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Overlapping Replicator Dynamics for Functional Subnetwork Identification [chapter]

Burak Yoldemir, Bernard Ng, Rafeef Abugharbieh
2013 Lecture Notes in Computer Science  
We refer to our approach as overlapping replicator dynamics (RDOL). On synthetic data, we show that RDOL achieves higher accuracy in subnetwork identification than state-of-the-art methods.  ...  To address this limitation, we propose a novel approach based on replicator dynamics that facilitates detection of sparse overlapping subnetworks.  ...  In this paper, we propose a novel approach based on replicator dynamics (RD) [10] for identifying overlapping subnetworks.  ... 
doi:10.1007/978-3-642-40763-5_84 fatcat:dvvc6f2tbfcrxpjjjkmurzn6oa

Coupled Stable Overlapping Replicator Dynamics for Multimodal Brain Subnetwork Identification [chapter]

Burak Yoldemir, Bernard Ng, Rafeef Abugharbieh
2015 Lecture Notes in Computer Science  
We thus refer to our technique as coupled stable overlapping replicator dynamics (CSORD).  ...  We propose a multimodal integration technique based on a sex-differentiated formulation of replicator dynamics for identifying subnetworks of brain regions that exhibit high inter-connectivity both functionally  ...  Coupled Stable Overlapping Replicator Dynamics Since CRD is deterministic, reapplying it with the same initialization will converge to the same local maximum.  ... 
doi:10.1007/978-3-319-19992-4_61 fatcat:qcbcy67ksrcf3e65twombeez7y

Coactivated Clique Based Multisource Overlapping Brain Subnetwork Extraction [article]

Chendi Wang, Rafeef Abugharbieh
2018 arXiv   pre-print
We proposed a multisource subnetwork extraction approach based on the co-activated clique, which (1) uses task co-activation and task connectivity strength information for clique identification, (2) automatically  ...  Recent studies indicated that certain brain regions are known to interact with multiple subnetworks. However, most existing methods are mainly for non-overlapping subnetwork extraction.  ...  Ncuts Normalized cuts OSLOM Order Statistics Local Optimization Method RD Replicator Dynamics ROI region of interest RW Random Walker SORD Stable Overlapping Replicator Dynamics  ... 
arXiv:1801.09589v1 fatcat:hcrdghhhcvh6ncwl5lxe3iq2ee

Network-based integration of epigenetic landscapes unveils molecular programs underlying human T follicular helper cell differentiation [article]

Vinay S Mahajan, Syed A Rahman, Vinayak V Viswanadham, Grace J Yuen, Na Sun, Hamid Mattoo, Shiv S Pillai, Jishnu Das
2021 bioRxiv   pre-print
We find that human Tfh cell subnetworks are functionally associated with specific immune signaling cascades including cytokine receptor driven pathways.  ...  These subnetworks captured known Tfh cell drivers to a greater extent than conventional gene-centric analyses would, and also revealed novel modules that may be required for Tfh cell differentiation.  ...  Estimation of functional overlap between Tfh cell subnetworks and pathway databases We examined the functional overlap (where functional overlap was defined as either shared or directly interacting with  ... 
doi:10.1101/2021.05.19.444859 fatcat:kn4vkupzs5bwpbzsjtk2hty7u4

Unraveling reproducible dynamic states of individual brain functional parcellation

Amal Boukhdhir, Yu Zhang, Max Mignotte, Pierre Bellec
2020 Network Neuroscience  
Data-driven parcellations are widely used for exploring the functional organization of the brain, and also for reducing the high dimensionality of fMRI data.  ...  Taken together, our results indicate that static functional parcellations are incorrectly averaging well-defined and distinct dynamic states of brain parcellations.  ...  Scripts used in this study are available on GitHub (https://github.com/SIMEXP/dynamic-states -parcellations).  ... 
doi:10.1162/netn_a_00168 pmid:33688605 pmcid:PMC7935036 fatcat:cfzl4mqlmfd7lb4d6vqqemme5q

Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network

Junjie Su, Byung-Jun Yoon, Edward R Dougherty
2010 BMC Bioinformatics  
The overlapping linear paths are then optimally combined into subnetworks that can potentially serve as effective diagnostic markers.  ...  To overcome this problem, we propose a novel method for identifying reliable subnetwork markers in a human protein-protein interaction (PPI) network.  ...  In this paper, we propose a new method for identifying effective subnetwork markers from a PPI network by performing a global search for differentially expressed linear paths using dynamic programming.  ... 
doi:10.1186/1471-2105-11-s6-s8 pmid:20946619 pmcid:PMC3026382 fatcat:5qs2ykizozca7cv6eu3dlgu4qe

Unraveling reproducible dynamic states of individual brain functional parcellation [article]

Amal Boukhdhir, Yu Zhang, Max Mignotte, Pierre Bellec
2020 bioRxiv   pre-print
AbstractData-driven parcellations are widely used for exploring the functional organization of the brain, and also for reducing the high dimensionality of fMRI data.  ...  Taken together, our results indicate that static functional parcellations are incorrectly averaging well defined and distinct dynamic states of brain parcellations.  ...  ) for making MSC dataset available for our analysis.  ... 
doi:10.1101/2020.03.02.972760 fatcat:n7tszu32hnautljgocxravngle

Identification of highly synchronized subnetworks from gene expression data

Shouguo Gao, Xujing Wang
2013 BMC Bioinformatics  
Methods: Here we propose a topology-phase locking (TopoPL) based scoring metric for identifying active PPI subnetworks from time series expression data.  ...  However the interaction dynamics during the biological process under study has not been sufficiently considered previously.  ...  These results suggest that degree and betweenness can be utilized to further improve the performance of functional gene module identification.  ... 
doi:10.1186/1471-2105-14-s9-s5 pmid:23901792 pmcid:PMC3698028 fatcat:ypolh6kzufenpphp4icyplr6me

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome [article]

Edward L Huttlin, Raphael J. Bruckner, José Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab, Melanie P. Gygi, Alexandra Thornock, Gabriela Zárraga, Stanley Tam, John Szpyt, Alexandra Panov (+14 others)
2020 bioRxiv   pre-print
Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome.  ...  These networks model the interactome at unprecedented scale, encoding protein function, localization, and complex membership.  ...  ACKNOWLEDGEMENTS We thank Marc Vidal and David Hill for ORFeome 8.1 and acknowledge the Nikon Imaging Center (Harvard Medical School) for imaging support.  ... 
doi:10.1101/2020.01.19.905109 fatcat:7j6x5gmto5ajpi2vleksdrx2ja

A Dynamic Neural Network Designed Using Analytical Methods Produces Dynamic Control Properties Similar to an Analogous Classical Controller

Wade W. Hilts, Nicholas S. Szczecinski, Roger D. Quinn, Alexander J. Hunt
2019 IEEE Control Systems Letters  
It is our hypothesis that the analytical methods we have developed, combined with classical control techniques will provide a reasonable starting point for developing dynamic neural controllers that can  ...  In previous work, we tested this hypothesis and demonstrated that a biologically constrained neural controller that replicates human balance control characteristics is achievable.  ...  METHODS FOR SYSTEM IDENTIFICATION AND CONTROLLER DESIGN A.  ... 
doi:10.1109/lcsys.2018.2871126 fatcat:gdxrppzv5bd73cc22fhpm5gh7u

Comparing host module activation patterns and temporal dynamics in infection by influenza H1N1 viruses [article]

Irina Nudelman, Daniil Kudrin, German Nudelman, Raamesh Deshpande, Boris M. Hartmann, Steven H. Kleinstein, Chad L. Myers, Stuart C. Sealfon, Elena Zaslavsky
2021 bioRxiv   pre-print
Understanding similarities and differences among activated functional pathways in the host responses can help elucidate therapeutic targets responsible for pathogenesis.  ...  To compare the types and timing of functional modules activated in host cells by four influenza viruses of varying pathogenicity, we developed a new DYNAmic MOdule (DYNAMO) method that addresses the need  ...  We then compared temporal dynamics and functional pathway activity, computed 259 as GO term enrichment of discovered modules, for all the strains.  ... 
doi:10.1101/2021.05.07.443162 fatcat:yl775ulb7zd6pivmadjoid5sdq

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data

Min Li, Xuehong Wu, Jianxin Wang, Yi Pan
2012 BMC Bioinformatics  
Identification of protein complexes and functional modules from protein-protein interaction (PPI) networks is crucial to understanding the principles of cellular organization and predicting protein functions  ...  A series of time-sequenced subnetworks (TSNs) is constructed according to the time that the interactions were activated.  ...  Acknowledgements The authors would like to thank Matthew Sartin for useful discussions and carefully proofreading the manuscript.  ... 
doi:10.1186/1471-2105-13-109 pmid:22621308 pmcid:PMC3434013 fatcat:6oe5dzytlvhankzfe6rjjsscce

Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens

Deborah Chasman, Kevin B. Walters, Tiago J. S. Lopes, Amie J. Eisfeld, Yoshihiro Kawaoka, Sushmita Roy, Christina S. Leslie
2016 PLoS Computational Biology  
Regulators with evidence for influenza relevance are shaded in pink.  ...  We used the networks to study time point and strain-specific subnetworks and to prioritize important regulators of host response.  ...  Acknowledgments We thank Dylan Pozorski for constructing the supporting website, Michael Ferris for sharing computational resources for ILP modeling and solving, and Center for High-Throughput Computing  ... 
doi:10.1371/journal.pcbi.1005013 pmid:27403523 pmcid:PMC4942116 fatcat:7nrdzkbzjjawvm3toqzv3b2xkm

Contextual connectivity: A framework for understanding the intrinsic dynamic architecture of large-scale functional brain networks [article]

Rastko Ciric, Jason Nomi, Lucina Uddin, Ajay Satpute
2016 bioRxiv   pre-print
Our assay for functional autonomy of coordinated neural systems is broadly applicable across populations, and our findings provide evidence of structure in temporal dynamics that complements the well-described  ...  Here, we used tools from connectivity dynamics to develop a synthesis that bridges these models.  ...  Second, whereas time-averaged approaches resolve networks into spatially non-overlapping subnetworks, our analysis permits spatial overlaps between nodes.  ... 
doi:10.1101/068320 fatcat:fyla5hhz4faidl7td4ksydyqmu

Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus

C. Li, A. Bankhead, A. J. Eisfeld, Y. Hatta, S. Jeng, J. H. Chang, L. D. Aicher, S. Proll, A. L. Ellis, G. L. Law, K. M. Waters, G. Neumann (+3 others)
2011 Journal of Virology  
Here, we leveraged a system approach to identify and statistically validate signaling subnetworks that define the dynamic transcriptional response of human bronchial epithelial cells after infection with  ...  for fatal HPAI H5N1 disease.  ...  Twelve modules were identified as host response subnetworks that are significantly connected using the topological overlap measure.  ... 
doi:10.1128/jvi.05792-11 pmid:21865398 pmcid:PMC3194976 fatcat:jdds3blxwfdu5mvcfmyeygis3e
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