Qunhua Li

Associate Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Professor of Statistics

Qunhua Li

Research Summary

Developing statistical and computational methods for analyzing complex omics data and improving quality and reproducibility of high-throughout data

Huck Graduate Students

Huck Affiliations

Links

Most Recent Publications

Methods to assess the reproducibility and similarity of Hi-C data

Tao 41. Yang, Xi He, Lin An, Qunhua Li,

Dissecting heritability, environmental risk, and air pollution causal effects using > 50 million individuals in MarketScan

Daniel McGuire, Havell Markus, Lina Yang, Jingyu Xu, Austin Montgomery, Arthur Berg, Qunhua Li, Laura Carrel, Dajiang J. Liu, Bibo Jiang, 2024, Nature Communications

Dissecting heritability, environmental risk, and air pollution causal effects using> 50 million individuals in MarketScan

D. McGuire, H. Markus, L. Yang, J. Xu, A. Montgomery, A Berg, Qunhua Li, L Carrel, D Liu, B Jiang, 2024, Nature communications on p. 1-14

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang, Xi He, Belinda M. Giardine, Kathryn J. Isaac, Kathryn Weaver, Dylan J. Taylor, Rajiv C. McCoy, Camden Jansen, Cheryl A. Keller, Alexander Q. Wixom, April Cockburn, Amber Reese Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F. Heuston, Stacie M. Anderson, Jing Luan, Marit W. Vermunt, Feng Yue, Michael E.G. Sauria, Michael C. Schatz, James Taylor, Berthold Göttgens, Berthoid Gottgens, Jim R. Hughes, Douglas R. Higgs, Mitchell J. Weiss, Yong Cheng, Gerd A. Blobel, David M. Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross C. Hardison, 2024, Genome Research on p. 1089-1105

Learning Robust Representations using a Change Point Framework

Ame 42. Osotsi, Qunhua Li, 2023, The 7th Workshop on Mining and Learning from Time Series (MiLeTS) at KDD 2021 on p. 8

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M. Saba, Katerina Kechris, 2023, PLoS Computational Biology

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

Souvik Seal, Qunhua Li, Elle Butler Basner, Laura Saba, Katerina Kechris, 2023, PLoS Computational Biology

CLIMB: High-dimensional association detection in large scale genomic data

H Koch, Cheryl Keller, G Xiang, B Giardine, F Zhang, Y Wang, Ross Hardison, Qunhua Li, 2022, Nature Communications on p. 6874

Assessing reproducibility of high-throughput experiments in the case of missing data

Roopali Singh, Feipeng Zhang, Qunhua Li, 2022, Statistics in Medicine on p. 1884-1899

Systematic Integration of Epigenomic Landscapes in Human and Mouse Blood Cells to Predict Activity and Targets of Regulatory Elements

Ross C. Hardison, Guanjue Xiang, Camden Jansen, Cheryl A. Keller, Belinda M. Giardine, April Cockburn, Xi He, Michael E. Sauria, Kathryn Weaver, Qunhua Li, Yu Zhang, 2022, FASEB Journal

Most-Cited Papers

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Tao Yang, Feipeng Zhang, Galip Gürkan Yardımci, Fan Song, Ross C. Hardison, William Stafford Noble, Feng Yue, Qunhua Li, 2017, Genome Research on p. 1939-1949

Measuring the reproducibility and quality of Hi-C data

Galip Gürkan Yardımcı, Hakan Ozadam, Michael E.G. Sauria, Oana Ursu, Koon Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R. Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng Yue, Job Dekker, William S. Noble, 2019, Genome Biology

OnTAD: Hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Lin An, Tao Yang, Jihao Yang, Johannes Nuebler, Guanjue Xiang, Ross Hardison, Qunhua Li, Yu Zhang, 2019, Genome Biology on p. 1-16

Epigenetic regulation of gene expression by Ikaros, HDAC1 and Casein Kinase II in leukemia

C. Song, X. Pan, Z. Ge, C. Gowda, Y. Ding, H. Li, Z. Li, G. Yochum, M. Muschen, Q. Li, K. J. Payne, S. Dovat, 2016, Leukemia on p. 1436-1440

A food-based approach that targets interleukin-6, a key regulator of chronic intestinal inflammation and colon carcinogenesis

Abigail Sido, Sridhar Radhakrishnan, Sung Woo Kim, Elisabeth Eriksson, Frank Shen, Qunhua Li, Vadiraja Bhat, Lavanya Reddivari, Jairam K.P. Vanamala, 2017, Nutrition Reports International on p. 11-17

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Guanjue Xiang, Cheryl A. Keller, Elisabeth Heuston, Belinda M. Giardine, Lin An, Alexander Q. Wixom, Amber Miller, April Cockburn, Michael E.G. Sauria, Kathryn Weaver, Jens Lichtenberg, Berthold Göttgens, Qunhua Li, David Bodine, Shaun Mahony, James Taylor, Gerd A. Blobel, Mitchell J. Weiss, Yong Cheng, Feng Yue, Jim Hughes, Douglas R. Higgs, Yu Zhang, Ross C. Hardison, 2020, Genome Research on p. 472-484

A continuous threshold expectile model

Feipeng Zhang, Qunhua Li, 2017, Computational Statistics and Data Analysis on p. 49-66

S3norm: Simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data

Guanjue Xiang, Cheryl A. Keller, Belinda Giardine, Lin An, Qunhua Li, Yu Zhang, Ross C. Hardison, 2020, Nucleic Acids Research on p. e43

Model-based assessment of replicability for genome-wide association meta-analysis

D McGuire, Y Jiang, M Liu, J Weissenkampen, S Eckert, L Yang, F Chen, A Berg, Mengzhen Liu, Yu Jiang, S Vrieze, Bibo Jiang, Robbee Wedow, Yue Li, Q Li, D Liu, David M. Brazel, Fang Chen, Gargi Datta, Jose Davila-Velderrain, Daniel McGuire, Chao Tian, Xiaowei Zhan, H. éléne Choquet, Anna R. Docherty, Jessica D. Faul, Johanna R. Foerster, Lars G. Fritsche, Maiken Elvestad Gabrielsen, Scott D. Gordon, Jeffrey Haessler, Jouke Jan Hottenga, Hongyan Huang, Seon Kyeong Jang, Philip R. Jansen, Yueh Ling, Reedik Ma ̈gi, Nana Matoba, George McMahon, Antonella Mulas, Valeria Orru, Teemu Palviainen, Anita Pandit, Gunnar W. Reginsson, Anne Heidi Skogholt, Jennifer A. Smith, Amy E. Taylor, Constance Turman, Gonneke Willemsen, Hannah Young, Kendra A. Young, Dajiang J. Liu, Arthur Berg, Qunhua Li, 2021, Nature Communications on p. 1964

Robust bent line regression

Feipeng Zhang, Qunhua Li, 2017, Journal of Statistical Planning and Inference on p. 41-55

News Articles Featuring Qunhua Li

Jul 30, 2024

Genes or environment? A new model for understanding disease risk factors

A new model more accurately predicts how genetics and air pollution levels causally influence disease development; may help better assess disease risk and intervention strategies.

Full Article

Jul 31, 2023

Penn State CTSI announces seven Bridges to Translation pilot funding recipients

Penn State Clinical and Translational Science Institute is helping to generate innovative health research ideas and promote collaboration through the awarding of pilot grants in its "Bridges to Translation" program.

Full Article

Nov 14, 2022

New statistical method improves genomic analyses

A new statistical method provides a more efficient way to uncover biologically meaningful changes in genomic data that span multiple conditions — such as cell types or tissues.

Full Article

Dec 17, 2019

New tool reveals DNA structures that influence disease

Disruption of certain DNA structures — called topologically associating domains, or TADs — is linked with the development of disease, including some cancers. With its newly created algorithm that quickly locates and helps elucidate the complex functions of TADs, an international team of researchers is making it easier to study these important structures and help prevent disease.

Full Article

Mar 26, 2019

CBIOS Trainee Hillary Koch Awarded NIH Fellowship

Koch's dissertation proposal, "Statistical Methods for Differential Peak Detection in Hi-C Data," was funded upon its first submission to the National Human Genome Research Institute.

Full Article