Charles Chen

Drought-tolerant phenotypes associated with patterns of deterministic microbiome assembly across peanut genotypes

The paper examines how drought-response phenotypes in peanut genotypes influence microbiome assembly patterns in different soil compartments under field conditions.

In Vitro Characterization of Extracellular Vesicles from the Medicinal Plant Centella asiatica for Aesthetic Applications

This study characterizes extracellular vesicles from Centella asiatica and shows they reduce oxidative stress, melanin, and inflammation in vitro and in a UVB-induced mouse model.

Development and Optimization of Expected Cross Value for Mate Selection Problems

This study develops an expected cross value (ECV) criterion and integer linear programming framework to optimize mate selection in breeding programs by maximizing desirable genetic inheritance while controlling inbreeding.

Gene-language models are whole genome representation learners

This paper introduces a gene-language model that generates whole-genome vector representations from bacterial species, achieving state-of-the-art accuracy in antibiotic resistance prediction.

Weighted Kernels Improve Multi-Environment Genomic Prediction

This paper develops a genomic selection framework using weighted kernels to improve multi-environment prediction by incorporating genetic associations and population characteristics, achieving up to 31% higher predictability in winter wheat.

Pan-genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

The paper predicts antibiotic resistance in Elizabethkingia using pan-genomic analysis and machine learning, achieving high F1 scores for clindamycin and vancomycin resistance.

Inter- and Intra-Generation Genomic Predictions for Douglas-fir Growth in Unobserved Environments

The paper improves genomic prediction accuracy for Douglas-fir growth in unobserved environments by incorporating environmental covariates and genotype-by-environment interactions in a reaction-norm model using ssGBLUP.

SNP Variable Selection by Generalized Graph Domination

This paper introduces a SNP variable selection method using k-dominating set graph theory and demonstrates its effectiveness in pedigree reconstruction and species delineation.

Genomic Surveillance for Antimicrobial Resistance in Mannheimia haemolytica Using Nanopore Single Molecule Sequencing Technology

The paper uses nanopore sequencing to identify antimicrobial resistance genes in Mannheimia haemolytica strains and validates their resistance phenotypes.