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Multi-comparative systems biology analysis reveals time-course biosignatures of in vivo bovine pathway responses to B.melitensis, S.enterica Typhimurium and M.avium paratuberculosis
2011
BMC Proceedings
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This paper presents the application of systems biology for the cross-comparative analysis and interactome modeling of three different infectious agents, leading to the identification of novel, unique and ...
: To decipher the complexity and improve the understanding of host-pathogen interactions, biologists must adopt new system level approaches in which the hierarchy of biological interactions and dynamics ...
Acknowledgements The animal study was supported by U.S. Department of Homeland Security ...
doi:10.1186/1753-6561-5-s4-s6
pmid:21645321
pmcid:PMC3108236
fatcat:jl4raavqkfdgbpbyobrj5qfvhu
Enhancing the role of veterinary vaccines reducing zoonotic diseases of humans: Linking systems biology with vaccine development
2011
Vaccine
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The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis as such are classic examples of worldwide zoonoses for application of a systems biology approach for enhanced ...
The goal of this paper is to evaluate the role of computational systems biology analysis of host:pathogen interactions (the interactome) as a tool for enhanced rational design of vaccines. ...
Department of Homeland Security -National Center of Excellence for Foreign Animal and Zoonotic Disease (FAZD) Defense grant ONR-N00014-04-1-0. ...
doi:10.1016/j.vaccine.2011.05.080
pmid:21651944
pmcid:PMC3170448
fatcat:j4imwmzm45bk5f4uqyde2s2y5e
The application of systems biology to drug discovery
2006
Current Opinion in Chemical Biology
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Acknowledgements We thank Mark S Boguski and Alan Buckler for their input and support during the writing of this review. ...
Experimental methods Experimental approaches in systems biology are generally aimed at identifying the components of a system and their interactions, and monitoring the effect of perturbations on these ...
mutations) represents a well established approach to study a system through the analysis of naturally occurring perturbations. ...
doi:10.1016/j.cbpa.2006.06.025
pmid:16822703
fatcat:7phoojuwvbeqhdfljt4oikcnaq
Systems biology approach: Panacea for unravelling host-virus interactions and dynamics of vaccine induced immune response
2016
Gene Reports
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Systems biology is an interdisciplinary research field in life sciences, which involves a comprehensive and quantitative analysis of the interactions between all of the components of biological systems ...
Hence the intricacies of signalling pathways can be dissected only by system level approaches. ...
Viral infection is a systems-level perturbation, and therefore systems biology approaches are naturally suited for studying the complexity of viral host interactions. ...
doi:10.1016/j.genrep.2016.08.002
pmid:32289096
pmcid:PMC7104209
fatcat:brqn4pgszvax5hqojrwzs75nle
A Parallel Algorithm for Reverse Engineering Gene Regulatory Networks
2012
Biophysical Journal
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Thus, 2D-diffusion of membrane-bound proteins, complexes and effectors plays a central role in signaling biology. ...
We have proposed that single molecule analysis of membrane protein diffusion on supported lipid bilayers could provide a powerful approach for studies of complex formation between membrane-associated proteins ...
are perturbed in each dataset) in the background of a varying number of other randomly perturbed genes. ...
doi:10.1016/j.bpj.2011.11.1000
fatcat:daelwvwi3zcdtool3xlzomfmaq
Systems biology approaches to dissect mammalian innate immunity
2011
Current Opinion in Immunology
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Together with computational analysis, these measurement and perturbation technologies have given rise to the field of systems biology, which seeks to discover, analyze and model the interactions of physical ...
Advances in experimental tools have allowed for the systematic identification of components and biological processes as well quantification of their activities over time. ...
Acknowledgments We would like to thank members of the lab for discussions and the National Institutes of Health grants AI074575, OD002230 and AI057159 for support of our work. ...
doi:10.1016/j.coi.2010.10.022
pmid:21111589
pmcid:PMC3746755
fatcat:4nzrxleujbertfmcbzglx4bdna
A systems biology approach to genetic studies of complex diseases
2005
FEBS Letters
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In this report, we propose a systems biology approach, which integrates omic data, to find genes responsible for complex diseases. ...
This approach consists of five steps: (1) generate a set of candidate genes using gene-gene interaction data sets; (2) reconstruct a genetic network with the set of candidate genes from gene expression ...
Selection of a set of candidate genes For ease of presentation, we use our studies of SSc as an example to describe a scheme of a systems biology approach to genetic studies of a complex disease. ...
doi:10.1016/j.febslet.2005.08.058
pmid:16182293
fatcat:oix5toajtzcytpsmpm4k7kayrq
Systems biology for identifying liver toxicity pathways
2009
BMC Proceedings
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Systems biology approaches were developed to integrate multi-level data, i.e., gene expression, metabolite profile, toxicity measurements and a priori knowledge to identify gene targets for modulating ...
The objective of this paper is to describe systems biology methods for identifying pathways involved in liver toxicity induced by free fatty acids (FFA) and tumor necrosis factor (TNF)-in human hepatoblastoma ...
Acknowledgements The research was supported in part through funding from National Science ...
doi:10.1186/1753-6561-3-s2-s2
pmid:19278558
pmcid:PMC2654485
fatcat:fy5nh2wakbgkjgv4y6rhbah7c4
A Systems Biology Approach Identifies Effective Tumor–Stroma Common Targets for Oral Squamous Cell Carcinoma
2014
Cancer Research
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Here, we propose a concept of common target perturbation (CTP). ...
To employ this concept, we design a systems biology strategy by combining experiment and computation to identify potential common target. ...
We develop a systems biology strategy that combines experiment and computation for identification of the epithelial-mesenchymal common targets (EMCTs). ...
doi:10.1158/0008-5472.can-13-2275
pmid:24556718
fatcat:3kav3kmeyrcqfatyflc2rxyxbi
A thematic review series: systems biology approaches to metabolic and cardiovascular disorders
2006
Journal of Lipid Research
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A major challenge of systems biology is to intersect these data sets. The lines between the stages illustrate the effects of a hypothetical genetic perturbation. ...
for the identification and functional analysis of genes involved in lipid metabolism. ...
doi:10.1194/jlr.e600004-jlr200
pmid:16924129
fatcat:n6ofgnrwx5ar5cfg3l4uzkzy74
Recent Advances in the Systems Biology of Aging
2018
Antioxidants and Redox Signaling
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Significance: Reductionist studies have contributed greatly to our understanding of the basic biology of aging in recent years but we still do not understand fundamental mechanisms for many identified ...
Use of systems approaches will help us move forward in our understanding of aging. ...
Acknowledgments DELP was supported in part by funding from the NIH (AG049494 and CA211160) and the National Science Foundation (DMS1561814). ...
doi:10.1089/ars.2017.7367
pmid:29020802
pmcid:PMC6104255
fatcat:ljogd7ooxrdedptfotvdb472xq
Multiple Co-Evolutionary Networks have Evolved on the Common Tertiary Scaffold of the LacI/GalR Proteins
2012
Biophysical Journal
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are perturbed in each dataset) in the background of a varying number of other randomly perturbed genes. ...
Nevertheless, many scoring methods use significance (e.g. p-value, q-value) to characterize the gene perturbation instead of more biology relevant measures such as fold change. ...
High-throughput proteomics has allowed for the drafting of large Protein-Interaction Networks and systems biology devotes a constant effort in the statistical analysis of these. ...
doi:10.1016/j.bpj.2011.11.1001
fatcat:rdx2hjadffe7jbvpwcszhpmkbe
In Silico Reconstruction of HIV Viral Fitness Landscapes
2012
Biophysical Journal
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are perturbed in each dataset) in the background of a varying number of other randomly perturbed genes. ...
Nevertheless, many scoring methods use significance (e.g. p-value, q-value) to characterize the gene perturbation instead of more biology relevant measures such as fold change. ...
High-throughput proteomics has allowed for the drafting of large Protein-Interaction Networks and systems biology devotes a constant effort in the statistical analysis of these. ...
doi:10.1016/j.bpj.2011.11.1003
fatcat:73257ocy5bektkmo3xgefp4qh4
An Improved Meta-Analysis Procedure Reveals Key Transcriptome Signatures Underlying a Renal Damage Phenotype
2012
Biophysical Journal
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are perturbed in each dataset) in the background of a varying number of other randomly perturbed genes. ...
Nevertheless, many scoring methods use significance (e.g. p-value, q-value) to characterize the gene perturbation instead of more biology relevant measures such as fold change. ...
High-throughput proteomics has allowed for the drafting of large Protein-Interaction Networks and systems biology devotes a constant effort in the statistical analysis of these. ...
doi:10.1016/j.bpj.2011.11.1002
fatcat:sokrge5oefa7djdczcapnzi4ue
How to Find Non Hub Important Nodes in Protein Networks?
2012
Biophysical Journal
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are perturbed in each dataset) in the background of a varying number of other randomly perturbed genes. ...
Nevertheless, many scoring methods use significance (e.g. p-value, q-value) to characterize the gene perturbation instead of more biology relevant measures such as fold change. ...
High-throughput proteomics has allowed for the drafting of large Protein-Interaction Networks and systems biology devotes a constant effort in the statistical analysis of these. ...
doi:10.1016/j.bpj.2011.11.1004
fatcat:qa3wgr7oonhq5l23tojhgt5z3i
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