Dear Colleagues,

Systems biology is an interdisciplinary research field that requires the combined contribution of many distinct and complementary areas of expertise to build up a strategy to unravel the molecular mechanisms behind complex living systems by integrating multiple types of quantitative molecular measurements with well-designed mathematical models.

The technological developments in high-throughput biology experienced in the last 20 years, vis-à-vis the reduction in the cost of using it have generated large-scale Multi-Omics datasets on plants’ development and their interaction with the environment. Datasets in genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, metabolomics, epigenomics, ionomics, phenomics—just to mention the most popular platforms—are piling up elsewhere intending to gain insights on the molecular mechanisms behind plant interaction with biotic and abiotic stresses.

At first, data from each platform were analyzed in isolation using statistical and machine learning methods. As the molecular complexity of the plant responses to specific environmental stress exists at several different levels, single-level analyses have shown limited power to deliver a more complete and accurate picture of the dynamics of the mechanisms behind those responses. In recent years, the scientific community has engaged in developing strategies to integrate these omics datasets and advances in learning how genes, non-coding RNAs, proteins, metabolites, and epigenetic factors influence the resulting phenotype in the context of the system.

Multi-Omics Integration (MOI) uses conceptual integration and element- (correlation, clustering, and multivariate analysis), pathway- (pathway mapping, co-expression analysis), or mathematical- (differential analysis, genome-scale analysis) based approaches to integrate omics datasets. MOI is a new window of opportunity facilitating the hypothesis generation leading to a further understanding of biological, molecular, and ecological functions and mechanisms, in addition to performing associations and correlations studies. However, MOI is well-accepted as a non-trivial challenge due to the complexity of biological systems, technological limits, the large number of variables usually involved, and the need for a relatively high number of biological samples.

This Special Issue of Plants seeks to stimulate and collect these kinds of MOI studies.  Groups applying MOI strategies to study plant responses to biotic (virus, bacteria, fungi, nematodes, insects and so on—alone or in combination) or abiotic (cold, heat, salinity, drought, heavy metals and so on—alone or in combination), or even the combination of both types of stresses, are welcome to submit the results of their studies. Studies using only conceptual integration strategies will not be considered for publication.

Prof. Dr. Manoel Teixeira Souza Júnior
Prof. Dr. Betania Ferraz Quirino
Dr. Carlos Antônio Ferreira de Sousa
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• environmental stress
• abiotic stress
• biotic stress
• multi-omics integration
• systems biology