Improved K-mer Based Prediction of Protein-Protein Interactions With Chaos Game Representation, Deep Learning and Reduced Representation Bias

Protein-protein interactions drive many biological processes, including the detection of phytopathogens by plants' R-Proteins and cell surface receptors. Many machine learning studies have attempted to predict protein-protein interactions but performance is highly dependent on training data; models have been shown to accurately predict interactions when the proteins involved are included in the training data, but achieve consistently poorer results when applied to previously unseen proteins. In addition, models that are trained using proteins that take part in multiple interactions can suffer from representation bias, where predictions are driven not by learned biological features but by learning of the structure of the interaction dataset. We present a method for extracting unique pairs from an interaction dataset, generating non-redundant paired data for unbiased machine learning. After applying the method to datasets containing _Arabidopsis thaliana_ and pathogen effector interations, we developed a convolutional neural network model capable of learning and predicting interactions from Chaos Game Representations of proteins' coding genes

Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires

Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers.https://doi.org/10.1186/s40104-019-0403-