Fei He

CLCNet: a contrastive learning and chromosome-aware network for genomic prediction in plants

CLCNet improves genomic prediction accuracy in plants by integrating contrastive learning and chromosome-aware feature selection, outperforming existing models across four crop species and ten traits.

Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

This study uses RNA-seq on 328 wheat lines to analyze gene expression diversity, identifying introgressed genes and their regulatory impacts on agronomic traits and disease resistance.

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

This study uses biGWAS to identify 65 Avr loci and 251 R loci in wheat and Blumeria graminis f. sp. tritici, revealing their interactions and implications for durable resistance breeding.

Reshaping epistatic network modules enhances wheat yield potential

This study identifies genetic modules and epistasis driving wheat yield improvement through GWAS and haplotype analysis across diverse environments.

Two divergent haploid nuclei shaped the landscape of population diversity in wheat stripe rust

The paper identifies two divergent haploid genomes in wheat stripe rust, showing their role in generating diversity and virulence through hybridization and recombination.

Multiplexed promoter and gene editing in wheat using the virus-based guide RNA delivery system

This study uses a virus-based guide RNA delivery system to enable efficient gene editing in wheat, demonstrating multiplexed editing of agronomic genes and heritable targeted deletions.

Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation

The paper develops a wheat haplotype graph database for efficient genotype storage and imputation, showing improved accuracy over existing methods.

The haplotype-based analysis of Aegilops tauschii introgression into hard red winter wheat and its impact on productivity traits

This study evaluates the impact of Aegilops tauschii introgression on wheat yield traits, identifying beneficial haplotypes associated with increased grain production and stability.

Expanding the range of editable targets in the wheat genome using the variants of the Cas12a and Cas9 nucleases

This study evaluates Cas12a and Cas9 variants for genome editing in wheat, showing LbCas12a and Cas9-NG can edit loci previously inaccessible to Cas9.

Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations.

The paper analyzes whole-genome sequences of 121 Puccinia triticina isolates to study lineage evolution and mutation patterns in asexual lineages.

Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes

The paper uses a differential nuclease sensitivity assay to analyze chromatin accessibility in wheat, revealing how repetitive and gene regions influence chromatin states and agronomic trait variation.

Multivariable regulation of gene expression plasticity in metazoans

This study quantifies gene expression plasticity across four metazoan species, identifies conserved regulatory elements, and links plasticity to gene function and disease.

Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat

This study uses gene editing and mutagenesis to show that TaGW2 homoeologues contribute additively to grain size and weight in wheat, with inter-cultivar differences in their effects.

The DOE Systems Biology Knowledgebase (KBase)

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

Pan- and core- network analysis of co-expression genes in a model plant

The paper analyzes 134 coexpression networks from Arabidopsis microarray datasets to show context-dependent gene coexpression patterns and introduces pan- and core-network concepts.