Systems Biology Using Host Responses To Diagnose Infections

Shannon Weiman

doi:10.1128/microbe.9.478.1

A Systems Biology Approach Investigating the Effect of Probiotics on the Vaginal Microbiome and Host Responses in a Double Blind, Placebo-Controlled Clinical Trial of Post-Menopausal Women

PLoS ONE ◽

10.1371/journal.pone.0104511 ◽

2014 ◽

Vol 9 (8) ◽

pp. e104511 ◽

Cited By ~ 27

Author(s):

Jordan E. Bisanz ◽

Shannon Seney ◽

Amy McMillan ◽

Rebecca Vongsa ◽

David Koenig ◽

...

Keyword(s):

Clinical Trial ◽

Systems Biology ◽

Host Responses ◽

Controlled Clinical Trial ◽

Vaginal Microbiome ◽

Double Blind ◽

Double Blind Placebo ◽

Menopausal Women ◽

Post Menopausal

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Systems Biology Analyses to Define Host Responses to HCV Infection and Therapy

Current Topics in Microbiology and Immunology - Systems Biology ◽

10.1007/82_2012_251 ◽

2012 ◽

pp. 143-167 ◽

Cited By ~ 1

Author(s):

Reneé C. Ireton ◽

Michael Gale

Keyword(s):

Systems Biology ◽

Hcv Infection ◽

Host Responses

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Systems Biology-Based Approaches Applied to Vaccine Development

Data Mining ◽

10.4018/978-1-4666-2455-9.ch058 ◽

2013 ◽

pp. 1131-1148

Author(s):

Patricio A. Manque ◽

Ute Woehlbier

Keyword(s):

Gene Expression ◽

Systems Biology ◽

Vaccine Development ◽

Cost Effective ◽

Host Responses ◽

Effective Vaccine ◽

Antigen Discovery ◽

Genomic Technologies ◽

History Of ◽

Genomic Revolution

Vaccines represent one of the most cost-effective ways to prevent and treat diseases. The use of vaccines in the control of viral diseases represents an important milestone in the history of medicine. The genomic revolution brought us the possibility to scan genomes in the search of new and more effective vaccine candidates and the advancement of bioinformatics provided the framework for the application of strategies that were focused not only on antigen discovery but also on comparative genomics, and pathogenic factor identification and data mining. In addition, the progress in post-genomic technologies including gene expression technologies such as microarray and proteomics gave us the opportunity to explore the host responses to vaccines leading to a better understanding of immune responses to pathogens and/or to vaccines, assisting in the development of new and better vaccines and adjuvants. This chapter will review how systems biology-based approaches including genomics, gene expression technologies, and bioinformatics have changed the way of thinking about antigen discovery and vaccine development. In addition, the chapter will discuss how the study of the host responses in combination with “in silico” approaches could help predict immunogenicity and improve the efficacy of vaccines.

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Systems Biology-Based Approaches Applied to Vaccine Development

Handbook of Research on Computational and Systems Biology ◽

10.4018/978-1-60960-491-2.ch003 ◽

2011 ◽

pp. 61-78

Author(s):

Patricio A. Manque ◽

Ute Woehlbier

Keyword(s):

Gene Expression ◽

Systems Biology ◽

Vaccine Development ◽

Cost Effective ◽

Host Responses ◽

Effective Vaccine ◽

Antigen Discovery ◽

Genomic Technologies ◽

History Of ◽

Genomic Revolution

Vaccines represent one of the most cost-effective ways to prevent and treat diseases. The use of vaccines in the control of viral diseases represents an important milestone in the history of medicine. The genomic revolution brought us the possibility to scan genomes in the search of new and more effective vaccine candidates and the advancement of bioinformatics provided the framework for the application of strategies that were focused not only on antigen discovery but also on comparative genomics, and pathogenic factor identification and data mining. In addition, the progress in post-genomic technologies including gene expression technologies such as microarray and proteomics gave us the opportunity to explore the host responses to vaccines leading to a better understanding of immune responses to pathogens and/or to vaccines, assisting in the development of new and better vaccines and adjuvants. This chapter will review how systems biology-based approaches including genomics, gene expression technologies, and bioinformatics have changed the way of thinking about antigen discovery and vaccine development. In addition, the chapter will discuss how the study of the host responses in combination with “in silico” approaches could help predict immunogenicity and improve the efficacy of vaccines.

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Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002911 ◽

2019 ◽

Vol 42 ◽

Author(s):

J. Alfredo Blakeley-Ruiz ◽

Carlee S. McClintock ◽

Ralph Lydic ◽

Helen A. Baghdoyan ◽

James J. Choo ◽

...

Keyword(s):

Systems Biology ◽

High Resolution ◽

Experimental Design ◽

Integrated Systems ◽

Microbiome Research ◽

Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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