Abstract: Disclosed herein are methods of improving agronomic traits in crop plants through editing sequences within the 5? untranslated region (UTR) of plant genomes.

Abstract: A method for generating a gene regulatory sequence with a desired endophenotype profile includes obtaining a plurality of gene regulatory sequences and inputting the plurality of gene regulatory sequences into a machine-learning model trained to obtain a plurality of effect predictions corresponding to a plurality of endophenotypes. The method further includes selecting one or more desired endophenotypes based on the plurality of endophenotypes and selecting a gene regulatory sequence in accordance with the one or more desired endophenotypes.

Abstract: A method for predicting endophenotypes of interacting partner genes includes obtaining one or more endophenotype profiles corresponding to a genotype, partitioning the one or more endophenotype profiles into a first set of endophenotypes and a second set of endophenotypes, and receiving an input to modify the first set of endophenotypes to a desired level. The method thus includes inputting the modified first set of endophenotypes and unmodified second set of endophenotypes into a trained machine-learning model to obtain a prediction of an updated second set of endophenotypes. The updated second set of endophenotypes represents an updated version of the second set of endophenotypes after interacting with the modified subset of the first set of endophenotypes.

Abstract: Provided herein are machine learning-based methods for assessing the combined impact of multiple genetic variants, as well as the uses of such methods for various applications, such as in synthetic biology, personalized medicine, agricultural breeding, and genetic engineering. Also provided herein are exemplar computer-readable storage media and electronic devices for performing such methods.

Abstract: Provided herein are methods for assessing genetic variants for use in genetically improving organisms and in human genetics and medicine. Also provided herein are systems for implementing such methods, as well as computer-readable storage media storing instructions for performing such methods.