Chris G. Daum

This study integrates multi-omic data with interpretable machine learning to identify genetic mechanisms underlying trait variation and phenotypic plasticity in switchgrass across environments.

The paper investigates how transcription factor binding site position and chromatin context influence gene regulation in plants, revealing distinct regulatory roles for different genomic locations.

The paper investigates DNA methylation-expression relationships in rice internode development using RNA-seq and bisulfite sequencing, finding specific methylation contexts correlate with gene expression patterns.

The paper catalogs structural and sequence variation in the pennycress pangenome, revealing contrasting evolutionary modes across genomic regions and highlighting the utility of pangenomic resources for crop development.

This study identifies hundreds of drought-responsive genes in sorghum using multi-season transcriptomic data from field experiments.

The paper establishes reproducible methods for plant-microbiome research using fabricated ecosystems across multiple laboratories.

The paper identifies NUC-1 as a bifunctional transcription factor regulating phosphate starvation response in Neurospora crassa, with NUC-3 acting as a brake on the response during prolonged starvation.

The paper presents a scalable TFBS assay to create an atlas of 3,000 genome-wide binding site maps for 360 TFs across 10 flowering plant species, revealing conservation and rewiring of regulatory elements.

The paper presents an improved haplotype-resolved genome assembly for Eucalyptus grandis, increasing gene annotation completeness and revealing structural variations and tandem duplicates.

The paper analyzes 739 Thlaspi arvense accessions to uncover genetic variation and adaptation mechanisms, identifying genomic regions linked to agronomic traits and climate resilience.

The paper describes a high-resolution microbial metagenome dataset collected over 22 days during a phytoplankton bloom cycle, including gene abundances and time-matched environmental data.

The paper sequenced twelve Camelina sativa genomes to study pangenomic variation in an allohexaploid species, finding minimal gene presence-absence variation but subgenome-specific gene content.

This study uses multi-omics analysis to characterize Neurospora intermedia in oncom, revealing its role in byproduct conversion and potential for waste-to-food upcycling.

The paper presents a chromosome-scale genome assembly of Aurantiochytrium limacinum, revealing novel subtelomeric rDNA repeats and herpes-like viral elements.

The paper analyzes a thousand-genome panel of Zymoseptoria tritici to trace its global spread and identify genetic changes associated with climatic adaptation.

The paper presents version 6 of the Chlamydomonas reinhardtii reference genome, improving assembly quality and revealing structural mutations in laboratory strains.

The paper maps meiotic recombination hotspots and sex-biased recombination in Populus trichocarpa using dense genetic mapping and haplotype reconstruction.

The paper develops a MAGIC population in maize to map flowering time and plant height, finding that predictive models perform better when trained on direct data rather than indirect data from hybrids.

This study uses long-read metagenomics and metatranscriptomics to analyze soil communities, revealing phylum-specific secondary metabolite dynamics during wetting events.

This study identifies genomic traits of ectomycorrhizal transitions in Boletales by comparing gene repertoires and reconstructing gene duplication/loss histories.

The paper uses RNA sequencing and DNA affinity purification sequencing to study the sulfur starvation response in Neurospora crassa, revealing CYS-3's role in regulating sulfur metabolism and related pathways.

The paper describes a metagenome processing workflow that includes assembly, annotation, and binning, and provides tools for researchers to apply it to their data.

The paper confirms a two-step hybridization model for the formation of hexaploidy in Brassiceae and shows subgenomes have distinct loss rates but functionally compatible genes.

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.

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.