Anthony J W Hall

Regulatory architecture tunes gene expression noise in the plant heat shock response

This study shows that the plant heat shock regulatory network controls both the magnitude and distribution of stress-responsive gene expression across cells.

Machine learning models reveal environmental and genetic factors associated with the plant circadian clock

This study develops ChronoGauge, a machine learning model that estimates plant circadian time from transcriptomic data, enabling analysis of environmental and genetic factors affecting the circadian clock.

Selective breeding for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.)

This study identifies QTLs for determinacy and photoperiod sensitivity in common bean, linking them to population structure and providing insights for breeding and genetic research.

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

This study presents a chromosome-scale genome assembly and annotation of Alopecurus aequalis, revealing its genetic similarity to barley and expansion of herbicide resistance genes.

De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

This study annotates the wheat pan-transcriptome de novo and identifies gene diversity and expression patterns across multiple wheat cultivars and tissues.

Introgressions lead to reference bias in wheat RNA-Seq analysis

The paper shows RNA-Seq in hexaploid wheat is biased by introgressed genes and proposes a pantranscriptome reference to reduce this bias.

Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines

This study uses whole genome sequencing to analyze hexaploid wheat/Ambylopyrum muticum introgression lines, identifying structural disruptions and gene expression patterns associated with introgression.

A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

The paper develops chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat doubled haploid introgression lines using whole genome sequencing and SNP discovery.

Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function

This paper uses machine learning to predict circadian gene expression in Arabidopsis using DNA sequence features, identifies key regulatory elements, and optimizes sampling strategies for circadian transcript prediction.

Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel

The paper maps trehalose biosynthetic pathway genes to yield traits in spring wheat, finding significant associations and heritability contributions.

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

The paper presents a chromosome-scale rye genome assembly to study genomic evolution and agronomic traits in Triticeae crops.

Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of hexaploid wheat and diploid Aegilops tauschii

A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene

The paper maps the Yr7 yellow rust resistance gene in wheat using QTL mapping, association mapping, and mapping-by-sequencing, narrowing the interval to a candidate gene.

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

This study uses nanopore direct RNA sequencing to map the m6A epitranscriptome in Arabidopsis, revealing its role in mRNA processing and circadian rhythms.

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency

The paper analyzes recombination patterns in hexaploid wheat, identifies genes controlling recombination and gene conversion, and highlights a novel RecQ helicase gene involved in gene conversion.

Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat

The paper presents and validates two capture probe sets for wheat to enable efficient and cost-effective re-sequencing of genes and promoters.

Hidden variation in polyploid wheat drives local adaptation

The paper identifies hidden genetic and epigenetic variation in polyploid wheat that contributes to local adaptation and suggests using methylation and transposon diversity for breeding.

Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression

The paper examines single-cell circadian rhythms in Arabidopsis seedlings, revealing robust oscillations and spatial waves of gene expression that coordinate clock activity across the plant.

A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample

The paper introduces a modified sequence capture method that enables simultaneous analysis of genotype and methylation from the same genomic DNA sample in wheat.