Iain C. Macaulay

EISCA and EISTA are pipelines for single-cell and spatial transcriptomics analysis that provide standardized, modular workflows for data processing and downstream analysis.

This study maps the telencephalon transcriptome of cleaner wrasse to identify conserved neural cell populations and gene networks involved in social behavior.

The paper shows that nitrogen responses in plant roots are cell-type specific and evolve across species, with NLP7 proteins modulating these responses in Arabidopsis and tomato.

This study uses spatial transcriptomics to analyze gene expression gradients in wheat inflorescences, revealing dynamic spatio-temporal organization along the apical-basal axis.

The paper shows that plant progeny inherit maternal climate adaptation through hormone transport, specifically via temperature-dependent ABA signaling during seed development.

This study compares long-read single-cell sequencing platforms, identifying common limitations and demonstrating their utility for isoform-resolved analyses.

The paper constructs a spatiotemporal atlas of wheat inflorescence development using single-cell omics, identifying cell types, genes, and chromatin regions involved in spikelet and floret formation.

This study shows that a low protein diet reduces liver damage from Salmonella infection by altering macrophage metabolism and autophagy.

The paper uses single-nucleus RNA sequencing to identify five distinct classes of anterolateral system neurons in the adult mouse spinal cord and their laminar distribution.

This paper introduces a method to profile the transcriptome of live cells over time, showing treatment induces transcriptionally stable cells in glioblastoma.

The paper generates a molecular map of the avian trunk and tailbud using single-cell and spatial transcriptomics, identifying cell lineages and spatially restricted genes.

The paper identifies a non-canonical genetic code in a ciliate where UAA and UAG codons specify different amino acids, challenging the universality of the genetic code.

This study uses single-cell genome-and-transcriptome sequencing to analyze the impact of chromosome instability on cellular states and development in human preimplantation embryos.

The paper presents a low-cost genomic DNA extraction method for soil samples, which produces high-quality DNA suitable for amplicon sequencing and downstream applications at a lower cost than commercial kits.

The paper uses single-cell genomics to analyze bacterial population structures in antibiotic stress experiments, revealing sub-populations and resistance development not detectable with bulk sequencing.

The paper identifies non-neuronal cell types in the olfactory system expressing SARS-CoV-2 entry genes, suggesting indirect mechanisms for COVID-19-associated anosmia.

The paper evaluates de novo genome assembly methods for a low-quality non-model mammal sample, finding that more data types do not always improve assembly quality.

This study combines short- and long-read scRNA-seq to analyze gene and isoform expression changes in hematopoietic stem and progenitor cells during differentiation and ageing.

This paper introduces Grid-seq, a cost-effective spatial transcriptomics method for plants, and demonstrates its ability to detect immune responses in Arabidopsis thaliana to flagellin-22.

This paper compares genome assembly technologies for the potato species S. verrucosum, evaluating their completeness, accuracy, cost, and computational requirements.