Qunhua Li

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

Publication Tags

Genes Dna Chromatin Genome Gene Expression Reproducibility Gene Methodology Experiment Epigenomics Analysis Encyclopedias Method Chromatin Immunoprecipitation Transcription Factors Datasets Measuring Chromatin Immunoprecipitation Sequencing Gata Transcription Factors Neoplasms Application Modification T Cells Paint Interleukin 6

Most 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

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

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 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

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 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

Condition-adaptive fused graphical lasso (CFGL)

Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris, Qunhua Li, 2018, PLoS Computational Biology

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

A user's guide to the Encyclopedia of DNA elements (ENCODE)

Richard M. Myers, John Stamatoyannopoulos, Michael Snyder, Ian Dunham, Ross C. 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 S. 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

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

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

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