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CellCircuits: a database of protein network models

H. C. Mak, M. Daly, B. Gruebel, T. Ideker
2007 Nucleic Acids Research  
CellCircuits ( is an openaccess database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases  ...  We demonstrate how such a repository of network models is a novel systems biology resource by performing several meta-analyses not currently possible with existing databases.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl937 pmid:17135207 pmcid:PMC1751555 fatcat:2jfmnrpwarakzm6f7noeedonsa

Update of KDBI: Kinetic Data of Bio-molecular Interaction database

P. Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, Y. Z. Chen
2009 Nucleic Acids Research  
Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein-protein, proteinnucleic acid, protein-ligand,  ...  simulation models of 63 pathways, and 2.3-fold increase of data (19 263 entries of 10 532 distinctive biomolecular binding and 11 954 interaction events, involving 2635 proteins/protein complexes, 847  ...  Kinetic data in KDBI have been manually collected from literatures, a substantial percentage of which are not yet available in other databases (e.g. some protein-protein interactions in thrombin, translation  ... 
doi:10.1093/nar/gkn839 pmid:18971255 pmcid:PMC2686478 fatcat:t4jlakihprgtvihi4xgui7dgzm

Taking Bioinformatics to Systems Medicine [chapter]

Antoine H. C. van Kampen, Perry D. Moerland
2016 Msphere  
Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing  ...  lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine.  ...  There have been some initial attempts in building databases of network models, for example the CellCircuits database [ 123 ] ( ) and the causal biological networks (CBN) database  ... 
doi:10.1007/978-1-4939-3283-2_2 pmid:26677177 pmcid:PMC7120931 fatcat:w2l6fz4iobg5nnxtz5lscjhe6y

Network-based classification of breast cancer metastasis

Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee, Trey Ideker
2007 Molecular Systems Biology  
Here, we apply a proteinnetwork-based approach that identifies markers not as individual genes but as subnetworks extracted from protein interaction databases.  ...  Although genes with known breast cancer mutations are typically not detected through analysis of differential expression, they play a central role in the protein network by interconnecting many differentially  ...  TI was additionally supported by a David and Lucille Packard Fellowship.  ... 
doi:10.1038/msb4100180 pmid:17940530 pmcid:PMC2063581 fatcat:x2j5b4cgovfz7mwrmdyp44ptbq

An Integrated Systems Analysis Implicates EGR1 Downregulation in Simian Immunodeficiency Virus Encephalitis-Induced Neural Dysfunction

M. Gersten, M. Alirezaei, M. C. G. Marcondes, C. Flynn, T. Ravasi, T. Ideker, H. S. Fox
2009 Journal of Neuroscience  
In this study we integrate gene expression data from uninfected and SIV-infected hippocampus with a human protein interaction network and discover modules of genes whose expression patterns distinguish  ...  Integration of expression data with protein interaction data to discover discriminatory modules of interacting proteins can be usefully used to prioritize differentially expressed genes for further study  ...  The human protein interaction network was compiled using the following sources: Human Protein Reference Database (HPRD, 01JAN07) (Peri et al., 2003) , Biomolecular Interaction Network Database (BIND,  ... 
doi:10.1523/jneurosci.3180-09.2009 pmid:19812322 pmcid:PMC2802851 fatcat:nuyrgaifo5gvlpbj73v72gfu7e


Wiwanitkit House, Viroj Wiwanitkit
2009 unpublished
In this work, a systematic network creation for human insulin receptor substrate 1 by systemic biology technique was performed.  ...  Of interest, the relation of diabetes to some identified genes can be seen. In addition, identified relation to some genes implies a correlation between IRS-1 and cancer.  ...  After validation of IRS-1 gene in PubMed, the procedure used by the author was the systematic search of molecular interactions in a publicly available database, using the CellCircuits software (  ... 

An Overview of Systems Biology [chapter]

Rka Albert, Sarah M. Assmann
Plant Systems Biology  
A representative sample of biological network models is provided, ranging from static models to dynamic models that incorporate how the status of the nodes changes in time.  ...  This chapter provides an overview of three crucial aspects of systems biology: constructing biological networks, analyzing and modeling the structure of biological networks, and modeling the dynamics of  ...  A recently developed database, CellCircuits, offers a repository of network models spanning yeast, worm, fly, Plasmodium falciparum, and human, and four types of interaction 140 .  ... 
doi:10.1002/9781444312249.ch2 fatcat:gkkofhnxs5glxhf2yjtnk66rnq

Orthologous pair transfer and hybrid Bayes methods to predict the protein-protein interaction network of the Anopheles gambiae mosquitoes

Qiuxiang Li, Andrea Crisanti, Stephen Muggleton, ORS Scholarship
interaction network of the Anopheles gambiae (A. gambiae) mosquitoes.  ...  The second strategy, namely the hybrid Bayes, is based on the domain composition of proteins, with which we utilize a probability model to build virtual domain-domain maps by integrating large-scale protein  ...  On the pathway side, CellCircuits [118] database provides free access to molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases  ... 
doi:10.25560/4635 fatcat:s3ny2ihss5fflbj4qw42kaabbi