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Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback

Gil Hornung, Naama Barkai
2008 PLoS Computational Biology  
Citation: Hornung G, Barkai N (2008) Noise propagation and signaling sensitivity in biological networks: A role for positive feedback. PLoS Comput Biol 4(1): e8.  ...  As the design of biological networks optimizes for multiple constraints, positive feedback can be used to improve sensitivity without a compromise in the ability to buffer propagated noise.  ...  We thank Andreas Doncic for helping with the screen design and critical review of the manuscript, and Nitzan Rosenfeld, Sagi Levi, Ran Kafri and members of our lab for comments and discussion.  ... 
doi:10.1371/journal.pcbi.0040008 pmid:18179281 pmcid:PMC2174979 fatcat:nev2jhjkajfjlfuwuzcju3tbgu

Noise propagation and signaling sensitivity in biological networks: A role for positive feedback

Gil Hornung, Naama Barkai
2005 PLoS Computational Biology  
Citation: Hornung G, Barkai N (2008) Noise propagation and signaling sensitivity in biological networks: A role for positive feedback. PLoS Comput Biol 4(1): e8.  ...  As the design of biological networks optimizes for multiple constraints, positive feedback can be used to improve sensitivity without a compromise in the ability to buffer propagated noise.  ...  We thank Andreas Doncic for helping with the screen design and critical review of the manuscript, and Nitzan Rosenfeld, Sagi Levi, Ran Kafri and members of our lab for comments and discussion.  ... 
doi:10.1371/journal.pcbi.0040008.eor fatcat:ygkfze6nzbha7jn34k37rtyydm

Noise Propagation in Gene Regulation Networks Involving Interlinked Positive and Negative Feedback Loops

Hui Zhang, Yueling Chen, Yong Chen, Kumar Selvarajoo
2012 PLoS ONE  
Interlinked positive and negative feedback loops are essential signal transduction motifs in biological networks.  ...  Here, by using the signal sensitivity (susceptibility) and noise amplification to quantify noise propagation, we analyze an abstract model of the Myc/E2F/MiR-17-92 network that is composed of a coupling  ...  Feedback loops play a critical role in noise propagation.  ... 
doi:10.1371/journal.pone.0051840 pmid:23284787 pmcid:PMC3527455 fatcat:6spu2xz4znbpnke6za3f5ynmjm

Defining Biological Networks for Noise Buffering and Signaling Sensitivity Using Approximate Bayesian Computation

Shuqiang Wang, Yanyan Shen, Changhong Shi, Tao Wang, Zhiming Wei, Hanxiong Li
2014 The Scientific World Journal  
By systematically analyzing three-component circuits, we rank these biological circuits and identify three-basic-biological-motif buffering noise while maintaining sensitivity to long-term changes in input  ...  Here, we employ the approximate Bayesian computation (ABC) method based on sequential Monte Carlo (SMC) to search for biological circuits that can maintain signaling sensitivity while minimizing noise  ...  Acknowledgment This work was supported by a GRF project from Hong Kong SAR (Cityu 117310).  ... 
doi:10.1155/2014/625754 pmid:24995358 pmcid:PMC4068073 fatcat:yg2j6svizrdjjjvn5f2vlyljcm

NEURAL NETWORK DYNAMICS

Tim P. Vogels, Kanaka Rajan, L.F. Abbott
2005 Annual Review of Neuroscience  
oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits.  ...  We also review propagation of stimulus-driven activity through spontaneously active networks.  ...  ACKNOWLEDGMENTS Research was supported by the National Science Foundation (IBN-0235463), an NIH Pioneer Award, and the Swartz Foundation.  ... 
doi:10.1146/annurev.neuro.28.061604.135637 pmid:16022600 fatcat:saonmh5e3zbjzgdbyiqehlxrvy

Modeling and Dynamical Analysis of Molecular Networks [chapter]

Ruiqi Wang, Xing-Ming Zhao, Zengrong Liu
2009 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
In recent years, many progress have been made in systematic approaches and high-throughput technologies for systematic studying complex molecular networks.  ...  This paper presents a brief survey on recent developments on modeling and analyzing complex molecular networks mainly from global and dynamical properties of complex molecular networks.  ...  Acknowledgements This work was supported by the National Natural Science Foundation of China (Youth Research Grant 10701052), Shanghai Pujiang Program, and the Innovation Fund of Shanghai University.  ... 
doi:10.1007/978-3-642-02469-6_90 fatcat:57tnb4skmvas3a4hppbti63ftu

Frequency Domain Analysis of a Stochastic Biological Network Motif with Delay [chapter]

Qi Wang, Shiwei Yan, Shengjun Liu, Xian Li
2009 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
The aim of this paper is to incorporate the effects of time delays and feedback into a general biological network motif.  ...  dynamics within a general biological network motif.  ...  Effect of Time Delay It has been well recognized that time delay plays a very significant role in the dynamics of biological networks.  ... 
doi:10.1007/978-3-642-02469-6_50 fatcat:6flnhygcg5eidnj27ahesf6lhy

The Computational Versatility of Proteomic Signaling Networks

Herbert Sauro
2004 Current Protoemics  
In this article I wish to summarize the great versatility of the basic protein cycle as a means to construct complex functional behaviors including the central role that feedback plays in determining the  ...  Almost all proteomic signaling networks in prokaryotes and eukaryotes are based on the simple phosphorylation/dephosporylation cycle; from this simple unit it is possible to construct a huge variety of  ...  There are now a number of instances where positive feedback plays a critical role in the functioning of signaling pathways.  ... 
doi:10.2174/1570164043488315 fatcat:7olvri25fja73k6w7yyzjithuu

Quantitative analysis of signaling networks

H SAURO
2004 Progress in Biophysics and Molecular Biology  
The response of biological cells to environmental change is coordinated by protein based signaling networks. These networks are to be found in both prokaryotes and eukaryotes.  ...  In eukaryotes the signaling networks can be highly complex, some networks comprising of sixty or more proteins.  ...  Acknowledgements We are very grateful to John Doyle, Hana El-Samad, Mustafa Khammash, Tau-Mu Yi and Chris Rao for useful and most simulating discussions.  ... 
doi:10.1016/j.pbiomolbio.2004.03.002 pmid:15261524 fatcat:ojdg7iqjerffnn7pq36xemvrvy

Digital signaling network drives the assembly of the AIM2-ASC inflammasome

Mariusz Matyszewski, Seamus R. Morrone, Jungsan Sohn
2018 Proceedings of the National Academy of Sciences of the United States of America  
Author contributions: J.S. designed research; M.M. and S.R.M. performed research; S.R.M. contributed new reagents/analytic tools; M.M., S.R.M., and J.S. analyzed data; and M.M., S.R.M., and J.S. wrote  ...  Greene Foundation and American Cancer Society Research Scholars Grant DMC-RG-15-224 (to J.S.).  ...  It is also noteworthy that positive feedback loops are known to promote binary responses, hysteresis, and noise attenuation in both biological and electrical pathways (5, 24, 33) .  ... 
doi:10.1073/pnas.1712860115 pmid:29440442 pmcid:PMC5834677 fatcat:mz6n2ck4dnf7varsvqfgd2e42a

The role of stochastic sequestration dynamics for intrinsic noise filtering in signaling network motifs [article]

Debdas Paul, Nicole Radde
2018 bioRxiv   pre-print
Overall, this study reveals a novel role of stochastic sequestration for dynamic noise filtering in signaling cascade motifs.  ...  The relation between design principles of signaling network motifs and their robustness against intrinsic noise still remains illusive.  ...  DP and NR designed the study and wrote the main part of the manuscript. All authors discussed the results and implications and commented on the manuscript at all stages of the project.  ... 
doi:10.1101/278929 fatcat:swgwx4wwovcbzip3yg4645w3me

A more biologically plausible learning rule for neural networks

P. Mazzoni, R. A. Andersen, M. I. Jordan
1991 Proceedings of the National Academy of Sciences of the United States of America  
The network behaves similarly to networks trained by using back-propagation and to neurons recorded in area 7a.  ...  These results show that a neural network does not require back propagation to acquire biologically interesting properties.  ...  Similarly, the noise in neuronal activity may play an important role in biological learning.  ... 
doi:10.1073/pnas.88.10.4433 pmid:1903542 pmcid:PMC51674 fatcat:fmkusfvkfzfg7piqa4wyagxnvu

Applications of Artificial Neural Networks: A Review

Rajan Dharwal, Loveneet Kaur
2016 Indian Journal of Science and Technology  
Findings: Artificial neural network has a significant role in medical area.  ...  Objectives: The objective of this research paper is study the different methods related to artificial neural network used for prediction and detection of the lung cancer in its early stages so that survival  ...  Biological neural networks are made up of these real biological neurons, one neuron makes connections with other neurons and signals are propagated between them.  ... 
doi:10.17485/ijst/2015/v8i1/106807 fatcat:iwpy2c47nfctrj52jomaw6vymy

Noise Filtering and Prediction in Biological Signaling Networks

David Hathcock, James Sheehy, Casey Weisenberger, Efe Ilker, Michael Hinczewski
2016 IEEE Transactions on Molecular, Biological and Multi-Scale Communications  
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter.  ...  The idea of a biochemical noise filter is actually more than just a metaphor: we describe recent work that has made an explicit mathematical connection between signaling fidelity in cellular circuits and  ...  ACKNOWLEDGMENT The authors would like to thank Dave Thirumalai, Shishir Adhikari, Tenglong Wang, Benjamin Kuznets-Speck, and Joseph Broderick for useful discussions.  ... 
doi:10.1109/tmbmc.2016.2633269 dblp:journals/tmbmc/HathcockSWIH16 fatcat:7fuofvwm5fezldcmc5z7aqd5oy

Noise-Driven Causal Inference in Biomolecular Networks

Robert J. Prill, Robert Vogel, Guillermo A. Cecchi, Grégoire Altan-Bonnet, Gustavo Stolovitzky, Alberto de la Fuente
2015 PLoS ONE  
A model that by design does not incorporate feedback loops, would likely fail to approximate reality when feedbacks indeed exist and play a role in the causal relationships.  ...  We report the first analysis of covariance elements documenting noise propagation from a kinase to a phosphorylated substrate in an endogenous mammalian signaling network. prohibited [3]-that represent  ...  The specific roles of these authors are articulated in the 'author contributions' section. R.V. and G.A.B. acknowledge support from NIH AI083408 and U54 CA148967.  ... 
doi:10.1371/journal.pone.0125777 pmid:26030907 pmcid:PMC4452541 fatcat:gh3qkw3f2ncuncjfs4ab7eom4y
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