Literature DB >> 16849202

Complex networks and simple models in biology.

Eric de Silva1, Michael P H Stumpf.   

Abstract

The analysis of molecular networks, such as transcriptional, metabolic and protein interaction networks, has progressed substantially because of the power of models from statistical physics. Increasingly, the data are becoming so detailed--though not always complete or correct--that the simple models are reaching the limits of their usefulness. Here, we will discuss how network information can be described and to some extent quantified. In particular statistics offers a range of tools, such as model selection, which have not yet been widely applied in the analysis of biological networks. We will also outline a number of present challenges posed by biological network data in systems biology, and the extent to which these can be addressed by new developments in statistics, physics and applied mathematics.

Mesh:

Substances:

Year:  2005        PMID: 16849202      PMCID: PMC1618496          DOI: 10.1098/rsif.2005.0067

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN: 1742-5662            Impact factor:   4.118


  57 in total

1.  Emergence of scaling in random networks

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

2.  Highly expressed genes in yeast evolve slowly.

Authors:  C Pál; B Papp; L D Hurst
Journal:  Genetics       Date:  2001-06       Impact factor: 4.562

3.  Clustering and preferential attachment in growing networks.

Authors:  M E Newman
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-07-26

4.  Spectra of "real-world" graphs: beyond the semicircle law.

Authors:  I J Farkas; I Derényi; A L Barabási; T Vicsek
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-07-20

5.  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

6.  Classification of scale-free networks.

Authors:  Kwang-Il Goh; Eulsik Oh; Hawoong Jeong; Byungnam Kahng; Doochul Kim
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-18       Impact factor: 11.205

7.  Subnets of scale-free networks are not scale-free: sampling properties of networks.

Authors:  Michael P H Stumpf; Carsten Wiuf; Robert M May
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-14       Impact factor: 11.205

8.  A map of the interactome network of the metazoan C. elegans.

Authors:  Siming Li; Christopher M Armstrong; Nicolas Bertin; Hui Ge; Stuart Milstein; Mike Boxem; Pierre-Olivier Vidalain; Jing-Dong J Han; Alban Chesneau; Tong Hao; Debra S Goldberg; Ning Li; Monica Martinez; Jean-François Rual; Philippe Lamesch; Lai Xu; Muneesh Tewari; Sharyl L Wong; Lan V Zhang; Gabriel F Berriz; Laurent Jacotot; Philippe Vaglio; Jérôme Reboul; Tomoko Hirozane-Kishikawa; Qianru Li; Harrison W Gabel; Ahmed Elewa; Bridget Baumgartner; Debra J Rose; Haiyuan Yu; Stephanie Bosak; Reynaldo Sequerra; Andrew Fraser; Susan E Mango; William M Saxton; Susan Strome; Sander Van Den Heuvel; Fabio Piano; Jean Vandenhaute; Claude Sardet; Mark Gerstein; Lynn Doucette-Stamm; Kristin C Gunsalus; J Wade Harper; Michael E Cusick; Frederick P Roth; David E Hill; Marc Vidal
Journal:  Science       Date:  2004-01-02       Impact factor: 47.728

9.  Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks.

Authors:  Ino Agrafioti; Jonathan Swire; James Abbott; Derek Huntley; Sarah Butcher; Michael P H Stumpf
Journal:  BMC Evol Biol       Date:  2005-03-18       Impact factor: 3.260

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

View more
  22 in total

1.  Modelling protein-protein interaction networks via a stickiness index.

Authors:  Natasa Przulj; Desmond J Higham
Journal:  J R Soc Interface       Date:  2006-10-22       Impact factor: 4.118

Review 2.  The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms.

Authors:  Gil Alterovitz; Taro Muso; Marco F Ramoni
Journal:  Brief Bioinform       Date:  2009-11-11       Impact factor: 11.622

3.  Statistical inference of the time-varying structure of gene-regulation networks.

Authors:  Sophie Lèbre; Jennifer Becq; Frédéric Devaux; Michael P H Stumpf; Gaëlle Lelandais
Journal:  BMC Syst Biol       Date:  2010-09-22

4.  Estimating the size of the human interactome.

Authors:  Michael P H Stumpf; Thomas Thorne; Eric de Silva; Ronald Stewart; Hyeong Jun An; Michael Lappe; Carsten Wiuf
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-12       Impact factor: 11.205

5.  Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins.

Authors:  William P Kelly; Michael P H Stumpf
Journal:  BMC Bioinformatics       Date:  2010-09-20       Impact factor: 3.169

6.  A differential network approach to exploring differences between biological states: an application to prediabetes.

Authors:  Beatriz Valcárcel; Peter Würtz; Nafisa-Katrin Seich al Basatena; Taru Tukiainen; Antti J Kangas; Pasi Soininen; Marjo-Riitta Järvelin; Mika Ala-Korpela; Timothy M Ebbels; Maria de Iorio
Journal:  PLoS One       Date:  2011-09-27       Impact factor: 3.240

7.  Detecting network communities: an application to phylogenetic analysis.

Authors:  Roberto F S Andrade; Ivan C Rocha-Neto; Leonardo B L Santos; Charles N de Santana; Marcelo V C Diniz; Thierry Petit Lobão; Aristóteles Goés-Neto; Suani T R Pinho; Charbel N El-Hani
Journal:  PLoS Comput Biol       Date:  2011-05-05       Impact factor: 4.475

8.  The effects of incomplete protein interaction data on structural and evolutionary inferences.

Authors:  Eric de Silva; Thomas Thorne; Piers Ingram; Ino Agrafioti; Jonathan Swire; Carsten Wiuf; Michael P H Stumpf
Journal:  BMC Biol       Date:  2006-11-03       Impact factor: 7.431

9.  Snazer: the simulations and networks analyzer.

Authors:  Tommaso Mazza; Gennaro Iaccarino; Corrado Priami
Journal:  BMC Syst Biol       Date:  2010-01-07

10.  Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

Authors:  Lev Guzmán-Vargas; Moisés Santillán
Journal:  BMC Syst Biol       Date:  2008-01-31
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.