Nancy Manchanda

The paper develops a pan-TE annotation tool to analyze TE variation in maize, finding that tropical maize has more TE sequences due to active and less methylated LTR retrotransposons.

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

GenomeQC evaluates genome assembly and gene annotation quality by integrating multiple metrics and allows benchmarking against reference genomes.