Personal Academic Portfolio

Qunhao Niu

Postdoctoral Associate in Animal & Avian Sciences at the University of Maryland, working on animal genomics, multi-omics analysis, and genomic prediction.

My research dissects the genetic basis of complex traits across livestock and poultry using GWAS, eQTL, TWAS, colocalization, chromatin accessibility, DNA methylation, RNA editing, and genomic prediction.

Animal & Avian Sciences Multi-omics Genomic Prediction
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Profile

Profile

About Me

I am a Postdoctoral Associate in the Department of Animal & Avian Sciences at the University of Maryland. My work focuses on computational and statistical genomics for animal breeding, connecting regulatory variant discovery, trait-associated genomic regions, and multi-layered biological priors for complex trait prediction.

I earned a Ph.D. in Animal Genetics, Breeding and Reproduction from the Graduate School of the Chinese Academy of Agricultural Sciences. As of 2026, my Google Scholar metrics include an h-index of 10 and i10-index of 10.

17 PubMed-indexed journal articles h-index 10 Google Scholar, 2026 i10-index 10 Google Scholar, 2026
Illustrated portrait of Qunhao Niu
Current Role
Postdoctoral Associate
Affiliation
Department of Animal & Avian Sciences, University of Maryland
Research Areas
Animal genomics, multi-omics, epigenomics, GWAS, eQTL, RNA editing, genomic prediction
Location
College Park, Maryland, United States
Email
niuqh97@umd.edu

Research Summary

Research Summary

01

Regulatory Genomics of Complex Traits

Identify regulatory variants and candidate genes associated with carcass, body weight, fatty acid composition, meat production, and host resistance traits.

02

Multi-omics Integration

Integrate RNA-seq, ATAC-seq, WGBS, ChIP-seq, long-read sequencing, MNase-seq, GWAS, eQTL, TWAS, and colocalization analyses.

03

Genomic Prediction and Breeding

Build biologically informed variant scoring and prediction strategies to improve genomic prediction accuracy for economically important traits.

Education

Academic Training

Ph.D. in Animal Genetics, Breeding and Reproduction

Institute of Animal Science, Graduate School of Chinese Academy of Agricultural Sciences

Thesis: Multi-omics Analysis of Genetic Basis for Carcass Traits in Beef Cattle and Genome Prediction.

Bachelor of Agronomy in Animal Science

College of Animal Science and Technology, South China Agricultural University

Thesis: Genetic Parameter Estimation of Growth Traits for Landrace Pigs.

Experience

Research Experience

Contact for Collaboration

Animal Functional Genomics and Epigenetics Group

Postdoctoral Associate, Department of Animal & Avian Sciences, University of Maryland

Investigate transcriptional regulation in chicken embryonic stem cells and primordial germ cells using long-read sequencing, MNase-seq, ChIP-seq, and other multi-omics approaches. Current work also profiles A-to-I RNA editing in Marek's disease of chickens to study host resistance and immune regulation.

Beef Cattle Multi-omics and Genomic Prediction

Institute of Animal Science, Chinese Academy of Agricultural Sciences

Dissected the genetic basis of body weight, carcass traits, and fatty acid composition through selection sweeps, GWAS, eQTL, TWAS, colocalization, chromatin accessibility, DNA methylation, and genomic prediction.

Functional Variant Scoring and Prediction

Meat production traits in beef cattle

Developed a comprehensive variant scoring strategy based on heritability partitioning across variant sets, then used high-ranking variants to improve genomic prediction accuracy.

Publications

Publications

Journal Article

Multi-omics dissection of the genetic regulation underlying fatty acid composition in cattle

Zhang T, Niu Q, Wang T, Wu J, Zhu B, Wang Z, Gao X, Chen Y, Gao H, Zhang L, Fu T, Gao T, Liu GE, Li J, Xu L

Genome Biology, 26, 432, 2025

PubMed DOI

Journal Article

Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle

Niu Q, Wu J, Wu T, Zhang T, Wang T, Zheng X, Zhao Z, Xu L, Wang Z, Zhu B, Zhang L, Gao H, Liu GE, Li J, Xu L

Genomics, Proteomics & Bioinformatics, 23(4), 2025

PubMed DOI

Journal Article

Multi-omics integration analysis reveals the regulatory impact of CNVs for slaughter traits in cattle

Wu J, Niu Q, Wu T, Su Y, Liu F, Zhao Z, Gao H, Li J, Xu L

International Journal of Biological Macromolecules, 321(Pt 2):146355, 2025

PubMed DOI

Journal Article

Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle

Zhu B, Wang T, Niu Q, Wang Z, Hay EH, Xu L, Chen Y, Zhang L, Gao X, Gao H, Cao Y, Zhao Y, Xu L, Li J

Communications Biology, 8(1):208, 2025

PubMed DOI

Journal Article

Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle

Zhao Z, Niu Q, Wu J, Wu T, Xie X, Wang Z, Zhang L, Gao H, Gao X, Xu L, Zhu B, Li J

Biology Direct, 19(1):147, 2024

PubMed DOI

Journal Article

Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle

Wu J, Wu T, Xie X, Niu Q, Zhao Z, Zhu B, Chen Y, Zhang L, Gao X, Niu X, Gao H, Li J, Xu L

Foods, 12(21), 2023

PubMed DOI

Journal Article

Evaluation of Linear Programming and Optimal Contribution Selection Approaches for Long-Term Selection on Beef Cattle Breeding

Zheng X, Wang T, Niu Q, Wu J, Zhao Z, Gao H, Li J, Xu L

Biology, 12(9), 2023

PubMed DOI

Journal Article

Identifying candidate genes for litter size and three morphological traits in Youzhou Dark goats based on genome-wide SNP markers

Sun X, Niu Q, Jiang J, Wang G, Zhou P, Li J, Chen C, Liu L, Xu L, Ren H

Genes, 14, 2023

PubMed DOI

Journal Article

Cis-eQTL analysis and functional validation of candidate genes for carcass yield traits in beef cattle

Wang T, Niu Q, Zhang T, Zheng X, Li H, Gao X, Chen Y, Gao H, Zhang L, Liu GE, Li J, Xu L

International Journal of Molecular Sciences, 23, 2022

PubMed DOI

Journal Article

Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts

Zhang T, Wang T, Niu Q, Zheng X, Li H, Gao X, Chen Y, Gao H, Zhang L, Liu GE, Li J, Xu L

BMC Genomics, 23(1):387, 2022

PubMed DOI

Journal Article

Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

Zhang T, Wang T, Niu Q, Xu L, Chen Y, Gao X, Gao H, Zhang L, Liu GE, Li J, Xu L

BMC Biology, 20(1):79, 2022

PubMed DOI

Journal Article

Comparative Transcriptomic Analysis Reveals Diverse Expression Pattern Underlying Fatty Acid Composition among Different Beef Cuts

Zhang T, Niu Q, Wang T, Zheng X, Li H, Gao X, Chen Y, Gao H, Zhang L, Liu GE, Li J, Xu L

Foods, 11(1), 2022

PubMed DOI

Journal Article

Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle

Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Zhang L, Gao H, Song J, Li J, Xu L

Genomics, 113:3325-3336, 2021

PubMed DOI

Journal Article

Identification of candidate variants associated with bone weight using whole genome sequence in beef cattle

Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Gao X, Chen Y, Zhang L, Gao H, Li J, Xu L

Frontiers in Genetics, 12:750746, 2021

PubMed DOI

Journal Article

Validation of the prediction accuracy for 13 traits in Chinese Simmental beef cattle using a preselected low-density SNP panel

Xu L, Niu Q, Chen Y, Wang Z, Xu L, Li H, Xu L, Gao X, Zhang L, Gao H, Cai W, Zhu B, Li J

Animals, 11, 2021

PubMed DOI

Journal Article

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

Zhao G, Liu Y, Niu Q, Zheng X, Zhang T, Wang Z, Xu L, Zhu B, Gao X, Zhang L, Gao H, Li J, Xu L

BMC Genomics, 22:678, 2021

PubMed DOI

Journal Article

Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle

Yang L, Niu Q, Zhang T, Zhao G, Zhu B, Chen Y, Zhang L, Gao X, Gao H, Liu GE, Li J, Xu L

Genomics, 113:812-820, 2021

PubMed DOI

Awards

Selected Honors

Honors

Outstanding Graduate Recognition

Beijing Outstanding Graduates and Outstanding Graduate of Chinese Academy of Agricultural Sciences, 2024.

Scholarship

National Scholarship for Doctoral Students

National Scholarship for Doctoral Students, Beijing, China, 2022; National Inspirational Scholarship, 2017.

Conference

Animal Genetics and Breeding Symposium

Excellent Poster Award and Young Traveler Award at the 22nd National Academic Symposium on Animal Genetics and Breeding, 2023.

Contact

Open to collaboration in animal genomics, multi-omics, and genomic prediction

Please reach out for research collaboration, data analysis, manuscript discussion, or academic opportunities.

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