Robert J. Schmitz

This study creates a spatial transcriptome atlas of poplar shoot-associated organs, revealing tissue organization and gene expression patterns across different developmental stages and anatomical contexts.

The paper uses single-cell sequencing to show that Id1 regulates flowering in maize by affecting chromatin remodeling and gene expression, with a genetic interaction between Id1 and Te1 that delays flowering.

The paper quantifies mutation rates in Arabidopsis DNA repair and chromatin mutants, finding differential pathway efficiencies and mutation rate changes in specific genomic regions.

This study analyzes genetic and epigenetic divergence in Arabidopsis thaliana Col-0 laboratory lineages over decades, revealing substantial divergence and functional consequences.

This study characterizes the soybean root response to cyst nematode infection using single-cell multi-omic profiling, identifying key transcription factors involved in syncytium formation and immune suppression.

The paper introduces PEAgent, a deep-learning framework predicting single-cell chromatin accessibility from DNA sequence in plants, revealing cell-type-specific cis-regulatory patterns and their conservation.

Easy-Multiome enables joint profiling of gene expression and chromatin accessibility in plant single cells with high efficiency and minimal workflow changes.

The paper introduces CASCADE, a method to identify promoter-associated regulatory motifs from cell-type-resolved DNA language model attributions in soybean.

The paper characterizes time-dependent transcriptomic changes in plant protoplasts across species and identifies stress-like cell states in single-cell RNA-seq data.

The paper presents a single-cell RNA-seq atlas of poplar shoots, identifies epidermal subclusters, and discovers new trichome-specific genes through integration with bulk transcriptome data.

This study investigates the lineage-specific evolution of regulatory elements in allopolyploid peanut and its diploid progenitors, revealing patterns of chromatin accessibility and histone modification conservation and divergence.

This paper introduces VAST, a method improving transient gene expression in plant seedlings, showing enhanced efficiency across multiple species.

This study uses nanorate sequencing to analyze somatic mutations in Arabidopsis shoots, finding a higher mutation rate and distinct mutational signatures compared to germline mutations.

This study uses single-cell genomics to analyze transcriptional and cis-regulatory divergence in duplicated genes of soybean, revealing how chromatin accessibility and duplication mechanisms shape expression patterns.

This study shows that faster tree growth increases the annual rate of somatic epimutations at CG dinucleotides, likely due to higher cell division rates.

The paper identifies trans-regulatory variants associated with chromatin accessibility in maize hybrids, revealing their role in heterosis and gene expression.

The paper uses single-cell ATAC-seq to show ZmWUS1 overexpression alters chromatin accessibility in maize inflorescence meristem, revealing its role in stem cell maintenance through context-dependent regulation.

The paper constructs a single-cell chromatin accessibility atlas in rice and compares it across grass species to study the evolution of cell-type-specific cis-regulatory elements.

The paper identifies three high-impact mutations in Arabidopsis thaliana that drive DNA methylation variation during colonization of the Cape Verde Islands.

The paper tracks DNA methylation across generations in Arabidopsis lineages to identify a genetic modifier that increases epimutation rates and supports a punctuated-equilibrium model of methylation evolution.

The paper identifies cell-type-specific cis-regulatory variants in maize using single-cell genomics and population genetics, revealing their role in local adaptation and flowering.

This study identifies polycistronic mRNA expression in Cryptosporidium parvum using long-read RNA-seq and ATAC-seq, revealing a novel gene regulation mechanism in apicomplexan parasites.

The paper constructs a spatially resolved multiomic single-cell atlas of soybean development, identifying cell types, chromatin regions, and gene regulatory networks involved in growth and nitrogen fixation.

This study uses single-cell ATAC-seq to analyze cis-regulatory elements in C4 photosynthesis across grass species, revealing cell-type-specific chromatin accessibility patterns and evolutionary dynamics.

The paper identifies that unstable transcripts are rare in plants and often originate from promoters, challenging the use of genome annotations to infer enhancers.

This study investigates the evolution of IBM1, an H3K9 demethylase, in flowering plants, showing its role in regulating gene body methylation and its dynamic evolution across species.

The paper shows that epigenetic mechanisms, including base J modification, regulate mono-allelic transcriptional silencing of adjacent polycistronic gene clusters in Trypanosoma brucei.

GenomicLinks predicts 3D chromatin loops in maize by identifying sequence features associated with transcription factor binding motifs, validated using single-cell co-accessibility data.

The paper introduces scifi-ATAC-seq, a method that increases single-cell ATAC-seq throughput by 20-fold using combinatorial fluidic indexing.

The paper uses a phased genome of the Fairchild mandarin to analyze how haplotype-specific chromatin states influence allele-specific gene expression.