Ronan C. O’Malley

Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants

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.

A global regulatory atlas of Streptomyces reveals conserved and diversified transcriptional networks across actinomycetes

The paper constructs a regulatory atlas of Streptomyces and related actinomycetes using DAP-seq and ChIP-seq, revealing conserved and divergent transcriptional networks.

Multi-season analysis reveals hundreds of drought-responsive genes in sorghum

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

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

This study shows that TOR inhibition in algae increases amino acid levels through transcriptional activation of biosynthesis pathways and identifies a conserved transcription factor involved in nitrogen metabolism.

Single-cell-level response to drought in Sorghum bicolor reveals novel targets for improving water use efficiency

The paper identifies single-cell transcriptional responses to drought in Sorghum bicolor and highlights shared regulatory mechanisms across cell types.

A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

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.

Recruitment, rewiring, and deep conservation in flowering plant gene regulation

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.

Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungus R. microsporus reveals pervasive DNA methyl adenine regulatory network

The paper uses DAP-seq to analyze TF binding sites in R. microsporus, revealing DNA methylation's role in gene regulation and expanding fungal motif catalogs.

An optimized ChIP-Seq framework for profiling of histone modifications in Chromochloris zofingiensis

The paper optimizes a ChIP-Seq framework for histone modification profiling in Chromochloris zofingiensis and identifies H3K4me3 enrichment at transcription start sites.

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

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

Genome wide profiling of histone H3 lysine 4 methylation during the Chlamydomonas cell cycle reveals stable and dynamic properties of lysine 4 trimethylation at gene promoters and near ubiquitous lysine 4 monomethylation

This study uses ChIP-Seq to profile H3K4 methylation across the Chlamydomonas cell cycle, revealing distinct patterns of mono- and trimethylation at gene promoters and their relationship to gene expression.

Aspects of the Neurospora crassa sulfur starvation response are revealed by transcriptional profiling and DNA affinity purification sequencing

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 DOE JGI Metagenome Workflow

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

A network of MAP-Kinase pathways and transcription factors regulates cell-to-cell communication and cell wall integrity in Neurospora crassa

The paper identifies a regulatory network involving MAP-Kinase pathways and transcription factors that maintain cell integrity and mediate communication and cell fusion in Neurospora crassa.