Understanding plant pathogen interactions using spatial and single-cell technologies

J Zhu, A Moreno-Pérez, G Coaker - Communications Biology, 2023 - nature.com
Plants are in contact with diverse pathogens and microorganisms. Intense investigation over
the last 30 years has resulted in the identification of multiple immune receptors in model and …

Resolving plant development in space and time with single-cell genomics

TM Nolan, R Shahan - Current opinion in plant biology, 2023 - Elsevier
Single-cell genomics technologies are ushering in a new research era. In this review, we
summarize the benefits and current challenges of using these technologies to probe the …

Spatially resolved transcriptomic analysis of the germinating barley grain

M Peirats-Llobet, C Yi, LC Liew… - Nucleic Acids …, 2023 - academic.oup.com
Seeds are a vital source of calories for humans and a unique stage in the life cycle of
flowering plants. During seed germination, the embryo undergoes major developmental …

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

C Grones, T Eekhout, D Shi, M Neumann… - The Plant …, 2024 - academic.oup.com
Single-cell and single-nucleus RNA-sequencing technologies capture the expression of
plant genes at an unprecedented resolution. Therefore, these technologies are gaining …

Lost in space: what single-cell RNA sequencing cannot tell you

K Adema, MA Schon, MD Nodine, W Kohlen - Trends in Plant Science, 2024 - cell.com
Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their
workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the …

Large language models in plant biology

HYI Lam, XE Ong, M Mutwil - Trends in Plant Science, 2024 - cell.com
Large language models (LLMs), such as ChatGPT, have taken the world by storm. However,
LLMs are not limited to human language and can be used to analyze sequential data, such …

Single-cell transcriptomics reveals heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions

R Tenorio Berrío, M Dubois - Journal of Experimental Botany, 2024 - academic.oup.com
Biotic and abiotic environmental cues are major factors influencing plant growth and
productivity. Interactions with biotic (eg symbionts and pathogens) and abiotic (eg changes …

The transcriptional integration of environmental cues with root cell type development

M Gouran, SM Brady - Plant Physiology, 2024 - academic.oup.com
Plant roots navigate the soil ecosystem with each cell type uniquely responding to
environmental stimuli. Below ground, the plant's response to its surroundings is orchestrated …

Exploring plant cis‐regulatory elements at single‐cell resolution: overcoming biological and computational challenges to advance plant research

JP Mendieta, A Sangra, H Yan, MAA Minow… - The Plant …, 2023 - Wiley Online Library
Cis‐regulatory elements (CREs) are important sequences for gene expression and for plant
biological processes such as development, evolution, domestication, and stress response …

ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images

L Jo, K Kajala - Journal of Experimental Botany, 2024 - academic.oup.com
As plant research generates an ever-growing volume of spatial quantitative data, the need
for decentralized and user-friendly visualization tools to explore large and complex datasets …