Michelle C. Stitzer

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

This study identifies 9 QTLs associated with freezing tolerance in Tripsacum dactyloides using bulk segregant analysis and regression-based allele frequency imputation.

The paper constructs a transcriptomic atlas of grass senescence to identify molecular mechanisms of nitrogen recycling, finding divergent underground sink networks in annual crops.

The paper identifies a conserved cis-regulatory code across 589 grass species and finds that motif conservation declines rapidly but remains significant over evolutionary time, with adaptive changes linked to ecological transitions.

This study investigates the origins and adaptive consequences of polyploidy in the prairie grass Andropogon gerardi, finding that whole genome duplication is common and provides fitness advantages in xeric climates.

GeneCAD improves gene annotation in plant genomes using a DNA foundation model, achieving higher accuracy than existing tools across diverse species.

The paper generates high-quality genome assemblies for three Bouteloua species and identifies polyploidy and transposable elements, providing genomic resources for comparative studies.

reelGene evaluates gene models using machine learning and evolutionary data, finding 28% of maize gene models are incorrectly annotated or nonfunctional.

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.

The paper compares genome fractionation patterns in maize and its wild relatives, finding distinct subgenome retention and gene loss trends between species.

The paper identifies genes under relaxed selection in cassava due to clonal propagation, highlighting pollen-related genes and their implications for breeding.

The paper introduces PlantCaduceus, a DNA language model for plants, showing high transferability across species and improved performance in mutation prediction and variant identification.

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

This paper introduces an age-adjusted site frequency spectrum to better assess selective constraints on transposable elements by accounting for transposition bursts and demographic changes.

AnchorWave improves genome alignment for genomes with high diversity, structural polymorphism, and whole-genome duplication by using a duplication-informed algorithm and gap cost strategy.

The paper develops a multiple genome alignment workflow for plants, showing that k-mer masking and parameter tuning improve alignment of functional regions.

The paper identifies poorly annotated genes in maize using a double triage approach combining quality metrics and gene tree visualization, revealing 4,000 novel annotations.

This study characterizes TE family transcript abundance in maize using RNA-seq data from over 800 libraries, revealing dynamic and tissue-specific expression patterns.

The paper identifies variable transposable element (TE) insertions across four maize genomes, showing their role in genome organization and gene content variation.

The paper describes a transgenerational epigenetic decline in vigor and viability in maize-teosinte backcross populations, termed 'hybrid decay', characterized by genomic instability and altered gene expression.

The paper investigates purging dynamics in selfed maize lines, finding increased homozygosity and genome size reduction due to purging of deleterious variants and transposable elements.

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.