Qunhua Li
Associate Chair, Intercollege Graduate Degree Program in Bioinformatics and Genomics; Associate Professor of Statistics
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Wartik Lab
University Park, PA - qul12@psu.edu
- 814-865-9468
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
Publication Tags
Genes Reproducibility Chromatin Gene Expression Genome Dna Statistical Models Experiment Gene High Throughput Interleukin 6 Change Point Epigenomics Galaxies Protein Proteins Methodology Simulation Datasets Chromatin Immunoprecipitation Sequencing Extrusion Heterogeneity Model Regression WorkflowMost Recent Publications
Methods to assess the reproducibility and similarity of Hi-C data
Tao Yang, Xi He, Lin An, Qunhua Li,
Learning Robust Representations using a Change Point Framework
Ame Osotsi, Qunhua Li, 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 Saba, Katerina Kechris, 2022, PLoS Computational biology
CLIMB: High-dimensional association detection in large scale genomic data
Hillary Koch, Cheryl A. Keller, Guanjue Xiang, Belinda Giardine, Feipeng Zhang, Yicheng Wang, Ross C. Hardison, Qunhua Li, 2022, Nature Communications
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
Segmented correspondence curve regression for quantifying covariate effects on the reproducibility of high-throughput experiments
Feipeng Zhang, Qunhua Li, 2022, Biometrics
Transcriptional Profiling of the Small Intestine and the Colon Reveals Modulation of Gut Infection with Citrobacter rodentium According to the Vitamin A Status
Zhi Chai, Yafei Lyu, Qiuyan Chen, Cheng Hsin Wei, I.M. Snyder, Lindsay M. Snyder, Veronika Weaver, Aswathy Sebastian, István Albert, Qunhua Li, Margherita T. Cantorna, Catharine Ross, A Ross, 2022, Nutrients on p. 1563
Methods to Assess the Reproducibility and Similarity of Hi-C Data
Tao Yang, Xi He, Lin An, Qunhua Li, 2022, on p. 17-37
Model-based assessment of replicability for genome-wide association meta-analysis
Daniel McGuire, Yu Jiang, Mengzhen Liu, J. Dylan Weissenkampen, Scott Eckert, Lina Yang, Fang Chen, Mengzhen Liu, Yu Jiang, Robbee Wedow, Yue Li, 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, Bibo Jiang, Qunhua Li, 2021, Nature Communications
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
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang, 2013, PLoS Computational Biology
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
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
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
Galaxy tools to study genome diversity
Oscar C. Bedoya-Reina, Aakrosh Ratan, Richard Burhans, Hie Lim Kim, Belinda Giardine, Cathy Riemer, Qunhua Li, Thomas L. Olson, Thomas P. Loughran, Bridgett M. vonHoldt, George H. Perry, Stephan C. Schuster, Webb Miller, 2013, GigaScience on p. 17
Robust bent line regression
Feipeng Zhang, Qunhua Li, 2017, Journal of Statistical Planning and Inference on p. 41-55
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 semi-parametric statistical model for integrating gene expression profiles across different platforms
Yafei Lyu, Qunhua Li, 2016, BMC Bioinformatics on p. 51
A continuous threshold expectile model
Feipeng Zhang, Qunhua Li, 2017, Computational Statistics and Data Analysis on p. 49-66
News Articles Featuring Qunhua Li
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