Qiongshi Lu

Statistical Geneticist
PhD Candidate in Biostatistics

See my work

About Me

Qiongshi is a fourth-year doctoral student in biostatistics at Yale School of Public Health. His thesis advisor is Dr. Hongyu Zhao. Qiongshi is currently leading several research projects in Yale Center for Statistical Genomics and Proteomics. He is also actively involved in multiple collaborative studies of human complex diseases.


2012 - 2017      Ph.D. in Biostatistics, Yale University
2008 - 2012      B.S. in Mathematics, Tsinghua University

Selected Honors and Awards

2016      Best Student Poster Award, The 30th New England Statistics Symposium
2016      Travel Fellowship, Alzheimer's Association International Conference
2016      Conference Travel Fellowship, Yale Graduate Student Assembly
2015      ASHG/Charles J. Epstein Trainee Award for Excellence in Human Genetics Research - Finalist
2012      Outstanding Graduate of Tsinghua University
2011      Torchbearer of the 26th Universiade in Shenzhen, China
2010      Tsinghua Xuetang Mathematics Program
2010      National Scholarship of China


Address:   60 College Street, New Haven, CT, 06520
Email:   qiongshi DOT lu AT yale DOT edu   


Yale Biostatistics
Dr. Hongyu Zhao's Lab | Center for Statistical Genomics and Proteomics


Qiongshi's research focuses on genomic functional annotations and their applications in human genetics. He is interested in developing statistical methods to leverage functional annotations in GWAS signal prioritization, functional variant fine mapping, and genetic risk prediction.


Asterisk * indicates equal contribution

Submitted Papers

[9] Hu Y.*, Lu Q.*, Powles R., Yao X., Yang C., Fang F., Xu X., Zhao H.
Leveraging functional annotations in genetic risk prediction for human complex diseases.

Published Papers

[8] Zhao B., Lu Q., Cheng Y., Belcher J., Siew E., Leaf D., Body S., Fox A., Waikar S., Collard C., Thiessen-Philbrook H., Ikizler T., Ware L., Edelstein C., Garg A., Choi M., Schaub J., Zhao H., Lifton R., Parikh C. for the TRIBE-AKI Consortium. (2016).
A genome-wide association study to identify single nucleotide polymorphisms for acute kidney injury.
American Journal of Respiratory and Critical Care Medicine, in press.

[7] Lu Q., Jin C., Sun J., Bowler R., Kechris K., Kaminski N., Zhao H. (2016).
Post-GWAS prioritization through data integration provides novel insights on chronic obstructive pulmonary disease.
Statistics in Biosciences, in press.

[6] Lu Q.*, Powles R.*, Wang Q., He B., Zhao H. (2016).
Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies.
PLOS Genetics, 12(4): e1005947.
Predoctoral Finalist of 2015 ASHG/Charles J. Epstein Trainee Award for Excellence in Human Genetics Research
Best Student Poster Award at the 30th New England Statistics Symposium

[5] Li M., Foli Y., Liu Z., Wang G., Hu Y., Lu Q., Selvaraj S., Lam W., Paintsil E. (2016).
High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals.
HIV Medicine, in press.

[4] Lu Q., Yao X., Hu Y., Zhao H. (2016).
GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation.
Bioinformatics, 32(4): 542-548.

[3] Lu Q., Hu Y., Sun J., Cheng Y., Cheung K., Zhao H. (2015).
A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.
Scientific Reports, 5, 10576.

[2] Wang Q.*, Lu Q.*, Zhao H. (2015).
A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing.
Frontiers in Genetics, 6:149.

[1] Lu Q., Ren S., Lu M., Zhang Y., Zhu D., Zhang X., Li T. (2013).
Computational prediction of associations between long non-coding RNAs and proteins.
BMC Genomics, 14(1), 651.



12/20/2016      The 10th ICSA International Conference, SJTU, Shanghai, China (Upcoming)
08/03/2016      JSM 2016, Chicago, IL
07/24/2016      Alzheimer's Association International Conference 2016, Toronto, Canada
10/08/2015      ASHG 2015, Baltimore, MD
07/06/2015      Workshop on Data Science in Biomedicine, HKBU, Hong Kong, China
05/12/2015      Bioinformatics Transition Workshop, SAMSI, Research Triangle Park, NC
02/16/2015      Omics Data Integration Workshop, SAMSI, Research Triangle Park, NC

Poster Presentations

10/21/2016      ASHG 2016, Vancouver, Canada (Upcoming)
07/26/2016      Alzheimer's Association International Conference 2016, Toronto, Canada  
04/23/2016      The 30th NESS, Yale University, New Haven, CT     Best Student Poster Award
06/29/2015      ENCODE 2015 Research Applications and Users Meeting, Potomac, MD  
04/25/2015      The 29th NESS, University of Connecticut, Storrs, CT  



Genetic risk prediction using large-scale GWAS summary data and integrative functional annotations.


GenoSkyline is a collection of tissue-specific functional annotations. The tissue-specific functionality is inferred through integrative analysis of Roadmap epigenomic data. Currently available tissue/cell types include brain, GI, lung, heart, blood, muscle, epithelium, breast, ESC, and fetal cells. The GenoSkyline framework is general so that it can be extended to cell types of your own interest.


GenoWAP (Genome Wide Association Prioritizer) is a GWAS signal prioritization method. It uses empirical Bayes techniques to evaluate the functional potential of each SNP in genome-wide association studies. The software as well as the source code can be accessed on its website.


GenoCanyon is a statistical framework to predict functional non-coding regions in the human genome through integrated analysis of computational and experimental annotation data. Pre-calculated functional scores for hg19 can be downloaded from the GenoCanyon website. We also provide a web application to visualize GenoCanyon scores.