The paper presents a haplotype-resolved genome assembly of the pomegranate cultivar 'Wonderful' using DNA from haploid pollen grains and long-read sequencing technologies.

bioRxiv · Jul 18, 2026 · PreprintGenomics

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads

Haoyu Cheng, Han Qu, Sean K. McKenzie, Katherine R. Lawrence, Rhydian Windsor, Mike Vella, Peter J. Park, Heng Li

The paper introduces hifiasm (ONT), an algorithm that enables near telomere-to-telomere genome assembly using standard ONT Simplex reads, reducing computational demands and improving chromosome reconstruction.

Nature · Feb 4, 2026Peer-reviewedBioinformatics

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

Yuwei Zhang, Han Qu, Qian Qin, Heng Li, Peter J. Park

This study evaluates diploid donor-specific assemblies for improving somatic structural variant detection in cancer genomes, finding they identify more variants and reduce artifacts compared to standard references.

bioRxiv · Oct 28, 2025 · PreprintGenomics

IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells

Han Qu, Ruidong Li, Lei Yu, Wei‐Ming Chen, Yuanfa Feng, Qiong Jia, Ryan C. Traband, Xuesong Wang, Shibo Wang, Luoxian He, Zixian Wang, Meng Qu, Sergio Pietro Ferrante, Jianguo Zhu, Weide Zhong, , Zhenyu Jia

IIIandMe improves haplotype phasing accuracy using three gametes, validated through simulation and citrus data.

bioRxiv · Dec 7, 2022 · PreprintBioinformatics

CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer

Ruidong Li, Han Qu, Shibo Wang, John M. Chater, Xuesong Wang, Yanru Cui, Lei Yu, Rui Zhou, Qiong Jia, Ryan C. Traband, Meiyue Wang, Weibo Xie, Dongbo Yuan, Jianguo Zhu, Weide Zhong, Zhenyu Jia

CancerMIRNome provides an interactive database for analyzing and visualizing miRNA expression data from cancer studies to identify dysregulated miRNAs and develop biomarkers.

Nucleic Acids Research · Sep 8, 2021Peer-reviewedBioinformatics

Extended Application of Genomic Selection to Screen Multi-Omics Data for Prognostic Signatures of Prostate Cancer

Ruidong Li, Shibo Wang, Yanru Cui, Han Qu, John M. Chater, Le Zhang, Julong Wei, Meiyue Wang, YANG CANG XU, Lei Ming Yu, Jianming Lü, Yuanfa Feng, Rui Zhou, Yuhan Huang, Renyuan Ma, , Zhenyu Jia

The paper applies genomic selection methods to multi-omics data to develop prognostic signatures for prostate cancer, showing improved predictability and computational efficiency.

Briefings in Bioinformatics · Aug 3, 2020Peer-reviewedBioinformatics

Inference of Chromosome-length Haplotypes Using Genomic Data of Three to Five Single Gametes

Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, John M. Chater, Le Zhang, Julong Wei, Yuan‐Ming Zhang, Chenwu Xu, Weide Zhong, Jianguo Zhu, Jianming Lü, Yuanfa Feng, Weiming Chen, Renyuan Ma, , Zhenyu Jia

Hapi infers chromosome-length haplotypes from 3-5 gametes, outperforming existing methods in accuracy, reliability, and cost efficiency.

Molecular Biology and Evolution · Jul 9, 2020Peer-reviewedBioinformatics

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC

Ruidong Li, Han Qu, Shibo Wang, Julong Wei, Le Zhang, Renyuan Ma, Jianming Lü, Jianguo Zhu, Weide Zhong, Zhenyu Jia

GDCRNATools provides an R/Bioconductor package for analyzing lncRNA, miRNA, and mRNA data from the GDC to study ceRNA regulatory networks in cancers.

Bioinformatics · Feb 28, 2018Peer-reviewedBioinformatics

Optimizing Trait Predictability in Hybrid Rice Using Superior Prediction Models and Selective Omic Datasets

Shibo Wang, Julong Wei, Ruidong Li, Han Qu, Weibo Xie, Zhenyu Jia

The paper evaluates prediction strategies for hybrid rice traits using various omic datasets and methods, finding genomic-metabolomic combinations and BLUP as most effective.

bioRxiv · Feb 7, 2018 · PreprintGenetics