Entire list of publications and citations is available from : G o o g l e Scholar:
* equal contributions, # corresponding authors

2024

1. Xuyuan Gao*, Ke Liu*, Songwen Luo*, Meifang Tang, Nianping Liu, Chen Jiang, Jingwen Fang, Shouzhen Li, Yanbing Hou, Chuang Guo#, Kun Qu#“Comparative analysis of methodologies for detecting extrachromosomal circular DNA”, Nature Communications, 2024.
2. Yinlei Hu*, Siyuan Wan*, Yuanhanyu Luo*, Yuanzhe Li, Tong Wu, Wentao Deng, Chen Jiang, Shan Jiang, Yueping Zhang, Nianping Liu, Zongcheng Yang, Falai Chen#, Bin Li# & Kun Qu#“Benchmarking algorithms for single-cell multi-omics prediction and integration”, Nature Methods, 2024.
3. Kaixing Chen*, Qiaoni Yu*, Qing Sha, Junyu Wang, Jingwen Fang, Xin Li, Xiaokun Shen, Binqing Fu, Chuang Guo#“Single-cell transcriptomic analysis of immune cell dynamics in the healthy human endometrium”, Biochemistry and Biophysics Reports, 2024.
4. Minghao Fang*, Jingwen Fang*, Songwen Luo, Ke Liu, Qiaoni Yu, Jiaxuan Yang, Youyang Zhou, Zongkai Li, Ruoming Sun, Chuang Guo#, Kun Qu#“eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data”, Briefings in Bioinformatics, 2024.

2023

1. Hao Xu*, Shuyan Wang*, Minghao Fang, Songwen Luo, Chunpeng Chen, Siyuan Wan, Rirui Wang, Meifang Tang, Tian Xue, Bin Li#, Jun Lin#, Kun Qu#“SPACEL: deep learning-based characterization of spatial transcriptome architectures”, Nature Communications, 2023.
2. Jun Lin*, Liang Dong*, Yi-Ming Liu*, Yi Hu, Chen Jiang, Ke Liu, Liu Liu, Yong-Hong Song, Mei Sun, Xing-Cheng Xiang, Kun Qu#, Yang Lu#, Long-Ping Wen#, Shu-Hong Yu#“Nickle-cobalt alloy nanocrystals inhibit activation of inflammasomes”, National Science Review, 2023.
3. Nianping Liu*, Chen Jiang*, Xinfeng Yao*, Minghao Fang, Xiaolong Qiao, Lin Zhu, Zongcheng Yang, Xuyuan Gao, Ying Ji, Chaoshi Niu, Chuandong Cheng#, Kun Qu#, Jun Lin#“Single-cell landscape of primary central nervous system diffuse large B-cell lymphoma”, Cell Discovery, 2023.
4. Min Wei*, Yanping Sun*, Shouzhen Li*, Yunuo Chen, Longfei Li, Minghao Fang, Ronghua Shi, Dali Tong, Jutao Chen, Yuqian Ma#, Kun Qu#, Mei Zhang#, Tian Xue#“Single-cell profiling reveals Müller glia coordinate retinal intercellular communication during light/dark adaptation via thyroid hormone signaling”, Protein & Cell, 2023.
5. Qiaoni Yu*, Xu Liu*, Jingwen Fang*, Huihui Wu*, Chuang Guo, Wen Zhang, Nianping Liu, Chen Jiang, Qing Sha, Xiao Yuan, Zhikai Wang#, Kun Qu#“Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution”, Science Advances, 2023.

2022

1. Chuang Guo*, Qian Liu*, Dandan Zong*, Wen Zhang, Zuqi Zuo, Qiaoni Yu, Qing Sha, Lin Zhu, Xuyuan Gao, Jingwen Fang, Jinhui Tao, Quan Wu, Xiaomei Li, Kun Qu#“Single-cell transcriptome profiling and chromatin accessibility reveal an exhausted regulatory CD4+ T cell subset in systemic lupus erythematosus”, Cell Reports, 2022.
2. Tiemin Jiang*, Wujianan Sun*, Tuerganaili Aji, Yingmei Shao, Chuang Guo, Chuanshan Zhang, Bo Ran, Jiao Hou, Aimaiti Yasen, Qiang Guo, Hui Wang#, Kun Qu#, Hao Wen#“Single-Cell Heterogeneity of the Liver-Infiltrating Lymphocytes in Individuals with Chronic Echinococcus multilocularis Infection”, Infection and Immunity, 2022.
3. Zhuoqiao Shen*, Minghao Fang*, Wujianan Sun*, Meifang Tang, Nianping Liu, Lin Zhu, Qian Liu, Bin Li, Ruoming Sun, Yu Shi, Chuang Guo#, Jun Lin# and Kun Qu#“A transcriptome atlas and interactive analysis platform for autoimmune disease”, Database, 2022.
4. Bin Li*, Wen Zhang*, Chuang Guo*, Hao Xu, Longfei Li, Minghao Fang, Yinlei Hu, Xinye Zhang, Xinfeng Yao, Meifang Tang, Ke Liu, Xuetong Zhao, Jun Lin, Linzhao Cheng, Falai Chen, Tian Xue and Kun Qu#“Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution”, Nature Methods, 2022.
5. Chuang Guo*, Mingming Wu*, Beibei Huang*, Rui Zhao, Linlin Jin, Binqing Fu, Ping Wang, Dongyao Wang, Meijuan Zheng, Jingwen Fang, Haiming Wei#, Kun Qu# and Fang Ni#“Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19”, Genome Medicine, 2022.

2021

1. Aimaiti Yasen*, Wujianan Sun*, Abudusalamu Aini, Tuerganaili Aji, Yingmei Shao, Hui Wang, Kun Li, Wending Li, Chuanshan Zhang, Ayifuhan Ahan, Tiemin Jiang, Zongding Wang, Wenbao Zhang, Cheng Sun, Kun Qu#, Hao Wen#“Single-Cell RNA Sequencing Reveals the Heterogeneity of Infiltrating Immune Cell Profiles in the Hepatic Cystic Echinococcosis Microenvironment”, Infection and Immunity, 2021.
2. Rendong Hu*, Wen Zhang*, Liang Li#, Zuqi Zuo, Min Ma, Jinfen Ma, Tingting Yin, Caiyue Gao, Shuhan Yang, Zhibin Zhao, Zijun Li, Guibin Qiao, Zhexiong Lian#, Kun Qu#“Chromatin accessibility analysis identifies the transcription factor ETV5 as a suppressor of adipose tissue macrophage activation in obesity” , Cell Death and Disease, 2021.
3. Nianping Liu*, Chen Jiang*, Pengfei Cai*, Zhuoqiao Shen, Wujianan Sun, Hao Xu, Minghao Fang, Xinfeng Yao, Lin Zhu, Xuyuan Gao, Jingwen Fang, Jun Lin, Chuang Guo#, Kun Qu#“Single-cell analysis of COVID-19, sepsis, and HIV infection reveals hyperinflammatory and immunosuppressive signatures in monocytes” , Cell Reports, 2021.
4. Yinlei Hu*, Bin Li*, Falai Chen#, Kun Qu#“Single-cell data clustering based on sparse optimization and low-rank matrix factorization” , G3-Genes Genomes Genetics, 2021.
5. Dandan Zong*, Beibei Huang*, Young Li#, Yichen Lu, Nan Xiang, Chuang Guo, Qian Liu, Qing Sha, Pengcheng Du, Qiaoni Yu, Wen Zhang, Pengfei Cai, Yanping Sun, Jinhui Tao, Xiaomei Li#, Shanbao Cai#, Kun Qu#“Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis” , BMC Biology, 2021.
6. Yinlei Hu*, Bin Li*, Wen Zhang, Nianping Liu, Pengfei Cai, Falai Chen#, Kun Qu#“WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition” , Briefings in Bioinformatics, 2021.
7. Young Li*, Kun Li*, Lianbang Zhu, Bin Li, Dandan Zong, Pengfei Cai, Chen Jiang, Pengcheng Du, Jun Lin, Kun Qu# “Development of double-positive thymocytes at single-cell resolution”, Genome Medicine , 2021.
8. Xianwen Ren*, Wen Wen*, Xiaoying Fan*, Wenhong Hou*, Bin Su*, Pengfei Cai*, Jiesheng Li*, Yang Liu*, Fei Tang*, Fan Zhang*, Yu Yang*, Jiangping He*, Wenji Ma*, Jingjing He*, Pingping Wang*, Qiqi Cao, Fangjin Chen, Yuqing Chen, Xuelian Cheng, Guohong Deng, Xilong Deng, Wenyu Ding, Yingmei Feng, Rui Gan, Chuang Guo, Weiqiang Guo, Shuai He, Chen Jiang, Juanran Liang, Yi-min Li, Jun Lin, Yun Ling, Haofei Liu, Jianwei Liu, Nianping Liu, Shu-Qiang Liu, Meng Luo, Qiang Ma, Qibing Song, Wujianan Sun, GaoXiang Wang, Feng Wang, Ying Wang, Xiaofeng Wen, Qian Wu, Gang Xu, Xiaowei Xie, Xinxin Xiong, Xudong Xing, Hao Xu, Chonghai Yin, Dongdong Yu, Kezhuo Yu, Jin Yuan, Biao Zhang, Peipei Zhang*, Tong Zhang, Jincun Zhao, Peidong Zhao, Jianfeng Zhou, Wei Zhou, Sujuan Zhong, Xiaosong Zhong, Shuye Zhang, Lin Zhu, Ping Zhu, Bin Zou, Jiahua Zou, Zengtao Zuo, Fan Bai, Xi Huang, Penghui Zhou#, Qinghua Jiang#, Zhiwei Huang#, Jin-Xin Bei#, Lai Wei#, Xiu-Wu Bian#, Xindong Liu#, Tao Cheng#, Xiangpan Li#, Pingsen Zhao#, Fu-Sheng Wang#, Hongyang Wang#, Bing Su#, Zheng Zhang#, Kun Qu#, Xiaoqun Wang#, Jiekai Chen#, Ronghua Jin#, Zemin Zhang# “COVID-19 immune features revealed by a large-scale single cell transcriptome atlas ”, Cell , 2021.
9. Chuang Guo*, Pengfei Cai*, Liying Jin*, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lu Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu# “Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss”, Cell Discovery, 2021.

2020

1. Kun Li*, Yang Wu*, Young Li, Qiaoni Yu, Zhigang Tian, Haiming Wei#, Kun Qu# “Landscape and dynamics of the transcriptional regulatory network during natural killer cell differentiation”, Genomics, Proteomics & Bioinformatics, 2020.
2. Qian Liu*, Lisa C. Zaba*, Ansuman T. Satpathy, Michelle Longmire, Wen Zhang, Kun Li, Jeffrey Granja, Chuang Guo, Jun Lin, Rui Li, Karen Tolentino, Gabriela Kania, Oliver Distler, David Fiorentino, Lorinda Chung, Kun Qu#, Howard Y. Chang# “Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis”, Nature Communications, 2020.
3. Chuang Guo*, Bin Li*, Huan Ma, Xiaofang Wang, Pengfei Cai, Qiaoni Yu, Lin Zhu, Liying Jin, Chen Jiang, Jingwen Fang, Qian Liu, Dandan Zong, Wen Zhang, Yichen Lu, Kun Li, Xuyuan Gao, Binqing Fu, Lianxin Liu, Xiaoling Ma, Jianping Weng, Haiming Wei, Tengchuan Jin#, Jun Lin#, Kun Qu# “Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm”, Nature Communications, 2020.
4. Bin Li*, Young Li*, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin, Kun Qu# “APEC: an accesson-based method for single-cell chromatin accessibility analysis”, Genome Biology, 2020.
5. Haohuan Xie*, Wen Zhang*, Mei Zhang*#, Tasneem Akhtar, Young Li, Wenyang Yi, Xiao Sun, Zuqi Zuo, Min Wei, Xin Fang, Ziqin Yao, Kai Dong, Suijuan Zhong, Qiang Liu, Yong Shen, Qian Wu, Xiaoqun Wang, Huan Zhao, Jin Bao, Kun Qu#, Tian Xue#“Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids”, Science Advances, 2020.
6. Pengfei Cai*, Auke B.C. Otten*, Binbin Cheng, Mitsuhiro A. Ishii, Wen Zhang, Beibei Huang, Kun Qu#, Bryan K. Sun# “A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis”, Genome Research, 2020.
7. Shi-Ting Li*, De Huang*, Shengqi Shen, Yongping Cai, Songge Xing, Gongwei Wu, Zetan Jiang, Yijie Hao, Mengqiu Yuan, Nana Wang, Lianbang Zhu, Ronghui Yan, Dongdong Yang, Lin Wang, Zhaoji Liu, Xin Hu, Rongbin Zhou, Kun Qu, Ailing Li, Xiaotao Duan#, Huafeng Zhang#, Ping Gao#“Myc-mediated SDHA acetylation triggers epigenetic regulation of gene expression and tumorigenesis”, Nature Metabolism, 2020.

2019

1. Jingwen Fang*, Qing Ma*, Ci Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Erisse Martin Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu#, Howard Y. Chang# “Functional classification of noncoding RNAs associated with distinct histone modifications by PIRCh-seq”, Genome Biology, 2019.
2. Cheen Euong Ang*, Qing Ma*, Orly L Wapinski*, ShengHua Fan, Ryan A Flynn, Qian Yi Lee, Bradley Coe, Masahiro Onoguchi, Victor Hipolito Olmos, Brian T Do, Lynn Dukes-Rimsky, Jin Xu, Koji Tanabe, LiangJiang Wang, Ulrich Elling, Josef M Penninger, Yang Zhao, Kun Qu, Evan E Eichler, Anand Srivastava, Marius Wernig#, Howard Y. Chang# “The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders”, eLIFE, 2019.
3. Jing Zhou, Hui Peng#, Kun Li, Kun Qu, Baohui Wang, Yuzhang Wu, Lilin Ye, Zhongjun Dong, Haiming Wei, Rui Sun, Zhigang Tian# “Liver-Resident NK Cells Control Antiviral Activity of Hepatic T Cells via the PD-1-PD-L1 Axis”, Immunity, 2019.
4. Haoyu Sun, Qiang Huang, Mei Huang, Hao Wen, Renyong Lin, Meijuan Zheng, Kun Qu, Kun Li, Haiming Wei, Weihua Xiao, Rui Sun, Zhigang Tian#, Cheng Sun# “Human CD96 Correlates to Natural Killer Cell Exhaustion and Predicts the Prognosis of Human Hepatocellular Carcinoma”, Hepatology, 2019.
5. Zuqi Zuo, Yonghao Jin, Wen Zhang, Yichen Lu, Bin Li#, Kun Qu# “ATAC-pipe: general analysis of genome-wide chromatin accessibility”, Briefings in Bioinformatics, 2019.

2018

1. Haoyu Sun, Jing Xu, Qiang Huang, Mei Huang, Kun Li, Kun Qu, Hao Wen, Renyong Lin, Meijuan Zheng, HaimingWei, Weihua Xiao, Rui Sun, Zhigang Tian#, Cheng Sun# “Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC”, Cancer Research, 2018.

2017

1. Kun Qu*, Lisa C. Zaba*, Ansuman T. Satpathy, Paul G. Giresi, Rui Li, Yonghao Jin, Randall Armstrong, Chen Jin, Nathalie Schmitt, Ziba Rahbar, Hideki Ueno, William J. Greenleaf, Youn H. Kim#, Howard Y. Chang# “Chromatin accessibility landscape of cutaneous T cell lymphoma and dynamic response to HDAC inhibitors”, Cancer Cell, 2017.
2. Gongwei Wu, Mengqiu Yuan, Shengqi Shen, Xiaoyu Ma, Jingwen Fang, Lianbang Zhu, Linchong Sun, Zhaoji Liu, Xiaoping He, De Huang, Tingting Li, Chenchen Li, Jun Wu, Xin Hu, Zhaoyong Li, Libing Song, Kun Qu, Huafeng Zhang#, Ping Gao#“Menin enhances c-Myc-mediated transcription to promote cancer progression” Nature Communications, 2017.
3. Xiaomin Bao#, Zurab Siprashvili, Brian J. Zarnegar, Rajani M. Shenoy, Eon J. Rios, Natalie Nady, Kun Qu, Angela Mah, Daniel E. Webster, Adam J. Rubin, Glenn G. Wozniak, Shiying Tao, Joanna Wysocka, Paul A. Khavari# “CSNK1a1 regulates PRMT1 to maintain the progenitor state in self-renewing somatic tissue”, Developmental Cell, 2017.
4. Wen Pan, Shu Zhu, Kun Qu, Katrina Meeth, Jijun Cheng, Kaixin He, Hongdi Ma, Yan Liao, Xizhi Wen, Christine Roden, Zuzana Tobiasova, Zheng Wei, Jun Zhao, Jun Liu, Ji Zheng, Bo Guo, Sajid A. Khan, Marcus Bosenberg, Richard A. Flavell, Jun Lu# “The DNA methylcytosine dioxygenase Tet2 sustains immunosuppressive function of tumor-infiltrating myeloid cells to promote melanoma progression”, Immunity, 2017.
5. Chen Jin, Kun Qu# “Application of bioinformatics techniques in revealing the mechanisms of epigenetic regulation“, SCIENTIA, 2017.

2016

1. Kun Qu*, Sara Garamszegi*, Felix Wu*, Helga Thorvaldsdottir, Ted Liefeld, Marco Ocana, Diego Borges-Rivera, Nathalie Pochet, James T Robinson, Barry Demchak, Tim Hull, Gil Ben-Artzi, Daniel Blankenberg, Galt P Barber, Brian T Lee, Robert M Kuhn, Anton Nekrutenko, Eran Segal, Trey Ideker, Michael Reich, Aviv Regev, Howard Y. Chang, Jill P Mesirov# “Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace”, Nature Methods, 2016.
2. Chunjiang He*#, Hanyang Hu*, Kitchener D. Wilson*, Haodi Wu, Jing Feng, Siyu Xia, Jared Churko, Kun Qu, Howard Y. Chang, Joseph C. Wu# “Systematic Characterization of Long Non-Coding RNAs Reveals the Contrasting Coordination of Cis- and Trans- Molecular Regulation in Human Fetal and Adult Heart”, Circulation: Cardiovascular Genetics, 2016.
3. Adam M. Schmitt, Julia T. Garcia, Tiffany Hung, Ryan A. Flynn, Ying Shen, Kun Qu, Alexander Y. Payumo, Ashwin Peres-da-Silva, Daniela Kenzelmann Broz, Rachel Baum, Shuling Guo, James K. Chen, Laura D. Attardi, Howard Y. Chang# “An inducible long noncoding RNA amplifies DNA damage signaling”, Nature Genetics, 2016.
4. Jin Xu, Robert C. Spitale, Linna Guan, Ryan A. Flynn, Eduardo A. Torre, Rui Li, Inbar Raber, Kun Qu, Dale Kern, Helen E. Knaggs, Howard Y. Chang, Anne LynnS. Chang# “Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing”, PloS one, 2016.
5. H. Efsun Arda, Lingyu Li, Jennifer Tsai, Eduardo A. Torre, Yenny Rosli, Heshan Peiris, Robert C. Spitale, Chunhua Dai, Xueying Gu, Kun Qu, Pei Wang, Jing Wang, Markus Grompe, Raphael Scharfmann, Michael S. Snyder, Rita Bottino, Alvin C. Powers, Howard Y. Chang, Seung K. Kim# “Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human b Cell Function”, Cell Metabolism, 2016.
6. Yue Wan#, Kun Qu, Zheng qing Ouyang, Howard Y. Chang “Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing”, Yeast Functional Genomics, 2016.

2015

1. Kun Qu*, Lisa C. Zaba*, Paul G. Giresi, Rui Li, Michelle Longmire, Youn H. Kim, William J. Greenleaf, Howard Y. Chang# “Individuality and variation of personal regulomes in primary human T cells”, Cell Systems, 2015.
2. Xiaomin Bao#, Adam J. Rubin, Kun Qu, Jiajing Zhang, Paul G. Giresi, Howard Y. Chang, Paul A. Khavari# “A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63”, Genome Biology, 2015.
3. Bryan K. Sun, Lisa D. Boxer, Julia D. Ransohoff, Zurab Siprashvili, Kun Qu, Vanessa Lopez-Pajares, S. Tyler Hollmig, Paul A. Khavari# “CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation”, Genes & Development, 2015.
4. Vanessa Lopez-Pajares, Kun Qu, Jiajing Zhang, Dan E. Webster, Brook C. Barajas, Zurab Siprashvili, Brian J. Zarnegar, Lisa D. Boxer, Eon J. Rios, Shiying Tao, Markus Kretz, Paul A. Khavari# “A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation”, Developmental Cell, 2015.
5. Meredith Corley, Amanda Solem, Kun Qu, Howard Y. Chang, Alain Laederach# “Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark”, Nucleic Acids Research, 2015.
6. Caroline Roost, Stephen R. Lynch, Pedro J. Batista, Kun Qu, Howard Y. Chang#, Eric T. Kool# “Structure and Thermodynamics of N6‑Methyladenosine in RNA: A Spring-Loaded Base Modification”, Journal of the American Chemical Society, 2015.
7. Ryan A. Flynn*, Lance Martin*, Robert C. Spitale, Brian T. Do, Selena M. Sagan, Brian Zarnegar, Kun Qu, Paul A. Khavari, Stephen R. Quake, Peter Sarnow, Howard Y. Chang# “Dissecting noncoding and pathogen RNA–protein interactomes”, RNA, 2015.

2014

1. Yue Wan*#, Kun Qu*, Qiangfeng Cliff Zhang, Ryan A. Flynn1, Ohad Manor, Zhengqing Ouyang, Jiajing Zhang ,Robert C. Spitale, Michael P. Snyder, Eran Segal, Howard Y. Chang# “Landscape and variation of RNA secondary structure across the human transcriptome”, Nature, 2014. (Highlighted in Nature News & Views)
2. Cecil M. Benitez, Kun Qu, Takuya Sugiyama, Philip T. Pauerstein, Yinghua Liu, Jennifer Tsai, Xueying Gu, Amar Ghodasara, H. Efsun Arda, Jiajing Zhang, Joseph D. Dekker, Haley O. Tucker, Howard Y. Chang, Seung K. Kim# “An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development”, PLoS Genetics, 2014.
3. Jeffrey J Quinn, Ibrahim A Ilik, Kun Qu, Plamen Georgiev, Ci Chu, Asifa Akhtar, Howard Y. Chang# “Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification”, Nature Biotechnology, 2014.
4. Pedro J. Batista, Benoit Molinie, Jinkai Wang, Kun Qu, Jiajing Zhang, Lingjie Li, Donna M. Bouley, Ernesto Lujan, Bahareh Haddad, Kaveh Daneshvar, Ava C. Carter, Ryan A. Flynn, Chan Zhou, Kok-Seong Lim, Peter Dedon, Marius Wernig, Alan C. Mullen, Yi Xing, Cosmas C. Giallourakis, Howard Y. Chang# “M6A RNA modification controls cell fate transition in mammalian embryonic stem cells”, Cell Stem Cell, 2014.
5. Yul W Yang*, Ryan A Flynn*, Yong Chen, Kun Qu, Bingbing Wan, Kevin C Wang, Ming Lei, Howard Y. Chang# “Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency”, Elife, 2014.

2013

1. Orly L. Wapinski*, Thomas Vierbuchen*, Kun Qu, Qian Yi Lee, Soham Chanda, Daniel R. Fuentes, Paul G. Giresi, Yi Han Ng, Samuele Marro, Norma F. Neff, Daniela Drechsel, Ben Martynoga, Diogo S. Castro, Ashley E. Webb, Thomas C. Su¨ dhof, Anne Brunet, Francois Guillemot, Howard Y. Chang#, Marius Wernig# “Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons”, Cell, 2013.
2. Yue Wan, Kun Qu, Zhengqing Ouyang, Howard Y. Chang# “Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing”, Nature Protocols, 2013.
3. Nicole A Rapicavoli, Kun Qu, Jiajing Zhang, Megan Mikhail, Remi-Martin Laberge, Howard Y. Chang# “A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics”, eLife, 2013.
4. Xiaomin Bao, Jiong Tang, Vanessa Lopez-Pajares, Shiying Tao, Kun Qu, Gerald R. Crabtree, Paul A. Khavari# “ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-Dependent induction of klf4”, Cell Stem Cell, 2013.
5. Markus Kretz, Zurab Siprashvili, Ci Chu, Dan E. Webster, Ashley Zehnder, Kun Qu, Carolyn S. Lee, Ross J. Flockhart, Abigail F. Groff, Jennifer Chow, Danielle Johnston, Grace E. Kim, Robert C. Spitale, Ryan A. Flynn, Grace X. Y. Zheng, Subhadra Aiyer, Arjun Raj, John L. Rinn, Howard Y. Chang#, Paul A. Khavari# “Control of somatic tissue differentiation by the long non-coding RNA TINCR”, Nature, 2013. (Faculty 1000) 
6. Lingjie Li, Bo Liu, Orly L. Wapinski, Miao-Chih Tsai, Kun Qu, Jiajing Zhang, Jeff C. Carlson, Meihong Lin, Fengqin Fang, Rajnish A. Gupta, Jill A. Helms, Howard Y. Chang# “Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression”, Cell Reports, 2013.
7. Anne Lynn S. Chang, Patrick H. Bitter Jr, Kun Qu, Meihong Lin, Nicole A. Rapicavoli, Howard Y. Chang# “Rejuvenation of gene expression pattern of aged human skin by broadband light treatment: a pilot study”, Journal of Investigative Dermatology, 2013.

2012

1. Ross J. Flockhart, Dan E. Webster, Kun Qu, Nicholas Mascarenhas, Joanna Kovalski, Markus Kretz, Paul A. Khavari# “BRAF^V600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration”, Genome Research, 2012. (Highlighted in Nature Reviews Cancer)
2. Yue Wan, Kun Qu, Zhengqing Ouyang, Michael Kertesz, Jun Li, Robert Tibshirani, Debora L. Makino, Robert C. Nutter, Eran Segal#, Howard Y. Chang# “Genome-wide measurement of RNA folding energies”, Molecular Cell, 2012. (Faculty 1000)
3. Aparna Bhaduri, Kun Qu, Carolyn S. Lee, Alexander Ungewickell, Paul A. Khavari# “Rapid identification of nonhuman sequencing in high throughput sequencing datasets”, Bioinformatics, 2012. (Faculty 1000)
4. Natalia Gomez-Ospina, Anne Lynn S. Chang, Kun Qu, Anthony E. Oro# “Translocation affecting sonic hedgehog gene in basal cell carcinomas”, The New England Journal of Medicine, 2012.
5. Carolyn S. Lee, Alexander Ungewickell, Aparna Bhaduri, Kun Qu, Dan E. Webster, Randall Armstrong, Wen-Kai Weng, Cody J. Aros, Angela Mah, Richard O. Chen, Meihong Lin, Uma Sundram, Howard Y. Chang, Markus Kretz, Youn H. Kim, Paul A. Khavari# “Transcriptome Sequencing in Sezary Syndrome Identifies Sezary Cell and Mycosis Fungoides-Associated lncRNAs and Novel Transcripts”, Blood, 2012.
6. Brian J. Zarnegar, Dan E. Webster, Vanessa Lopez-Pajares, Brook Vander Stoep Hunt, Kun Qu, Karen J. Yan, David R. Berk, George L. Sen, Paul A. Khavari# “Genomic Profiling of a Human Organotypic Model of AEC Syndrome Reveals ZNF750 as an Essential Downstream Target of Mutant TP63”, The American Journal of Human Genetics, 2012.
7. Pei Wang, Kristen D. McKnight, David J. Wong, Ryan T. Rodriguez, Takuya Sugiyama, Xueying Gu, Amar Ghodasara, Kun Qu, Howard Y. Chang, Seung K. Kim#“A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells”, Stem Cells and Development, 2012.
8. Laurie E. Littlepage, Adam S. Adler, Hosein Kouros-Mehr, Guiqing Huang, Jonathan Chou, Sheryl R. Krig, Obi L. Griffith, James E. Korkola, Kun Qu, Devon A. Lawson,Qing Xue, Mark D. Sternlicht, Gerrit J. P. Dijkgraaf, Paul Yaswen, Hope S. Rugo,Colleen A. Sweeney, Colin C. Collins, Joe W. Gray, Howard Y. Chang, Zena Werb# “The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression”, Cancer Discovery, 2012.
9. George L. Sen, Lisa D. Boxer, Dan E. Webster, Rose T. Bussat, Kun Qu, Brian J. Zarnegar, Danielle Johnston, Zurab Siprashvili, Paul A. Khavari# “ZNF750 Is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation”, Developmental Cell, 2012.
10. Markus Kretz*, Dan E. Webster*, Ross J. Flockhart, Carolyn S. Lee, Ashley Zehnder, Vanessa Lopez-Pajares, Kun Qu, Grace X.Y. Zheng, Jennifer Chow, Grace E. Kim, John L. Rinn, Howard Y. Chang, Zurab Siprashvili, Paul A. Khavari#“Suppression of progenitor differentiation requires the long noncoding RNA ANCR”, Genes & Development, 2012.

2011

1. Ci Chu, Kun Qu, Franklin L. Zhong, Steven E. Artandi, Howard Y. Chang# “Genomic maps of lncRNA occupancy reveal principles of RNA-chromatin interactions”, Molecular Cell, 2011. (Cover Article, Highlighted in Nature Reviews Genetics and Nature Methods, Faculty 1000)
2. Samuele Marro, Zhiping P. Pang, Nan Yang, Miao-Chih Tsai, Kun Qu, Howard Y. Chang, Thomas C. Sudhof, Marius Wernig# “Direct lineage conversion of terminally differentiated hepatocytes to functional neurons”, Cell Stem Cell, 2011. (Cover Article, Faculty 1000, and Highlighted in Nature Biotechnology)
3. Tiara L. A. Kawahara, Nicole A. Rapicavoli, Angela R. Wu, Kun Qu, Stephen R. Quake, Howard Y.Chang# “Dynamic chromatin localization of Sirt6 shapes stress-and aging-related transcriptional networks”, PLoS Genet, 2011.
4. Zhenbin Chen, Zheng Liu, Wenyan Li, Kun Qu, Xutao Deng, Madhulika G. Varma, Alessandro Fichera, Alessio Pigazzi, Julio Garcia-Aguilar# “Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer”, Genes, Chromosomes and Cancer, 2011.

2007~2010

1. Kun Qu, Anastasia M. Yesnik, Peter J. Ortoleva# “Alternative splicing regulatory network reconstruction from exon array data”, Journal of Theoretical Biology, 2010.
2. Kun Qu, Peter J. Ortoleva# “Understanding stem cell differentiation through self-organization theory”, Journal of Theoretical Biology, 2008.
3. Kun Qu, Alaa Abi Haidar, Jianmiao Fan, Lisa Ensman, Kagan Tuncay, Michael Jolly, Peter J. Ortoleva# “Cancer onset and progression: a genome-wide, nonlinear dynamical systems perspective on onconetworks”, Journal of Theoretical Biology, 2007.