Impact factor: 3.969

7.  Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection.

Authors:  Yoshihisa Tanaka; Kako Higashihara; Mai Adachi Nakazawa; Fumiyoshi Yamashita; Yoshinori Tamada; Yasushi Okuno
Journal:  Sci Rep       Date:  2021-05-27       Impact factor: 4.379

  7 in total

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