Dataset Information

Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases.

ABSTRACT: Biomarkers have gained immense scientific interest and clinical value in the practice of medicine. With unprecedented advances in high-throughput technologies, research interest in identifying novel and customized disease biomarkers for early detection, diagnosis, or drug responses is rapidly growing. Biomarkers can be identified in different levels of molecular biomarkers, networks biomarkers and dynamical network biomarkers (DNBs). The latter is a recently developed concept which relies on the idea that a cell is a complex system whose behavior is emerged from interplay of various molecules, and this network of molecules dynamically changes over time. A DNB can serve as an early-warning signal of disease progression, or as a leading network that drives the system into the disease state, and thus unravels mechanisms of disease initiation and progression. It is therefore of great importance to identify DNBs efficiently and reliably. In this work, the problem of DNB identification is defined as a multi-objective optimization problem, and a framework to identify DNBs out of time-course high-throughput data is proposed. Temporal gene expression data of a lung injury with carbonyl chloride inhalation exposure has been used as a case study, and the functional role of the discovered biomarker in the pathogenesis of lung injury has been thoroughly analyzed.

SUBMITTER: Vafaee F

PROVIDER: S-EPMC4764930 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases.

Vafaee Fatemeh F

Scientific reports 20160224

Biomarkers have gained immense scientific interest and clinical value in the practice of medicine. With unprecedented advances in high-throughput technologies, research interest in identifying novel and customized disease biomarkers for early detection, diagnosis, or drug responses is rapidly growing. Biomarkers can be identified in different levels of molecular biomarkers, networks biomarkers and dynamical network biomarkers (DNBs). The latter is a recently developed concept which relies on the ...[more]

PMID: 26906975

Similar Datasets

Project description:Agricultural landscapes provide many functions simultaneously including food production, regulation of water and regulation of greenhouse gases. Thus, it is challenging to make land management decisions, particularly transformative changes, that improve on one function without unintended consequences for other functions. To make informed decisions the trade-offs between different landscape functions must be considered. Here, we use a multi-objective optimization algorithm with a model of crop production that also simulates environmental effects such as nitrous oxide emissions to identify trade-off frontiers and associated possibilities for agricultural management. Trade-offs are identified in three soil types, using wheat production in the UK as an example, then the trade-off for combined management of the three soils is considered. The optimization algorithm identifies trade-offs between different objectives and allows them to be visualised. For example, we observed a highly non-linear trade-off between wheat yield and nitrous oxide emissions, illustrating where small changes might have a large impact. We used a cluster analysis to identify distinct management strategies with similar management actions and use these clusters to link the trade-off curves to possibilities for management. There were more possible strategies for achieving desirable environmental outcomes and remaining profitable when the management of different soil types was considered together. Interestingly, it was on the soil capable of the highest potential profit that lower profit strategies were identified as useful for combined management. Meanwhile, to maintain average profitability across the soils, it was necessary to maximise the profit from the soil with the lowest potential profit. These results are somewhat counterintuitive and so the range of strategies supplied by the model could be used to stimulate discussion amongst stakeholders. In particular, as some key objectives can be met in different ways, stakeholders could discuss the impact of these management strategies on other objectives not quantified by the model.

Dataset Information

Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases.

Publications

Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets