Nathan M. Springer

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.

DNA repair under heat: DNA Polymerase {lambda} modulates heat stress-induced mutagenesis in plants

This study shows heat stress increases mutation rates in plants, with DNA Polymerase λ mediating mutagenesis, particularly in heterochromatic regions and through 1-bp insertions.

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.

Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions

The paper tests gene regulatory network predictions in maize by analyzing transcriptomic and metabolic changes in TF mutants, finding limited phenotypic impacts but some altered target gene expression.

Temporally resolved growth patterns reveal novel information about the polygenic nature of complex quantitative traits

This study uses high-temporal-resolution plant height data to show that genetic and environmental factors influence plant growth differently across the growing season.

Dissecting the temporal phenomics and genomics of maize canopy cover using UAV mediated image capture

This study uses UAV imagery to track maize canopy cover over time, revealing its genetic and environmental influences and the limitations of single-time-point phenotyping.

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.

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

The paper trains deep learning models on ATAC-seq and DNA methylation data from 12 and 10 angiosperm species to predict chromatin accessibility and methylation across species, finding strong conservation of chromatin mechanisms.

The maize gene maternal derepression of r1 (mdr1) encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in endosperm

This paper identifies MDR1 as a DNA glycosylase in maize that demethylates DNA and reduces siRNA expression in endosperm, challenging the role of demethylation in transposon repression and genomic imprinting.

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

This paper presents a chromosome-level genome assembly of maize inbred line A188 and identifies structural variations and gene expression differences compared to the reference line B73.

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

The paper uses DNA methylation profiles from a single tissue to identify unmethylated regions (UMRs) that mark expressed genes and cis-regulatory elements in plant genomes.

Using multiple reference genomes to identify and resolve annotation inconsistencies

The paper identifies and resolves split-gene misannotations across multiple maize reference genomes using RNAseq data and a simulation framework.

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids

This study characterizes sRNA variation and inheritance in maize inbreds and F1 hybrids, revealing genotype and developmental influences on sRNA expression and non-additive inheritance patterns.

Dynamic patterns of transcript abundance of transposable element families in maize

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

Transposable elements contribute to dynamic genome content in maize

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

Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

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.

Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids

The paper analyzes gene expression in maize hybrids and inbreds to show that single-parent expression is genotype- and tissue-specific, with implications for heterosis.

Genotype-by-Environment Interactions Affecting Heterosis in Maize

This study examines how genotype-by-environment interactions affect heterosis in maize hybrids and their inbred parents across 16 environments and 25 traits.

Improved maize reference genome with single molecule technologies

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