Nagarajan Kathiresan

The paper presents an HPC-based workflow for genome variant calling using GATK, demonstrating SNP detection in four plant species and identifying novel SNPs in rice.

The paper constructs a pan-genome inversion index for Asian rice using 16 genomes and finds a high inversion rate with functional implications.

DeepSVP prioritizes pathogenic structural variants by integrating genotype and phenotype data using deep learning, improving benchmark performance and identifying novel variants in consanguineous families.

This study compares deep learning models for splice site identification, finding that shallow models outperform deep ones and introduces a new shallow ResNet variant.