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The Interplay between Microscopic and Mesoscopic Structures in Complex Networks

Jörg Reichardt, Roberto Alamino, David Saad, Olaf Sporns
2011 PLoS ONE  
Disentangling single node from group properties is crucial for network modeling and structural inference.  ...  Furthermore, the inclusion of hitherto neglected group specific effects in models used to assess the statistical significance of small subgraph (motif) distributions in networks may be sufficient to explain  ...  White, and J.P. Crutchfield for stimulating discussions. J.R. thanks the members of the Complexity Sciences Center at UC Davis for their hospitality. Author Contributions  ... 
doi:10.1371/journal.pone.0021282 pmid:21829597 pmcid:PMC3148213 fatcat:v66tzbzat5fdtppgyx6cuqdmum

Generating confidence intervals on biological networks

Thomas Thorne, Michael PH Stumpf
2007 BMC Bioinformatics  
It can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central.  ...  which reflect the relative importance of intra-category versus inter-category connections.  ...  In order to assess the CIs for motifs, however, an explicit incorporation of the network is generally necessary and only the third approach can be used.  ... 
doi:10.1186/1471-2105-8-467 pmid:18053130 pmcid:PMC2241843 fatcat:ebcbyfdjirhmjdqdbv3bx4bhzu

The limits of subfunctionalization

Thomas MacCarthy, Aviv Bergman
2007 BMC Evolutionary Biology  
The duplication-degeneration-complementation (DDC) model has been proposed as an explanation for the unexpectedly high retention of duplicate genes.  ...  We distinguish between subfunctionalization at the regulatory level and at the product level (e.g within temporal or spatial expression domains).  ...  Clearly, if H i declines and connectivity remains the same (D = 0), then neofunctionalization must be playing an important role.  ... 
doi:10.1186/1471-2148-7-213 pmid:17988397 pmcid:PMC2213666 fatcat:nkxtn4bgebdf5ipr3stiecox74

Molecular Evolution of Helix–Turn–Helix Proteins

James A. Rosinski, William R. Atchley
1999 Journal of Molecular Evolution  
The consequences of such an origin for a diverse group of proteins, and guidelines for the identification of future members of the HTH family are discussed.  ...  Herein, we analyze this large and diverse family with a combination of traditional phylogenetic techniques and newer sequence analysis tools to determine whether the helix-turn-helix family arose from  ...  Jeff Thorne, and Dr. Kurt Wollenberg for numerous helpful discussions and comments on the manuscript. This work was supported by NIH Grant 5-46472.  ... 
doi:10.1007/pl00006552 pmid:10473770 fatcat:sbqldyrkhzhwjdpozggq32akoa

A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining

Bor-Sen Chen, Shih-Kuang Yang, Chung-Yu Lan, Yung-Jen Chuang
2008 BMC Medical Genomics  
Elucidating the mechanisms underlying systemic inflammation has long been an important topic in basic and clinical research.  ...  Such network will be essential for us to extract valuable information from the complex and chaotic network under diseased conditions.  ...  This study was supported by an NSC grant No. NSC 96-2627-B-007-004  ... 
doi:10.1186/1755-8794-1-46 pmid:18823570 pmcid:PMC2567339 fatcat:57j4weua7rdr7mu7qd37izvswi

Mechanisms of Zero-Lag Synchronization in Cortical Motifs

Leonardo L. Gollo, Claudio Mirasso, Olaf Sporns, Michael Breakspear, Boris S. Gutkin
2014 PLoS Computational Biology  
Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain.  ...  The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free  ...  Honey for technical assistance and helpful discussions, and Andrew Zalesky for discussions and a careful reading of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1003548 pmid:24763382 pmcid:PMC3998884 fatcat:q6wmuwfti5dnxlqyfxe6lepjmq

Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes

Melanie J. Pierson, Rosa Martinez-Arias, Barbara R. Holland, Neil J. Gemmell, Matthew E. Hurles, David Penny
2006 Molecular biology and evolution  
Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a  ...  To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes  ...  Thanks are also due to Glenn Conner for implementing the changes to the MMS program and to Lisa Matisoo-Smith for valuable discussions and guidance on issues in Pacific prehistory and scholarship support  ... 
doi:10.1093/molbev/msl063 pmid:16855009 pmcid:PMC2674580 fatcat:5olqnfyd7bgs5cim2o3zqebifu

Discovering functions and revealing mechanisms at molecular level from biological networks

Shihua Zhang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen
2007 Proteomics  
The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function  ...  prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.  ...  As an important challenging problem of reverse engineering, a variety of models have been developed for this problem, such as the simple Boolean network model and dynamic Bayesian network model [100,  ... 
doi:10.1002/pmic.200700095 pmid:17703505 fatcat:spdclsqf4rdjxkxa7sts4c5u6q

A bioinformatics approach reveals novel interactions of the OVOL transcription factors in the regulation of epithelial – mesenchymal cell reprogramming and cancer progression

Hernan Roca, Manjusha Pande, Jeffrey S Huo, James Hernandez, James D Cavalcoli, Kenneth J Pienta, Richard C McEachin
2014 BMC Systems Biology  
Conclusions: We find significant evidence of the OVOL, AP1, STAT1, STAT3, and NFKB1 TFs having important roles in MET, and more broadly in cancer.  ...  Reflecting these results back to the OI-MET model, we found that binding motifs for the TF pair AP1/MYC are more frequent than expected and that the AP1/MYC pair is significantly enriched in binding in  ...  Acknowledgements We thank our colleagues, Melissa Coon and Brendan Tarrier at the University of Michigan DNA Sequencing Core.  ... 
doi:10.1186/1752-0509-8-29 pmid:24612742 pmcid:PMC4008156 fatcat:oqmvy6d5zfcqplzeoym62tozbi

A Survey of Graph Mining Techniques for Biological Datasets [chapter]

S. Parthasarathy, S. Tatikonda, D. Ucar
2010 Managing and Mining Graph Data  
The field of bioinformatics has emerged as important application area in this context. Examples abound ranging from the analysis of protein interaction networks to the analysis of phylogenetic data.  ...  We conclude this article with a discussion of the key results and identify some interesting directions for future research.  ...  Thus, identifying and studying groups of highly-interacting genes in co-expression networks is an important step towards characterizing genes at a global scale.  ... 
doi:10.1007/978-1-4419-6045-0_18 dblp:series/ads/ParthasarathyTU10 fatcat:aeu53r3dbzd67d5whkjypv64uq

Neuron Geometry Underlies a Universal Local Architecture in Neuronal Networks [article]

Eyal Gal, Rodrigo Perin, Henry Markram, Michael London, Idan Segev
2019 bioRxiv   pre-print
We concluded that the local geometry of cortical neurons imposes an innate, highly structured, global network structure, a skeleton upon which fine-grained structural and functional plasticity processes  ...  Using graph-theoretical and machine-learning tools, we developed a series of progressively more complex generative models for circuit connectivity that considers the geometry of cortical neurons.  ...  ACKNOWLEDGEMENTS We thank Oren Amsalem, Toviah Moldwin, Hanan Shteingart and all lab members of the Segev and London labs for many fruitful discussions and valuable feedback regarding this work.  ... 
doi:10.1101/656058 fatcat:vf4elmkn5zcercjm6pnschx46q

Estimating gene regulatory networks with pandaR

Daniel Schlauch, Joseph N Paulson, Albert Young, Kimberly Glass, John Quackenbush
2017 Bioinformatics  
PANDA is used to estimate networks for each experimental group and the network models are then compared between groups to explore transcriptional processes that distinguish the groups.  ...  PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that begins with a model of transcription factor-target gene interactions and uses message  ...  National Cancer Institute [5P50CA127003, 1R35CA197449, 1U01CA190234, 5P30CA006516]; and the National Institute of Allergy and Infectious Disease [5R01AI099204].  ... 
doi:10.1093/bioinformatics/btx139 pmid:28334344 pmcid:PMC5870629 fatcat:56tkf7q7vzhrnib4y5vyxxnbbi

The diversity bonus in pooling local knowledge about complex problems

Payam Aminpour, Steven A. Gray, Alison Singer, Steven B. Scyphers, Antonie J. Jetter, Rebecca Jordan, Robert Murphy, Jonathan H. Grabowski
2021 Proceedings of the National Academy of Sciences of the United States of America  
Evaluation via stochastic network analysis also indicated that a diverse group more adequately modeled complex feedbacks and interdependencies than homogeneous groups.  ...  We also highlight that diversity must be moderated through a proper aggregation process, leading to more complex yet parsimonious models.  ...  We thank all the fishers, managers, and the fisheries scientific experts who participated in our study; the Marine Science Center at Northeastern University; and many other colleagues for assistance and  ... 
doi:10.1073/pnas.2016887118 pmid:33495329 fatcat:zuyau4gakbfibfxv66dg2lp7qi

Complex networks and simple models in biology

Eric de Silva, Michael P.H. Stumpf
2005 Journal of the Royal Society Interface  
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.  ...  Here, we will discuss how network information can be described and to some extent quantified.  ...  In part a of figure 2 we show the possible motifs that can occur between three nodes in a directed network; part b of the same figure shows the four-node motifs in an undirected network.  ... 
doi:10.1098/rsif.2005.0067 pmid:16849202 pmcid:PMC1618496 fatcat:y4ttvdajwfaxlpt62v2q5isj3u

Model of interactions in biology and application to heterogeneous network in yeast

Serge Smidtas, Anastasia Yartseva, Vincent Schächter, François Képès
2006 Comptes rendus. Biologies  
Here, MIB, the Model of Interactions in Biology, a bipartite model of biological networks, is introduced, and its use for topological analysis of the heterogeneous network is presented.  ...  Heterogeneous loops and links between synexpression pattern and underlying molecular mechanisms are proposed. Resumé Modèle de réseaux d'Interactions Biologiques.  ...  An occurrence of a motif M in the MIB model N = {(X N , Y N ), E N } is a sub network O = {(X O ⊂ X N , Y O ⊂ Y N ), E O ⊂ E N } and two bijections B X : X O → X M and B Y : Y O → Y M can be established  ... 
doi:10.1016/j.crvi.2006.06.010 pmid:17126798 fatcat:g3hpwc5puvcfjhjd3lbynnmmrm
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