Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Sci. Signal., 28 July 2009
Vol. 2, Issue 81, p. pe44
[DOI: 10.1126/scisignal.281pe44]


Understanding Modularity in Molecular Networks Requires Dynamics

Roger P. Alexander1,2,3, Philip M. Kim4,5,6,7, Thierry Emonet1,2,8*, and Mark B. Gerstein1,3,9*

1 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
2 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
3 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
4 Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
5 Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
6 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.
7 Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada.
8 Department of Physics, Yale University, New Haven, CT 06520, USA.
9 Department of Computer Science, Yale University, New Haven, CT 06520, USA.

Abstract: The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as nongenetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics—and therefore to behavior—remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular—that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function.

* Corresponding authors. E-mail, thierry.emonet{at} (T.E.); mark.gerstein{at} (M.B.G.)

Citation: R. P. Alexander, P. M. Kim, T. Emonet, M. B. Gerstein, Understanding Modularity in Molecular Networks Requires Dynamics. Sci. Signal. 2, pe44 (2009).

Read the Full Text

A fluorescent reporter for mapping cellular protein-protein interactions in time and space.
D. Moreno, J. Neller, H. A. Kestler, J. Kraus, A. Dunkler, and N. Johnsson (2014)
Mol Syst Biol 9, 647
   Abstract »    Full Text »    PDF »
Biological network analysis: insights into structure and functions.
X. Ma and L. Gao (2012)
Briefings in Functional Genomics 11, 434-442
   Abstract »    Full Text »    PDF »
Load-Induced Modulation of Signal Transduction Networks.
P. Jiang, A. C. Ventura, E. D. Sontag, S. D. Merajver, A. J. Ninfa, and D. Del Vecchio (2011)
Science Signaling 4, ra67
   Abstract »    Full Text »    PDF »
Network-Based Tools for the Identification of Novel Drug Targets.
I. J. Farkas, T. Korcsmaros, I. A. Kovacs, A. Mihalik, R. Palotai, G. I. Simko, K. Z. Szalay, M. Szalay-Beko, T. Vellai, S. Wang, et al. (2011)
Science Signaling 4, pt3
   Abstract »    Full Text »    PDF »
The Evolution of the Phage Shock Protein Response System: Interplay between Protein Function, Genomic Organization, and System Function.
M. Huvet, T. Toni, X. Sheng, T. Thorne, G. Jovanovic, C. Engl, M. Buck, J. W. Pinney, and M. P. H. Stumpf (2011)
Mol. Biol. Evol. 28, 1141-1155
   Abstract »    Full Text »    PDF »
Information processing by biochemical networks: a dynamic approach.
C. G. Bowsher (2011)
J R Soc Interface 8, 186-200
   Abstract »    Full Text »    PDF »
Toward the dynamic interactome: it's about time.
T. M. Przytycka, M. Singh, and D. K. Slonim (2010)
Brief Bioinform
   Abstract »    Full Text »    PDF »
Science Signaling Podcast: 28 July 2009.
M. B. Yaffe and A. M. VanHook (2009)
Science Signaling 2, pc14
   Abstract »    Full Text »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882