These counts present many statistical challenges, including overdispersion, depth dependence, and uncertain DNA concentrations. In the massively parallel reporter assay (MPRA), short barcodes are counted by sequencing DNA libraries transfected into cells and the cell’s output RNA in order to simultaneously measure the shifts in transcription induced by thousands of genetic variants. High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged. For example, scalarization methods (e.g., reference point methods, tabu search) are particularly useful for a priori or interactive stakeholder integration whereas Pareto-based approaches (e.g., evolutionary algorithms) are appropriate for trade-off analyses and a posteriori stakeholder involvement.NGS studies have uncovered an ever-growing catalog of human variation while leaving an enormous gap between observed variation and experimental characterization of variant function. Finally, we provide recommendations for the use of the different optimization methods. We explore their relative abilities for the integration of stakeholders and the identification of ecosystem service trade-offs since these are especially pertinent to land use planners. To enhance the applicability of optimization techniques for real-world case studies, this study provides an overview of optimization methods used for targeting land use decisions in agricultural areas. Optimization techniques have been especially prevalent for solving land use problems however, there is no guideline supporting the selection of an appropriate method. Optimal land use allocation with the intention of ecosystem services provision and biodiversity conservation is one of the key challenges in agricultural management.
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