N. M. Springer

Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration

This paper develops a framework to prioritize maize metabolic gene regulators by integrating multi-omic data, identifying over 3,000 TFs and predicting new regulators of hormone, developmental, and metabolic processes.

Mutator transposon insertions within maize genes often provide a novel outward reading promoter

The study identifies Mu transposon insertions in maize genes that create outward-reading promoters, leading to complex transcripts and gene expression patterns similar to wild-type.

Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel

The paper identifies cis- and trans-acting eQTLs influencing heat stress gene expression in maize and maps transcription factor binding footprints to prioritize functional genomic regions.

Conserved and variable responses of the HEAT SHOCK FACTOR transcription factor family in maize and Setaria viridis

The paper compares the HSF transcription factor family in maize and Setaria viridis, identifying conserved and variable heat stress responses and chromatin state differences.

Critical Role of Insertion Preference for Invasion Trajectory of Transposons

The paper investigates how transposon insertion preferences affect their copy number and host population extinction risk through simulations.

Drastic differential CRISPR-Cas9 induced mutagenesis influenced by DNA methylation and chromatin features

This study shows that chromatin features and DNA methylation significantly affect CRISPR-Cas9 mutagenesis efficiency and mutation profiles in Arabidopsis thaliana.

Limited consequences for loss of RNA-directed DNA methylation in Setaria viridis domains rearranged methyltransferase (DRM) mutants

This study examines the effects of losing RNA-directed DNA methylation in Setaria viridis by analyzing methylation patterns and gene expression in drm1ab mutants, finding limited morphological and transcriptional consequences.

Plant trait heterosis is quantitatively associated with expression heterosis of plastid ribosomal proteins

This study identifies chloroplast ribosomal protein expression heterosis as a quantitative predictor of plant height heterosis in maize hybrids.

Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

The paper uses transcriptome profiling of maize under heat and cold stress to identify cis-regulatory elements and develop models predicting gene expression responses.

Whole Genome Variation of Transposable Element Insertions in a Maize Diversity Panel

This study analyzes TE insertion polymorphisms across 509 maize inbred lines using short read sequencing, revealing patterns of TE frequency, nesting, and SNP tagging.

Genetic and epigenetic contributions to variation in transposable element expression responses to abiotic stress in maize

This study examines how genetic and epigenetic factors influence transposable element expression in maize under abiotic stress conditions.

Utilizing Temporal Measurements from UAVs to Assess Root Lodging in Maize and its Impact on Productivity

The paper uses UAV-collected temporal plant height data to assess root lodging in maize and its impact on yield, finding growth rates and storm exposure timing predict lodging severity.

Cis-regulatory elements within TEs can influence expression of nearby maize genes

The paper identifies TE insertions that influence gene expression in maize by disrupting or carrying accessible chromatin regions, showing TEs can create novel regulatory elements.

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

This paper develops a multiplexed CRISPR/Cas9 system with Trex2 exonuclease to improve genome editing efficiency in Setaria viridis, achieving high mutation rates and MMEJ-mediated repair.

Widespread imprinting of transposable elements and young genes in the maize endosperm

The paper identifies widespread maternal expression of genes and transposable elements in maize endosperm using whole genome assemblies from reciprocal crosses, revealing imprinted expression patterns and fused transcripts.

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

This study investigates DNA methylation variation during maize domestication using WGS and WGBS, identifying DMRs linked to gene regulation and adaptation.

Utilizing top-down hyperspectral imaging for monitoring genotype and growth conditions in maize

This paper demonstrates that top-down hyperspectral imaging of maize seedlings, combined with leaf segmentation, improves classification of genotypes and abiotic stress conditions in field settings.

Maternal genome dominance in early plant embryogenesis

The paper investigates maternal genome dominance in early Arabidopsis embryogenesis using mutants and reciprocal crosses, finding maternal alleles play a predominant role through preferential zygotic transcription.

UAV Based Imaging Platform for Monitoring Maize Growth Throughout Development

This study evaluates UAV-based imaging for high-temporal-resolution maize height monitoring, comparing it to manual measurements and proposing methods to improve their correspondence.

Characterizing allele-by-environment interactions using maize introgression lines

This study examines how small genomic introgressions affect plant traits across different environments, finding significant allele-by-environment interactions in various growth stages.

The Genomic Ecosystem of Transposable Elements in Maize

The paper analyzes the ecological and evolutionary dynamics of transposable element families in maize genomes, revealing diverse strategies and interactions among TE families.

Classifying cold stress responses of inbred maize seedlings using RGB imaging

This study uses RGB imaging and PlantCV to classify cold stress responses in maize seedlings, identifying three genotype clusters with distinct growth and necrosis patterns.

Targeted epigenomic changes to the maize methylome resulting from tissue culture

This study identifies targeted epigenomic changes in maize methylomes due to tissue culture, showing consistent gains and losses of DNA methylation across multiple independent lines.

Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation

The paper identifies genes and transposons affected by context-specific DNA methylation changes in maize mutants, revealing distinct regulatory patterns for CMT and RdDM pathways.

Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

The paper investigates differential fractionation in maize inbred lines and finds it contributes little to presence/absence variation and functional phenotypic differences.