John P. Hamilton

Time-dependent transcriptomic changes following protoplast isolation in plants

The paper characterizes time-dependent transcriptomic changes in plant protoplasts across species and identifies stress-like cell states in single-cell RNA-seq data.

A Comprehensive Epidermal Map from a Poplar Single-Cell Shoot Atlas Reveals New Trichome-Specific Genes

The paper presents a single-cell RNA-seq atlas of poplar shoots, identifies epidermal subclusters, and discovers new trichome-specific genes through integration with bulk transcriptome data.

Engineering carotenoid and steroidal glycoalkaloid depleted tomato fruit for heterologous production of high value terpenes

This study engineers tomato fruit to produce high-value terpenes by modifying genes involved in specialized metabolism.

Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding

The paper develops a resource of 97 dihaploid potato clones to aid diploid breeding, identifies diversity in the maturity locus, and highlights structural genomic variation.

Chromosome-scale genome assembly for Yellow Wood sorrel, Oxalis stricta

This paper presents a chromosome-scale genome assembly for Oxalis stricta, revealing its allotetraploid nature and synteny with related species.

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience

This study creates a gene atlas for tetraploid potato, identifying genes involved in tuberization and stress resilience through coexpression modules and structural variation analysis.

High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes

This study analyzes diel transcriptomes of autotetraploid potato to reveal conservation of cyclic gene expression and function across tissues and conditions.

Single cell multi-omics reveals rare biosynthetic cell types in the medicinal tree Camptotheca acuminata

The paper uses single-cell multi-omics to identify rare cell types involved in camptothecin biosynthesis in Camptotheca acuminata.

Discovery of iridoid cyclase completes the iridoid pathway in asterids

The paper identifies an enzyme, ICYC, that catalyzes the cyclization of an enol intermediate in the iridoid biosynthesis pathway in asterids, completing the pathway and enabling metabolic engineering of iridoid compounds.

Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato

This study presents a phased chromosome-level genome assembly of sweetpotato, revealing its origin from a wild tetraploid relative and identifying genetic relationships with other progenitors.

Jan and mini-Jan, a model system for potato functional genomics

The paper introduces Jan and mini-Jan, two potato lines with improved traits for functional genomics research, including a high homozygosity genome and CRISPR-edited compact growth.

A reference-quality NLRome for the hexaploid sweetpotato and diploid wild relatives

The paper catalogs NLR diversity in sweetpotato and wild relatives using RenSeq, identifying 800-1,200 NLRs and highlighting CNL diversity and conservation across genotypes.

Physiological and Molecular Responses of Projected Future Temperatures on Potato Tuberization

This study investigates how future temperature projections affect potato tuberization by analyzing physiological responses and transcriptomic changes under heat stress.

Cell-type aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus

The paper constructs a cell-type-aware gene regulatory network for MIA biosynthesis in C. roseus using single-cell multi-omics data, identifying a novel idioblast-specific TF that regulates late-stage biosynthetic genes.

K-mer Genome-wide Association Study for Anthracnose and BCMV Resistance in the Andean Diversity Panel

This paper uses k-mer-based GWAS to identify disease resistance associations in common beans, revealing pan-genomic variation and improved resolution compared to traditional SNP methods.

Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression

The paper presents a chromosome-scale genome assembly of Chia pinta and identifies population structure and interspecies introgression in Salvia species.

Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR

The paper develops a mid-density targeted GBS assay for potato using DArTag technology and evaluates its performance with polyBreedR software for imputation and trait tracking.

Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis

The paper identifies genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis and finds shared and unique transcriptional responses to heat, salt, and drought stresses.

Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain

This study evaluates prediction models for tocochromanol content in maize grain using genomic and transcriptomic data, finding that incorporating biological knowledge improves predictive ability.

Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain

The paper combines GWAS and TWAS to identify 13 candidate causal genes for tocochromanol levels in maize grain, including five previously unassociated genes.

Transcriptome-wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels

This study uses transcriptome-wide association and prediction to identify genes related to carotenoid and tocochromanol levels in sweet corn and shows transcriptomic data improve predictive models.

Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

This study identifies genetic factors influencing zinc and cadmium concentrations in sweet corn kernels through genome-wide association analysis.

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

The paper identifies eleven biosynthetic genes explaining most of the natural variation in carotenoid levels in maize grain through QTL analysis and expression correlation.