Omics and Systems Biology: Integration of Production and Omics Data in Systems Biology

2018 ◽  
pp. 463-485 ◽  
Author(s):  
Kasper Hettinga ◽  
Lina Zhang
Keyword(s):  
Systems Biology ◽  
Omics Data

scholarly journals Integration of ‘omics’ data in aging research: from biomarkers to systems biology

Aging Cell ◽  
2015 ◽  
Vol 14 (6) ◽  
pp. 933-944 ◽  
Author(s):  
Jonas Zierer ◽  
Cristina Menni ◽  
Gabi Kastenmüller ◽  
Tim D. Spector
Keyword(s):  
Systems Biology ◽  
Omics Data ◽  
Aging Research

scholarly journals Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Metabolites ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 76 ◽  
Author(s):  
Farhana R. Pinu ◽  
David J. Beale ◽  
Amy M. Paten ◽  
Konstantinos Kouremenos ◽  
Sanjay Swarup ◽  
...  
Keyword(s):  
New Zealand ◽  
Systems Biology ◽  
Life Science ◽  
Biological Systems ◽  
Research Community ◽  
Data Sets ◽  
Omics Data ◽  
Omics Integration ◽  
Traditional Approaches ◽  
Multiple Interactions

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent ‘Australian and New Zealand Metabolomics Conference’ (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

scholarly journals The Promises and the Challenges of Integrating Multi-Omics and Systems Biology in Comparative Stress Biology

2020 ◽  
Vol 60 (1) ◽  
pp. 89-97 ◽  
Author(s):  
Tonia S Schwartz
Keyword(s):  
Systems Biology ◽  
Physiological Responses ◽  
Model Organisms ◽  
Omics Data ◽  
Holistic Understanding ◽  
Stress Biology

Abstract Comparative stress biology is inherently a systems biology approach with the goal of integrating the molecular, cellular, and physiological responses with fitness outcomes. In this way, the systems biology approach is expected to provide a holistic understanding of how different stressors result in different fitness outcomes, and how different individuals (or populations or species) respond to stressors differently. In this perceptive article, I focus on the use of multiple types of -omics data in stress biology. Targeting students and those researchers who are considering integrating -omics approaches in their comparative stress biology studies, I discuss the promise of the integration of these measures for furthering our holistic understanding of how organisms respond to different stressors. I also discuss the logistical and conceptual challenges encountered when working with -omics data and the current hurdles to fully utilize these data in studies of stress biology in non-model organisms.

scholarly journals MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 288
Author(s):  
Julia Koblitz ◽  
Dietmar Schomburg ◽  
Meina Neumann-Schaal
Keyword(s):  
Experimental Data ◽  
Systems Biology ◽  
Metabolic Pathways ◽  
Common Knowledge ◽  
Numerical Data ◽  
Omics Data ◽  
Web Based ◽  
Ongoing Research ◽  
Complex Interactions ◽  
Biology Research

Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.

scholarly journals An Integrative Approach to Assessing Diet–Cancer Relationships

Metabolites ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 123 ◽  
Author(s):  
Rachel Murphy
Keyword(s):  
Systems Biology ◽  
Health Professionals ◽  
Biomarker Discovery ◽  
Integrative Approach ◽  
Omics Data ◽  
The Public ◽  
The Past ◽  
Diet And Cancer ◽  
The Relationship ◽  
Considerable Body

The relationship between diet and cancer is often viewed with skepticism by the public and health professionals, despite a considerable body of evidence and general consistency in recommendations over the past decades. A systems biology approach which integrates ‘omics’ data including metabolomics, genetics, metagenomics, transcriptomics and proteomics holds promise for developing a better understanding of how diet affects cancer and for improving the assessment of diet through biomarker discovery thereby renewing confidence in diet–cancer links. This review discusses the application of multi-omics approaches to studies of diet and cancer. Considerations and challenges that need to be addressed to facilitate the investigation of diet–cancer relationships with multi-omic approaches are also discussed.

scholarly journals Systems Biology and Experimental Model Systems of Cancer

2020 ◽  
Vol 10 (4) ◽  
pp. 180
Author(s):  
Gizem Damla Yalcin ◽  
Nurseda Danisik ◽  
Rana Can Baygin ◽  
Ahmet Acar
Keyword(s):  
Systems Biology ◽  
Experimental Model ◽  
High Throughput Sequencing ◽  
Critical Role ◽  
Genetic Alterations ◽  
Model Systems ◽  
Treatment Modalities ◽  
Omics Data ◽  
Cancer Systems Biology ◽  
Experimental Model Systems

Over the past decade, we have witnessed an increasing number of large-scale studies that have provided multi-omics data by high-throughput sequencing approaches. This has particularly helped with identifying key (epi)genetic alterations in cancers. Importantly, aberrations that lead to the activation of signaling networks through the disruption of normal cellular homeostasis is seen both in cancer cells and also in the neighboring tumor microenvironment. Cancer systems biology approaches have enabled the efficient integration of experimental data with computational algorithms and the implementation of actionable targeted therapies, as the exceptions, for the treatment of cancer. Comprehensive multi-omics data obtained through the sequencing of tumor samples and experimental model systems will be important in implementing novel cancer systems biology approaches and increasing their efficacy for tailoring novel personalized treatment modalities in cancer. In this review, we discuss emerging cancer systems biology approaches based on multi-omics data derived from bulk and single-cell genomics studies in addition to existing experimental model systems that play a critical role in understanding (epi)genetic heterogeneity and therapy resistance in cancer.

Sign in / Sign up

Export Citation Format

Share Document