Lukas A. Mueller

Breedbase 2.0 introduces new features for managing plant breeding data, including improved data handling, user permissions, trial quality control, and tools for transgenics and field layout.

DeltaBreed is a breeding data management system that integrates with BrAPI-compliant applications and provides interoperability test cases and future development plans.

This study analyzes the evolution of deleterious mutations and structural variants in tomato domestication, finding reduced genetic diversity and increased deleterious alleles, with implications for breeding.

The paper improves genomic prediction of agronomic traits in maize by integrating spatio-temporal modeling of multi-spectral aerial images with genetic data.

The paper presents a chromosome-level genome assembly and manual annotation of Diaphorina citri, along with transcriptome and endosymbiont genomes, providing genomic resources for pest control research.

The paper analyzes the genome and population genomics of Coffea arabica to reveal its diversification history and breeding-related genetic changes.

The paper uses isotope-labeled crosslinkers to analyze protein interactions and posttranslational modifications in Diaphorina citri across life stages, revealing developmental changes in chromatin structure.

This paper presents a chromosome-scale genome assembly for Solanum lycopersicoides and maps introgression lines to support genetic studies of traits in tomato.

The paper annotates Hox genes and their cofactors in the Asian citrus psyllid, revealing a split in the Hox cluster and an additional copy of the extradenticle gene.

The paper manually annotates twenty-seven genes potentially associated with circadian rhythm in Diaphorina citri, suggesting a circadian model similar to Danaus plexippus.

The paper manually curates and phylogenetically analyzes chitinase family genes in the Asian citrus psyllid to identify novel classes and inform pest control strategies.

The paper annotates 15 ubiquitin-proteasome pathway genes in Diaphorina citri to identify potential RNAi targets for managing HLB disease spread.

The paper annotates genes in glycolysis, gluconeogenesis, and trehaloneogenesis pathways in the Asian citrus psyllid to identify potential targets for controlling the pest.

The paper annotates and compares V-ATPase subunits in Diaphorina citri to support therapeutic development against citrus greening disease vectors.

The paper presents a population-based transcriptomics atlas of cassava, identifying differentially expressed genes and gene modules related to disease resistance and physiological traits.

The paper quantifies transcriptome responses of Diaphorina citri to citrus greening disease using a new genome assembly, showing tissue-specific gene expression changes.

The paper annotates 24 segmentation gene homologs in the Asian citrus psyllid, identifying most expected genes but missing eagle and invected.

The paper characterizes four chitin deacetylase genes in the Diaphorina citri genome, providing a foundation for future studies on their potential roles in exoskeleton formation and bacterial defense.

The paper develops an open-source R package, waves, for spectral data analysis in plant breeding and integrates it into the Breedbase database to enhance spectral data handling and analysis.

The paper annotates and analyzes the yellow gene family in the Asian citrus psyllid genome to identify potential targets for pest control.

The paper presents a high-quality genome of Solanum pimpinellifolium and identifies structural variants that underlie important tomato breeding traits.

The paper annotates three chitin synthesis pathway genes in Diaphorina citri, revealing one CHS gene and two UAP genes with distinct expression patterns.

The paper identifies and characterizes 24 Wnt signaling genes in Diaphorina citri using genome analysis and phylogenetic classification.

The paper identifies genetic loci associated with cyanide content in cassava, finding two major genes contributing to HCN levels and developing markers for breeding.

The paper introduces a web portal integrating pathosystem-wide resources and tools for studying citrus greening disease, enabling data sharing and analysis across multiple omics data types.

A PacBio and Hi-C tomato genome rebuild shrinks gaps from 81.71Mb to 44Kb; the matching ITAG4.0 annotation adds 4,794 genes and updates most carried-over models.

The paper presents a high-quality zucchini genome assembly and identifies a whole genome duplication in the Cucurbita genus.

This study identifies rapid gene and metabolite changes in maize leaves after caterpillar feeding, showing early defense responses and the role of benzoxazinoids and jasmonic acid pathways.

The paper manually curates gene models in the Asian citrus psyllid genome to improve annotation for HLB control research.