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Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast

Ping Ye, Brian D Peyser, Forrest A Spencer, Joel S Bader
2005 BMC Bioinformatics  
Recently available large-scale data sets of genetic interactions and protein interactions in Saccharomyces cerevisiae provide a unique opportunity to elucidate the topological structure of biological pathways  ...  We have defined congruent genes as pairs of genes with similar sets of genetic interaction partners and constructed a genetic congruence network by linking congruent genes.  ...  networks.  ... 
doi:10.1186/1471-2105-6-270 pmid:16283923 pmcid:PMC1310633 fatcat:ivrgvexqbfaodnc56nxigmhvbi

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites

Manoj Tyagi, Ratna R. Thangudu, Dachuan Zhang, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko, Vladimir N. Uversky
2012 PLoS ONE  
of crystal parameters of the query protein.  ...  At the same time, about half of biological interfaces that are not present in the protein crystallographic asymmetric unit can be reconstructed by IBIS from homologous complexes without the prior knowledge  ...  At the same time about 45% of biological interfaces that are not present in the PDB asymmetric unit can be reconstructed by IBIS without the prior knowledge of crystal parameters of the query protein.  ... 
doi:10.1371/journal.pone.0028896 pmid:22303436 pmcid:PMC3269416 fatcat:662tgug3ujgwdktzkc5axdusl4

SIMCOMP/SUBCOMP: chemical structure search servers for network analyses

M. Hattori, N. Tanaka, M. Kanehisa, S. Goto
2010 Nucleic Acids Research  
The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks  ...  One of the greatest challenges in bioinformatics is to shed light on the relationship between genomic and chemical significances of metabolic pathways.  ...  ACKNOWLEDGEMENTS We thank Tomohiro Ohya and Yusuke Sugihara for helpful discussions on the graph isomorphism problem of chemical compounds. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq367 pmid:20460463 pmcid:PMC2896122 fatcat:7occz6qrlvg7dm5osg5eyhw5u4

Modeling cellular machinery through biological network comparison

Roded Sharan, Trey Ideker
2006 Nature Biotechnology  
The final mode of comparison is network querying, in which a given network is searched for subnetworks that are similar to a subnetwork query of interest 18 .  ...  However, and although sequence comparison has long been a staple of biological research, the development of a similar toolbox for comparing biological networks is still in its infancy.  ...  ., by the David and Lucille Packard Foundation. This work was also supported by the National Center for Research Resources (RR018627) and the National Science Foundation (NSF 0425926).  ... 
doi:10.1038/nbt1196 pmid:16601728 fatcat:4dlkuaeapvcgfjlbaf2rie5jza

The RCSB Protein Data Bank: redesigned web site and web services

P. W. Rose, B. Beran, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, J. D. Westbrook, J. Young, B. Yukich (+3 others)
2010 Nucleic Acids Research  
of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural  ...  This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export  ...  Finally, we thank other RCSB PDB staff past and present for suggestions, critical review and testing of new features.  ... 
doi:10.1093/nar/gkq1021 pmid:21036868 pmcid:PMC3013649 fatcat:aciwaivaenfubmhs2r3tc37qiu

An effective statistical evaluation of ChIPseq dataset similarity

Maria D. Chikina, Olga G. Troyanskaya
2012 Computer applications in the biosciences : CABIOS  
Our method is insensitive to non-biological variation in datasets such as peak width, and can rigorously model peak location biases by evaluating similarity conditioned on a restricted set of genomic regions  ...  By comparing ChIPseq data in an asymmetric way, we are able to observe clear interaction differences between cofactors such as p300 and factors that bind DNA directly.  ...  A principal difference between our method and alternative methods for determining statistical significance of peak distribution similarity is that our comparison is essentially asymmetric (the query and  ... 
doi:10.1093/bioinformatics/bts009 pmid:22262674 pmcid:PMC3339511 fatcat:5sqy2nz255gjdg2g2ere3lc6pe

Corbi: a new R package for biological network alignment and querying

Qiang Huang, Ling-Yun Wu, Xiang-Sun Zhang
2013 BMC Systems Biology  
best accuracy in terms of both nodes and networks.  ...  But the huge amount of network data have not been fully utilized due to the limited biological network analysis tools.  ...  The main extensions in this paper include the simulated data experiments and implementation of that methods in R package and web services.  ... 
doi:10.1186/1752-0509-7-s2-s6 pmid:24565104 pmcid:PMC3851956 fatcat:h7f75v7vofbzxhhdljq3uq2rzi

Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality

Yan Qi, Ping Ye, Joel S Bader
2005 BMC Bioinformatics  
Optimal choice of one single model parameter allows construction of gene networks with different levels of confidence.  ...  The impact of hub genes the generic probabilistic framework of GIMF may be used to group other types of biological entities such as proteins based on stochastic motifs.  ...  YQ acknowledges support from Institute for Pure and Applied Mathematics for a relevant workshop, IBM for a Ph.D fellowship and Dr. Jianbo Gao for stimulating discussions.  ... 
doi:10.1186/1471-2105-6-288 pmid:16332255 pmcid:PMC1334220 fatcat:ftxtaw3tfbcxdb74a5gtbgjwra


2013 Biocomputing 2014  
heterogeneous genomic and proteomic data sources. [8] [9] [10] [11] Here, one is given a set of genes (query) with a given annotation, and asked to find genes similar to the query.  ...  Experiments on multiple functional interaction networks from three species (mouse, fly, C.elegans) with tens of thousands of nodes and hundreds of binary prediction tasks demonstrate the efficacy of our  ...  Acknowledgments SV was supported by a Natural Science and Engineering Research Council of Canada operating grant to QM.  ... 
doi:10.1142/9789814583220_0037 fatcat:ios6qefnznfx3gixbdiy7obf4e

Rank-based edge reconstruction for scale-free genetic regulatory networks

Guanrao Chen, Peter Larsen, Eyad Almasri, Yang Dai
2008 BMC Bioinformatics  
In addition, in comparison with the Bayesian Network approach, the results show that the proposed algorithm gives much better recovery of the underlying network when sample size is much smaller relative  ...  Results: In this study, an algorithm that explores the scale-free topology of networks was proposed based on the modification of a rank-based algorithm for network reconstruction.  ...  Min Zou and Dr. Jing Yu for kindly sharing their source code and data [9, 33] . Additional file 1 Matlab fit() function.  ... 
doi:10.1186/1471-2105-9-75 pmid:18237422 pmcid:PMC2275249 fatcat:qs63sx2bvvdddn6qfrbfkf62xy

Idology and Its Applications in Public Security and Network Security [chapter]

Shenghui Su, Jianhua Zheng, Shuwang Lü, Zhiqiu Huang, Zhoujun Li, Zhenmin Tang
2017 Lecture Notes in Computer Science  
Draw a comparison between a symmetric identity and an asymmetric identity, and emphasize that a symmetric identity cannot guard against inside jobs.  ...  In this paper, the authors first propose the concept of idology  a systematic and scientific study of identifications of persons and things, and give the definitions of a symmetric identity and an asymmetric  ...  asymmetric identity such as a BFID and a biological characteristic.  ... 
doi:10.1007/978-3-319-57463-9_9 fatcat:zliukq3a2zbehjxt3y3dfxzcoa

Predicting genetic interactions with random walks on biological networks

Kyle C Chipman, Ambuj K Singh
2009 BMC Bioinformatics  
We apply our method to S. cerevisiae and C. elegans datasets and, using a decision tree classifier, integrate diverse biological networks and show that our method outperforms established methods.  ...  Building on previous studies that analyzed properties of network topology to predict genetic interactions, we apply random walks on biological networks to accurately predict pairwise genetic interactions  ...  Acknowledgements AS and KC designed the experiment. KC implemented the software and carried out the experiments. Both authors read and approved the final manuscript.  ... 
doi:10.1186/1471-2105-10-17 pmid:19138426 pmcid:PMC2653491 fatcat:bwgeuwi5kzdevgi4uclcxli3oq

Gene co-expression network analysis reveals pathways associated with graft healing by asymmetric profiling in tomato

Lulu Xie, Chunjuan Dong, Qingmao Shang
2019 BMC Plant Biology  
A large proportion of modules were related to Position, and represent asymmetric expression networks from different pathways.  ...  Conclusions: The present work provides a comprehensive understanding of graft healing-related gene networks in tomato.  ...  Authors' contributions QS and CD designed the research and collected the samples. LX analysed data and wrote the manuscript. All authors have read and approved the manuscript.  ... 
doi:10.1186/s12870-019-1976-7 fatcat:itrvah7z4bdj5h7ktuaupfidhm

Computational Inference of DNA Folding Principles: From Data Management to Machine Learning [chapter]

Luca Nanni
2022 SpringerBriefs in Applied Sciences and Technology  
We demonstrate a correlation between chromatin topology and co-expression, shedding a new light on this debated topic and providing a novel computational framework for the study of co-expression networks  ...  For this reason, understanding the mechanisms of genome folding is a major biological research problem.  ...  strategies and comparison with baselines.  ... 
doi:10.1007/978-3-030-85918-3_7 fatcat:yfcesphw3jdc5nsewcrd5lfjvy

A Scalable SDN Architecture for Underwater Networks Security Authentication

Qiuli CHEN, Ming HE, Xiang ZHENG, Fei DAI, Yuntian FENG
2018 IEICE transactions on information and systems  
Compared to some existing schemes, BSAM and SAM-PP can effectively distinguish between legal nodes and malicious nodes, save the storage space of nodes greatly, and improve the efficiency of network operation  ...  It realizes an organic combination of the knowledge level, control level, and data level. The new nodes can easily access the network, which could be conducive to large-scale deployment.  ...  The network used asymmetric key and hash function to realize the authentication of mobile cluster head. It had a high degree of security.  ... 
doi:10.1587/transinf.2017edp7359 fatcat:7tibmc4ljfezjkycmic6eke5xy
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