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
Chromatin Genes Genome Dna Gene Expression Extrusion Epigenomics Reproducibility Chromatin Immunoprecipitation Regulation Gene Transcription Factors Vitamin A Change Point Domain Structure Divergence Modification Measuring Gata Transcription Factors Interleukin 6 Colon Galaxies Chromatin Immunoprecipitation Sequencing Histone PaintMost Recent Papers
Model-based Assessment of Replicability of Association Signals: Applications to Genome-wide Association Meta-analysis of Smoking and Drinking Phenotypes in 1.2 Million Individuals
D. McGuire1, Y. Jiang, M. Liu, J Weissenkampen, Scott Eckert1, Lina Yang, F Chen, GWAS, Sequencing Alcohol, Nicotine Use (GSCAN), A Berg, Scott Vrieze, B Jiang, Qunhua Li, D Liu, Nature communications
Methods to Assess the Reproducibility and Similarity of Hi-C Data
Tao Yang, Xi He, Lin An, Qunhua Li, 2022, on p. 17-37
RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes
Zhi Chai, Yafei Lyu, Qiuyan Chen, Cheng Hsin Wei, Lindsay M. Snyder, Veronika Weaver, Aswathy Sebastian, István Albert, Qunhua Li, Margherita T. Cantorna, A. Catharine Ross, 2021, Nutrition Reports International
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
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
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells
Ross C. Hardison, Yu Zhang, Cheryl A. Keller, Guanjue Xiang, Elisabeth F. Heuston, Lin An, Jens Lichtenberg, Belinda M. Giardine, David Bodine, Shaun Mahony, Qunhua Li, Feng Yue, Mitchell J. Weiss, Gerd A. Blobel, James Taylor, Jim Hughes, Douglas R. Higgs, Berthold Göttgens, 2020, Biochemistry and Molecular Biology International on p. 27-38
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
OnTAD
Lin An, Tao Yang, Jiahao Yang, Johannes Nuebler, Guanjue Xiang, Ross C. Hardison, Qunhua Li, Yu Zhang, 2019, Genome Biology on p. 1-16
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
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells
R Hardison, Y Zhang, Cheryl Keller, Guanjue Xiang, Elisabeth Heuston, Lin An, Jens Lichtenberg, Belinda Giardine, David Bodine, S Mahony, others, 2019, bioRxiv on p. 730358
Most-Cited Papers
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham, Anshul Kundaje, Shelley F. Aldred, Patrick J. Collins, Carrie A. Davis, Francis Doyle, Charles B. Epstein, Seth Frietze, Jennifer Harrow, Rajinder Kaul, Jainab Khatun, Bryan R. Lajoie, Stephen G. Landt, Bum Kyu Lee, Florencia Pauli, Kate R. Rosenbloom, Peter Sabo, Alexias Safi, Amartya Sanyal, Noam Shoresh, Jeremy M. Simon, Lingyun Song, Nathan D. Trinklein, Robert C. Altshuler, Ewan Birney, James B. Brown, Chao Cheng, Sarah Djebali, Xianjun Dong, Jason Ernst, Terrence S. Furey, Mark Gerstein, Belinda Giardine, Melissa Greven, Ross C. Hardison, Robert S. Harris, Javier Herrero, Michael M. Hoffman, Sowmya Iyer, Manolis Kellis, Pouya Kheradpour, Timo Lassmann, Qunhua Li, Xinying Lin, Georgi K. Marinov, Angelika Merkel, Ali Mortazavi, Stephen C.J. Parker, Timothy E. Reddy, Joel Rozowsky, 2012, Nature on p. 57-74
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt, Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, Peter Bickel, James B. Brown, Philip Cayting, Yiwen Chen, Gilberto DeSalvo, Charles Epstein, Katherine I. Fisher-Aylor, Ghia Euskirchen, Mark Gerstein, Jason Gertz, Alexander J. Hartemink, Michael M. Hoffman, Vishwanath R. Iyer, Youngsook L. Jung, Subhradip Karmakar, Manolis Kellis, Peter V. Kharchenko, Qunhua Li, Tao Liu, X. Shirley Liu, Lijia Ma, Aleksandar Milosavljevic, Richard M. Myers, Peter J. Park, Michael J. Pazin, Marc D. Perry, Debasish Raha, Timothy E. Reddy, Joel Rozowsky, Noam Shoresh, Arend Sidow, Matthew Slattery, John A. Stamatoyannopoulos, Michael Y. Tolstorukov, Kevin P. White, Simon Xi, Peggy J. Farnham, Jason D. Lieb, Barbara J. Wold, Michael Snyder, 2012, Genome Research on p. 1813-1831
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
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
Systematic evaluation of factors influencing ChIP-seq fidelity
Yiwen Chen, Nicolas Negre, Qunhua Li, Joanna O. Mieczkowska, Matthew Slattery, Tao Liu, Yong Zhang, Tae Kyung Kim, Housheng Hansen He, Jennifer Zieba, Yijun Ruan, Peter J. Bickel, Richard M. Myers, Barbara J. Wold, Kevin P. White, Jason D. Lieb, X. Shirley Liu, 2012, Nature Methods on p. 609-614
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
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
OnTAD
Lin An, Tao Yang, Jiahao Yang, Johannes Nuebler, Guanjue Xiang, Ross C. Hardison, Qunhua Li, Yu Zhang, 2019, Genome Biology on p. 1-16
Robust bent line regression
Feipeng Zhang, Qunhua Li, 2017, Journal of Statistical Planning and Inference on p. 41-55
News Articles Featuring Qunhua Li
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