J. R. Ecker

Single nuclei sequencing reveals C4 photosynthesis is based on rewiring of ancestral cell identity networks

The paper uses single nuclei sequencing to show C4 photosynthesis evolves through rewiring of cell identity networks from C3 plants.

Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

The paper presents a time-resolved single-cell and spatial gene regulatory atlas of Arabidopsis thaliana infected by bacterial pathogens, revealing immune responses and gene regulatory logic.

A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

The paper creates a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development using over 800,000 nuclei across ten stages, revealing transcriptional conservation and heterogeneity in cell types.

Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways

The paper constructs a cross-regulation network of plant hormone signaling pathways by analyzing transcription factor activity and dynamic regulatory models in Arabidopsis seedlings.

Stress Recovery Triggers Rapid Transcriptional Reprogramming and Activation of Immunity in Plants

This study shows that drought recovery in plants rapidly activates immune responses, enhancing pathogen resistance across multiple tomato species.

Arabidopsis transcriptome responses to low water potential using high throughput plate assays

The paper compares transcriptional responses in Arabidopsis to different water potential reduction methods and introduces a high-throughput hard agar assay.

PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue

PHYTOMap enables low-cost, transgene-free single-cell spatial gene expression analysis in plant tissue, demonstrating its ability to identify cell types in Arabidopsis roots.

Single nucleus multi-omics regulatory atlas of the murine pituitary

The paper creates a single nucleus multi-omics atlas of the murine pituitary, revealing cell type-specific regulatory mechanisms and identifying a cis-regulatory region linked to fertility.

Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth

This study analyzes the genome and time-of-day transcriptome of Wolffia australiana to link its extreme morphological minimization with reduced circadian regulation and continuous growth.

A new plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for begomoviruses

This paper identifies a plant-specific syntaxin-6 protein, NISP, that facilitates begomovirus intracellular transport by interacting with viral proteins and forming a complex for DNA translocation.

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

The paper develops an integrated multi-omic framework to study the plant response to jasmonic acid, identifying new regulatory components and crosstalk points with other signaling pathways.

The complex architecture and epigenomic impact of plant T-DNA insertions

This study characterizes the structural complexity and epigenomic impact of T-DNA insertions in Arabidopsis using long-read sequencing technologies.