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A new computational model captures fundamental architectural features of diverse biological networks

Al-Anzi, Bader and Olsman, Noah and Ormerod, Christopher and Gerges, Sherif and Piliouras, Georgios and Ormerod, John and Zinn, Kai (2016) A new computational model captures fundamental architectural features of diverse biological networks. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20160516-072304246

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Abstract

Complex biological systems are often represented by network graphs. However, their structural features are not adequately captured by existing computational graph models, perhaps because the datasets used to assemble them are incomplete and contain elements that lack shared functions. Here, we analyze three large, near-complete networks that produce specific cellular or behavioral outputs: a molecular yeast mitochondrial regulatory protein network, and two anatomical networks of very different scale, the mouse brain mesoscale connectivity network, and the C. elegans neuronal network. Surprisingly, these networks share similar characteristics. All consist of large communities composed of modules with general functions, and topologically distinct subnetworks spanning modular boundaries responsible for their more specific phenotypical outputs. We created a new model, SBM-PS, which generates networks by combining communities, followed by adjustment of connections by a path selection mechanism. This model captures fundamental architectural features that are common to the three networks.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1101/046813DOIDiscussion Paper
ORCID:
AuthorORCID
Zinn, Kai0000-0002-6706-5605
Additional Information:The copyright holder for this preprint is the author/funder. All rights reserved. No reuse allowed without permission. bioRxiv preprint first posted online Apr. 2, 2016. This work was supported by a grant from the NIH, R21NS083874, to K. Z., and by the Della Martin Foundation. We also like to acknowledge NVIDIA Corporation for generously donating the NVIDIA GTX980 Graphics Card used in this study.
Funders:
Funding AgencyGrant Number
NIHR21NS083874
Della Martin FoundationUNSPECIFIED
NVIDIAUNSPECIFIED
Record Number:CaltechAUTHORS:20160516-072304246
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160516-072304246
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:67094
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:16 May 2016 18:50
Last Modified:03 Oct 2019 10:02

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