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
Dna Chromatin Reproducibility Experiment Genes Genome Methodology Experiments Analysis High Throughput Mass Spectrometry Interleukin 6 Measuring Scoring Clone Gene Expression Method Peptides T Cells Change Point Proteins Model Encyclopedias Extrusion SoftwareMost Recent Papers
S3norm
Guanjue Xiang, Cheryl A. Keller, Belinda Giardine, Lin An, Qunhua Li, Yu Zhang, Ross C. Hardison, 2020, Nucleic acids research on p. e43
Individualized Modeling to Distinguish Between High and Low Arousal States Using Physiological Data
Ame Osotsi, Zita Oravecz, Qunhua Li, Joshua Smyth, Timothy R. Brick, 2020, Journal of Healthcare Informatics Research on p. 91-109
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
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells
Ross Hardison, Y Zhang, Cheryl Keller, G Xiang, E Heuston, L An, J Lichtenberg, B Giardine, D Bodine, Shaun Mahony, Q Li, F Yue, M Weiss, G Blobel, J Taylor, J Hughes, D Higgs, B Göttgens, 2020, IUBMB life on p. 27-38
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
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Guanjue Xiang, Cheryl Keller, Elisabeth Heuston, Belinda Giardine, Lin An, Alexander Wixom, Amber Miller, April Cockburn, Jens Lichtenberg, Berthold Gottgens, others, David Bodine, Shaun Mahony, James Taylor, Gerd Blobel, Mitchell Weiss, Yong Cheng, Feng Yue, Jim Hughes, Douglas Higgs, Yu Zhang, Ross Hardison, 2019, bioRxiv
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 hematopoietic cells
Ross Hardison, Yu Zhang, Cheryl Keller, Guanjue Xiang, Elisabeth Heuston, Lin An, Jens Lichtenberg, Belinda Giardine, David Bodine, Shaun Mahony, Qunhua Li, Feng Yue, Mitchell Weiss, Gerd Blobel, James Taylor, Jim Hughes, Douglas Higgs, Berthold Gottgens, 2019, IUBMB LIFE
powerTCR
Hillary Koch, Dmytro Starenki, Sara J. Cooper, Richard M. Myers, Qunhua Li, 2018, PLoS computational biology
A regression framework for assessing covariate effects on the reproducibility of high-throughput experiments
Qunhua Li, Feipeng Zhang, 2018, Biometrics on p. 803-813
Most-Cited Papers
A user's guide to the Encyclopedia of DNA elements (ENCODE)
Richard M. Myers, John Stamatoyannopoulos, Michael Snyder, Ian Dunham, Ross Cameron Hardison, Bradley E. Bernstein, Thomas R. Gingeras, W. James Kent, Ewan Birney, Barbara Wold, Gregory E. Crawford, Charles B. Epstein, Noam Shoresh, Jason Ernst, Tarjei S. Mikkelsen, Pouya Kheradpour, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Lucas D. Ward, Robert C. Altshuler, Michael F. Lin, Manolis Kellis, Carrie A. Davis, Philipp Kapranov, Alexander Dobin, Christopher Zaleski, Felix Schlesinger, Philippe Batut, Sudipto Chakrabortty, Sonali Jha, Wei Lin, Jorg Drenkow, Huaien Wang, Kim Bell, Ian Bell, Hui Gao, Erica Dumais, Jacqueline Dumais, Stylianos E. Antonarakis, Catherine Ucla, Christelle Borel, Roderic Guigo, Sarah Djebali, Julien Lagarde, Colin Kingswood, Paolo Ribeca, Micha Sammeth, Tyler Alioto, Angelika Merkel, Hagen Tilgner, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann, Hazuki Takahashi, Rehab F. Abdelhamid, Gregory Hannon, Katalin Toth Fejes, Jonathan Preall, Assaf Gordon, Vihra Sotirova, Alexandre Reymond, Cedric Howald, Emilie Aït Yahya Graison, Jacqueline Chrast, Yijun Ruan, Xiaoan Ruan, Atif Shahab, Wan Ting Poh, Chia Lin Wei, Terrence S. Furey, Alan P. Boyle, Nathan C. Sheffield, Lingyun Song, Yoichiro Shibata, Teresa Vales, Deborah Winter, Zhancheng Zhang, Darin London, Tianyuan Wang, Damian Keefe, Vishwanath R. Iyer, Bum Kyu Lee, Ryan M. McDaniell, Zheng Liu, Anna Battenhouse, Akshay A. Bhinge, Jason D. Lieb, Linda L. Grasfeder, Kimberly A. Showers, Paul G. Giresi, Seul K.C. Kim, Christopher Shestak, Florencia Pauli, Timothy E. Reddy, Jason Gertz, E. Christopher Partridge, Preti Jain, Rebekka O. Sprouse, Anita Bansal, Barbara Pusey, Michael A. Muratet, Katherine E. Varley, Kevin M. Bowling, Kimberly M. Newberry, Amy S. Nesmith, Jason A. Dilocker, Stephanie L. Parker, Lindsay L. Waite, Krista Thibeault, Kevin Roberts, Devin M. Absher, Ali Mortazavi, Brian Williams, Georgi Marinov, Diane Trout, Brandon King, Kenneth McCue, Anthony Kirilusha, Gilberto DeSalvo, Katherine Aylor Fisher, Henry Amrhein, Shirley Pepke, Jost Vielmetter, Gavin Sherlock, Arend Sidow, Serafim Batzoglou, Rami Rauch, Anshul Kundaje, Max Libbrecht, Elliott H. Margulies, Stephen C.J. Parker, Laura Elnitski, Eric D. Green, Tim Hubbard, Jennifer Harrow, Stephen Searle, Felix Kokocinski, Browen Aken, Adam Frankish, Toby Hunt, Gloria Despacio-Reyes, Mike Kay, Gaurab Mukherjee, Alexandra Bignell, Gary Saunders, Veronika Boychenko, Michael Brent, M. J. van Baren, Randall H. Brown, Mark Gerstein, Ekta Khurana, Suganthi Balasubramanian, Hugo Lam, Philip Cayting, Rebecca Robilotto, Zhi Lu, Thomas Derrien, Andrea Tanzer, David G. Knowles, Marco Mariotti, David Haussler, Rachel Harte, Mark Diekhans, Mike Lin, Alfonso Valencia, Michael Tress, Stephen G. Landt, Debasish Raha, Minyi Shi, Ghia Euskirchen, Fabian Grubert, Maya Kasowski, Jin Lian, Phil Lacroute, Youhan Xu, Hannah Monahan, Dorrelyn Patacsil, Teri Slifer, Xinqiong Yang, Alexandra Charos, Brian Reed, Linfeng Wu, Raymond K. Auerbach, Lukas Habegger, Manoj Hariharan, Joel Rozowsky, Alexej Abyzov, Sherman M. Weissman, Kevin Struhl, Nathan Lamarre-Vincent, Marianne Lindahl-Allen, Benoit Miotto, Zarmik Moqtaderi, Joseph D. Fleming, Peter Newburger, Peggy J. Farnham, Seth Frietze, Henriette O'Geen, Xiaoqin Xu, Kim R. Blahnik, Alina R. Cao, Sushma Iyengar, Rajinder Kaul, Robert E. Thurman, Hao Wang, Patrick A. Navas, Richard Sandstrom, Peter J. Sabo, Molly Weaver, Theresa Canfield, Kristen Lee, Shane Neph, Vaughan Roach, Alex Reynolds, Audra Johnson, Eric Rynes, Erika Giste, Shinny Vong, Jun Neri, Tristan Frum, Eric D. Nguyen, Abigail K. Ebersol, Minerva E. Sanchez, Hadar H. Sheffer, Dimitra Lotakis, Eric Haugen, Richard Humbert, Tanya Kutyavin, Tony Shafer, William S. Noble, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, Kate R. Rosenbloom, Timothy R. Dreszer, Brian J. Raney, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Melissa S. Cline, Katrina Learned, Vanessa K. Swing, Ann S. Zweig, Brooke Rhead, Pauline A. Fujita, Krishna Roskin, Donna Karolchik, Robert M. Kuhn, Steven P. Wilder, Daniel Sobral, Javier Herrero, Kathryn Beal, Margus Lukk, Alvis Brazma, Juan M. Vaquerizas, Nicholas M. Luscombe, Peter J. Bickel, Nathan Boley, James B. Brown, Qunhua Li, Haiyan Huang, Andrea Sboner, Kevin Y. Yip, Chao Cheng, Koon Kiu Yan, Nitin Bhardwaj, Jing Wang, Lucas Lochovsky, Justin Jee, Theodore Gibson, Jing Leng, Jiang Du, Robert Scott Harris, Giltae Song, Webb Miller, Bernard Suh, Benedict Paten, Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Xianjun Dong, Jie Wang, Hualin Xi, Scott A. Tenenbaum, Frank Doyle, Sridar Chittur, Luiz O. Penalva, Thomas D. Tullius, Kevin P. White, Subhradip Karmakar, Alec Victorsen, Nader Jameel, Nick Bild, Robert L. Grossman, Patrick J. Collins, Nathan D. Trinklein, Morgan C. Giddings, Jainab Khatun, Chris Maier, Ting Wang, Troy W. Whitfield, Xian Chen, Yanbao Yu, Harsha Gunawardena, Elise A. Feingold, Rebecca F. Lowdon, Laura A.L. Dillon, Peter J. Good, Brian Risk, 2011, PLoS biology on p. e1001046
Measuring reproducibility of high-throughput experiments
Qunhua Li, James B. Brown, Haiyan Huang, Peter J. Bickel, 2011, Annals of Applied Statistics on p. 1752-1779
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
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
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
Tao Yang, Feipeng Zhang, Galip Gürkan Yardımci, Fan Song, Ross Cameron 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
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, Journal of Nutritional Biochemistry on p. 11-17
Robust bent line regression
Feipeng Zhang, Qunhua Li, 2017, Journal of Statistical Planning and Inference on p. 41-55
A likelihood-based scoring method for peptide identification using mass spectrometry
Qunhua Li, Jimmy K. Eng, Matthew Stephens, 2012, Annals of Applied Statistics on p. 1775-1794
A continuous threshold expectile model
Feipeng Zhang, Qunhua Li, 2017, Computational Statistics and Data Analysis on p. 49-66
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