Yiheng Hu

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

The paper curates and presents a collection of long-read genome assemblies for Arabidopsis thaliana accessions to enhance plant genome research.

Biotic interactions shape infection outcomes in Arabidopsis

This study identifies key microbial taxa associated with health and disease in Arabidopsis by analyzing microbiome data and using machine learning to distinguish infected from uninfected plants.

Inferring species compositions of complex fungal communities from long- and short-read sequence data

The paper compares methods for identifying fungal species from sequencing data and finds that aligning sequences to a fungi-specific database with coverage cutoffs improves accuracy.

Linked machine learning classifiers improve species classification of fungi when using error-prone long-reads on extended metabarcodes

This paper demonstrates that linked machine learning classifiers improve species classification of fungi using error-prone long-reads on extended metabarcodes, achieving high recall and low false positives.

Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina

The paper identifies and corrects phase switches in Hi-C data for dikaryotic fungus assemblies using Nanopore and HiFi sequencing, showing HiFi's superiority in phasing low heterozygosity genomes.