Research Topic

Analysis of Bioinformatics Tools in Systems Genetics

About this Research Topic

With the advancement of omics data technologies and the development of computational methods, researchers can decipher the relationships between genotype and phenotype with a systems genetics approach rather than single-gene approaches. Furthermore, complex traits involve the interactions between multiple genes or between genes and environments. Researchers have developed many computational methods and applied systems genetics to study numerous traits. The datasets are usually massive, and the computational methods are often sophisticated.

Here, we hope to collect a set of reliable tools, protocols, and databases which can be adopted widely in the field.First, though researchers have proposed many methods for the study of each data type (e.g., gene-by-gene interactions, gene-by-environment interactions, omics data integrations, etc.), most of the methods are inaccessible to biological practitioners due to being unreliable or user-unfriendly. We welcome research that comprehensively investigates the tools associated with each data type and makes unbiased recommendations for their use or improvement. Second, similar methods have recurrently developed for different data types (e.g., DNA methylation, RNA expression, proteomics, and metagenomics). We welcome studies that examine or propose methods and models that can be applied to multiple data types within systems genetics. Third, while network models are popular to link omics data to phenotypes, we welcome studies detailing best practices for network construction and interpretation. Fourth, the tools used in systems genetics are often inadequate to integrate multi-omics data. We wish to see protocols for the integration of multi-omics data for complex trait studies. In addition, we hope to see carefully curated databases for complex traits as the databases will lay solid basis for tool development in system genetics.

This Research Topic welcomes Original Research and Reviews related, but not limited, to the following subtopics:
• Comprehensive assessment of system genetics tools.
• Methods and models applicable to the multiple data types in system genetics.
• Network models that link omics data to phenotypes in system genetics.
• Tools, methods, or models to integrate multi-omics data in system genetics.
• Carefully curated databases for complex traits.

Topic Editor Sandro José de Souza holds patents related to the Research Topic subject. All other Topic Editors declare no competing interests.


Keywords: systems genetics, omics data, trans-omics, data integration


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

With the advancement of omics data technologies and the development of computational methods, researchers can decipher the relationships between genotype and phenotype with a systems genetics approach rather than single-gene approaches. Furthermore, complex traits involve the interactions between multiple genes or between genes and environments. Researchers have developed many computational methods and applied systems genetics to study numerous traits. The datasets are usually massive, and the computational methods are often sophisticated.

Here, we hope to collect a set of reliable tools, protocols, and databases which can be adopted widely in the field.First, though researchers have proposed many methods for the study of each data type (e.g., gene-by-gene interactions, gene-by-environment interactions, omics data integrations, etc.), most of the methods are inaccessible to biological practitioners due to being unreliable or user-unfriendly. We welcome research that comprehensively investigates the tools associated with each data type and makes unbiased recommendations for their use or improvement. Second, similar methods have recurrently developed for different data types (e.g., DNA methylation, RNA expression, proteomics, and metagenomics). We welcome studies that examine or propose methods and models that can be applied to multiple data types within systems genetics. Third, while network models are popular to link omics data to phenotypes, we welcome studies detailing best practices for network construction and interpretation. Fourth, the tools used in systems genetics are often inadequate to integrate multi-omics data. We wish to see protocols for the integration of multi-omics data for complex trait studies. In addition, we hope to see carefully curated databases for complex traits as the databases will lay solid basis for tool development in system genetics.

This Research Topic welcomes Original Research and Reviews related, but not limited, to the following subtopics:
• Comprehensive assessment of system genetics tools.
• Methods and models applicable to the multiple data types in system genetics.
• Network models that link omics data to phenotypes in system genetics.
• Tools, methods, or models to integrate multi-omics data in system genetics.
• Carefully curated databases for complex traits.

Topic Editor Sandro José de Souza holds patents related to the Research Topic subject. All other Topic Editors declare no competing interests.


Keywords: systems genetics, omics data, trans-omics, data integration


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

18 September 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

18 September 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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