Manisha Munasinghe

Promoter Structural Variants are Drivers of Genome-Wide Differential Expression in Maize

The paper identifies promoter structural variants in maize that are associated with differential gene expression across tissues, often involving transposable elements.

Genome-wide selection on transposable elements in maize

This study uses long-read genome assemblies from maize to develop a new method for detecting selection on transposable elements, identifying factors like gene distance and DNA methylation levels that influence TE selection.

SWIF-TE: identifying novel transposable element insertions from short read data

SWIF-TE identifies novel transposable element insertions from short read data with high efficiency and precision.

Structural variants contribute to phenotypic variation in maize

The paper identifies structural variants in maize using whole genome alignment and short-read sequencing, linking them to life history traits and genotype-by-environment interactions.

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

The paper analyzes transposable elements and structural variation in maize genomes, finding that deletions of transposable elements contribute more to genomic differences than insertions.