Entire list of publications and citations is available from : Google Scholar:
* equal contributions, # co-corresponding authors


  1. C. Guo*, B. Li*, H. Ma, X. Wang, P. Cai, Q. Yu, Lin. Zhu, L. Jin, C. Jiang, J. Fang, Q. Liu, D. Zong, W. Zhang, Y. Lu, K. Li, X. Gao, B. Fu, L. Liu, X. Ma, J. Weng, H. Wei, T. Jin#, J. Lin#, K. Qu# “Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm”, Nature Communications, 2020.
  2. B. Li*, Y. Li*, K. Li, L. Zhu, Q. Yu, P. Cai, J. Fang, W. Zhang, P. Du, C. Jiang, J. Lin, K. Qu# “APEC: an accesson-based method for single-cell chromatin accessibility analysis”, Genome Biology, 2020.
  3. H. Xie*, W. Zhang*, M. Zhang*, T. Akhtar, Y. Li, W. Yi, X. Sun, Z. Zuo, M. Wei, X. Fang, Z. Yao, K. Dong, S. Zhong, Q. Liu, Y. Shen, Q. Wu, X. Wang, H. Zhao, J. Bao, K. Qu#, T. Xue#“Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids”, Science Advances, 2020.
  4. P. Cai*, Auke BC Otten*, B. Cheng, Mitsuhiro A. Ishii, W. Zhang, B. Huang, K. Qu#, Bryan K. Sun# “A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis”, Genome Research, 2020.
  5. S. Li*, D. Huang*, S. Shen, Y. Cai, S. Xing, G. Wu, Z. Jiang, Y. Hao, M. Yuan, N. Wang, L. Zhu, R. Yan, D. Yang, L. Wang, Z. Liu, X. Hu, R. Zhou, K. Qu, A. Li, X. Duan#, H. Zhang#, P. Gao#“Myc-mediated SDHA acetylation triggers epigenetic regulation of gene expression and tumorigenesis”, Nature Metabolism, 2020.
  6. P. Du, P. Cai, B. Huang, C. Jiang, Q. Wu#, B. Li#, K. Qu#“SMAtool reveals sequences and structural principles of protein-RNA interaction”, Biochemical and Biophysical Research Communications, 2020.


  1. J. Fang*, Q. Ma*, C. Chu, B. Huang, L. Li, P. Cai, P. Batista, K. Tolentino, J. Xu, R. Li, P. Du, K. Qu#, H. Chang# “Functional classification of noncoding RNAs associated with distinct histone modifications by PIRCh-seq”, Genome Biology, 2019.
  2. C. Ang*, Q. Ma*, O. Wapinski*, S. Fan, R. Flynn, Q. Lee, B. Coe, M. Onoguchi, V. Olmos, B. Do, L. Dukes-Rimsky, J. Xu, K. Tanabe, L. Wang, U. Elling, J. Penninger, Y. Zhao, K. Qu, E. Eichler, A. Srivastava, M. Wernig#, H. Chang# “The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders”, eLIFE, 2019.
  3. J. Zhou, H. Peng#, K. Li, K. Qu, B. Wang, Y. Wu, L. Ye, Z. Dong, H. Wei, R. Sun, Z. Tian# “Liver-Resident NK Cells Control Antiviral Activity of Hepatic T Cells via the PD-1-PD-L1 Axis”, Immunity, 2019.
  4. H. Sun, Q. Huang, M. Huang, H. Wen, Re. Lin, M. Zheng, K. Qu, K. Li, H. Wei, W. Xiao, R. Sun, Z. Tian#, C. Sun# “Human CD96 Correlates to Natural Killer Cell Exhaustion and Predicts the Prognosis of Human Hepatocellular Carcinoma”, Hepatology, 2019.
  5. K. Li*, Y. Wu*, Y. Li, Q. Yu, Z. Tian, H. Wei#, K. Qu# “Landscape and dynamics of the transcriptional regulatory network during natural killer cell differentiation”, Genomics, Proteomics & Bioinformatics, 2019.


  1. Z. Zuo, Y. Jin, W. Zhang, Y. Lu, B. Li#, K. Qu# “ATAC-pipe: general analysis of genome-wide chromatin accessibility”, Briefings in Bioinformatics, 2018.
  2. H. Sun, J. Xu, Q. Huang, M. Huang, K. Li, K. Qu, H. Wen, R. Lin, M. Zheng, H. Wei,W. Xiao, R. Sun, Z. Tian#, C. Sun# “Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC”, Cancer Research, 2018.


  1. K. Qu, L. Zaba, A. Satpathy, P. Giresi, R. Li, Y. Jin, R. Armstrong, C. Jin, N. Schmitt, Z. Rahbar, H. Ueno, W. Greenleaf, Y. Kim#, H. Chang# “Chromatin accessibility landscape of cutaneous T cell lymphoma and dynamic response to HDAC inhibitors”, Cancer Cell, 2017.
  2. G. Wu, M. Yuan, S. Shen, X. Ma, J. Fang, L. Zhu, L. Sun, Z. Liu, X. He, D. Huang, T. Li, C. Li, J. Wu, X. Hu, Z. Li, L. Song, K. Qu, H. Zhang#, P. Gao# “Menin enhances c-Myc-mediated transcription to promote cancer progression” Nature Communications, 2017.
  3. X. Bao#, Z. Siprashvili, B. Zarnegar, R. Shenoy, E. Rios, N. Nady, K. Qu, A. Mah, D. Webster, A. Rubin, G. Wozniak, S. Tao, J. Wysocka, P. Khavari# “CSNK1a1 regulates PRMT1 to maintain the progenitor state in self-renewing somatic tissue”, Developmental Cell, 2017.
  4. W. Pan, S. Zhu, K. Qu, K. Meeth, J. Cheng, K. He, H. Ma, Y. Liao, X. Wen, C. Roden, Z. Tobiasova, Z. Wei, J. Zhao, J. Liu, J. Zheng, B. Guo, S. Khan, M. Bosenberg, R. Flavell, J. Lu# “The DNA methylcytosine dioxygenase Tet2 sustains immunosuppressive function of tumor-infiltrating myeloid cells to promote melanoma progression”, Immunity, 2017.
  5. C. Jin, K. QuApplication of bioinformatics techniques in revealing the mechanisms of epigenetic regulation, SCIENTIA, 2017.


  1. K. Qu, S. Garamszegi, F. Wu, et al, J. Mesirov# “Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace”, Nature Methods, 2016.
  2. C. He*#, H. Hu*, Kitchener D. Wilson*, H. Wu, J. Feng, S. Xia, J. Churko, K. Qu, H. Chang, J. 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. A. Schmitt, J. Garcia, T. Hung, R. Flynn, Y. Shen, K. Qu, A. Payumo, A. Peres-da-Silva1, D. Broz, R. Baum, S. Guo, J. Chen, L. Attardi, H. Chang# “An inducible long noncoding RNA amplifies DNA damage signaling”, Nature Genetics, 2016.
  4. J. Xu, R. Spitale, L. Guan, R. Flynn, E. Torre, R. Li, I. Raber, K. Qu, D. Kern, H. Knaggs, H. Chang, A. Chang# “Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing”, PloS one, 2016.
  5. H. Arda, L. Li, J. Tsai, E. Torre, Y. Rosli, H. Peiris, R. Spitale, C. Dai, X. Gu, K. Qu, P. Wang, J. Wang, M. Grompe, R. Scharfmann, M. Snyder, R. Bottino, A. Powers, H. Chang, S. Kim# “Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human b Cell Function”, Cell Metabolism, 2016.
  6. Y. Wan#, K. Qu, Z. Ouyang, H. Chang “Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing”, Yeast Functional Genomics, 2016.


  1. K. Qu*, L. Zaba*, P. Giresi, R. Li, M. Longmire, Y. Kim, W. Greenleaf, H. Chang# “Individuality and variation of personal regulomes in primary human T cells”, Cell Systems, 2015.
  2. X Bao, A. Rubin, K. Qu, J. Zhang, P. Giresi, H. Chang#, P. 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. B. Sun, L. Boxer,J. Ransohoff, Z. Siprashvili, K. Qu, V. Lopez-Pajares,S. Hollmig, P. Khavari# “CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation”, Genes & Development, 2015.
  4. V. Lopez-Pajares, K. Qu, J. Zhang, D. Webster, B. Barajas, Z. Siprashvili,B. Zarnegar, L. Boxer, E. Rios, S. Tao, M. Kretz, P. Khavari# “A LncRNA-MAF:MAFB Transcription Factor Network Regulates Epidermal Differentiation”, Developmental Cell, 2015.
  5. M. Corley, A. Solem, K. Qu, H. Chang#, A. Laederach “Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark”, Nucleic Acids Research, 2015.
  6. C. Roost, S. Lynch, P. Batista, K. Qu, H. Chang#, E. Kool# “Structure and Thermodynamics of N6
    ‑Methyladenosine in RNA: A Spring-Loaded Base Modification”
    , Journal of the American Chemical Society, 2015.
  7. R. FLYNN*, L. MARTIN*, R. SPITALE, B. DO, S. SAGAN, B. ZARNEGAR, K. Qu, P. KHAVARI, S. QUAKE, P. SARNOW, H. CHANG, E. Kool# “Dissecting noncoding and pathogen RNA–protein interactomes”, RNA, 2015.


  1. Y. Wan*, K. Qu*, Q. Zhang, R. Flynn, O. Manor, Z. Ouyang, J. Zhang, R. Spitale, M. Snyder, E. Segal#, H. Chang# “Landscape and variation of RNA secondary structure across the human transcriptome”, Nature, 2014. (Highlighted in Nature News & Views)
  2. C. Benitez, K. Qu, T. Sugiyama, P. Pauerstein, Y. Liu, J. Tsai, X. Gu, A. Ghodasara, H. Arda, J. Zhang, J. Dekker, H. Tucker, H. Chang, S. Kim# “An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development”, PLoS Genetics, 2014.
  3. J. Quinn, I. Ilik, K. Qu, P. Georgiev, C. Chu, A. Akhtar, H. Chang# “Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification”, Nature Biotechnology, 2014.
  4. P. Batista, B. Molinie, J. Wang, K. Qu, et al., H. Chang# “M6A RNA modification controls cell fate transition in mammalian embryonic stem cells”, Cell Stem Cell, 2014.
  5. J. Quinn, I. Ilik, K. Qu, P. Georgiev, et al., H. Chang# “Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification”, Nature Biotechnology, 2014.
  6. Yu. Yang*, R. Flynn*, Y. Chen, K. Qu, B. Wan, K. Wang, M. Lei, H. Chang# “Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency”, Elife, 2014.
  7. K. Paik, K. Qu, B. Hsueh, E. Torre, R. Flynn, M. Chung, A. Spencley, K. Wang, J. Wu, M. Longaker, H. Chang, D. Wan# “Identification of BMP-Responsive Long Noncoding RNAs in Pluripotent Cells”, Plastic and Reconstructive Surgery, 2014.


  1. O. Wapinski, T. Vierbuchen, K. Qu, et al., H. Chang, and M. Wernig# “Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons”, Cell, 2013.
  2. Y. Wan, K. Qu, Z. Ouyang, and H. Chang# “Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing”, Nature Protocols, 2013.
  3. N. Rapicavoli, K. Qu, et al., H. Chang# “A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics”, eLife, 2013.
  4. X. Bao, J. Tang, V. Lopaz-Pajares, S. Tao, K. Qu, G. Crabtree, P. Khavari# “ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-Dependent induction of klf4”, Cell Stem Cell, 2013.
  5. M. Kretz, D. Webster, C. Chu, Z. Siprashvili, A. Zehnder, K. Qu, et al., H. Chang, and P. Khavari# “Control of somatic tissue differentiation by the long non-coding RNA TINCR”, Nature, 2013. (Faculty 1000
  6. L. Li, B. Liu, O. Wapinski, M. Tsai, K. Qu, J. Zhang, J. Carlson, M. Lin, F. Fang, R. Gupta, J. Helms, H. Chang# “Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression”, Cell Reports, 2013.
  7. A. Chang, P. Bitter Jr, K. Qu, M. Lin, N. Rapicavoli, H. Chang# “Rejuvenation of gene expression pattern of aged human skin by broadband light treatment: a pilot study”, Journal of Investigative Dermatology, 2013.


  1. R. Flockhart, D. Webster, K. Qu, et al., P. Khavari# “BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration”, Genome Research, 2012. (Highlighted in Nature Reviews Cancer)
  2. Y. Wan, K. Qu, Z. Ouyang, et al., E. Segal, H. Chang# “Genome-wide measurement of RNA folding energies”, Molecular Cell, 2012. (Faculty 1000)
  3. A. Bhaduri, K. Qu, et al., and P. Khavari# “Rapid identification of nonhuman sequencing in high throughput sequencing datasets”, Bioinformatics, 2012. (Faculty 1000)
  4. N. Gomez-Ospina, A. Chang, K. Qu, A. Oro# “Translocation affecting sonic hedgehog gene in basal cell carcinomas”, The New England Journal of Medicine, 2012.
  5. C. Lee, A. Ungewickell, A. Bhaduri, K. Qu, D. Webster, R. Armstrong, W. Weng, C. Aros, A. Mah, R. Chen, M. Lin, U. Sundram, H. Chang, M. Kretz, Y. Kim, P. Khavari# “Transcriptome Sequencing in Sezary Syndrome Identifies Sezary Cell and Mycosis Fungoides-Associated lncRNAs and Novel Transcripts”, Blood, 2012.
  6. B. Zarnegar, D. Webster, V. Lopez-Pajares, B. Hunt, K. Qu, K. Yan, D. Berk, G. Sen, P. 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. P. Wang, K. McKnight, D. Wong, R. Rodriguez, T. Sugiyama, X. Gu, A. Ghodasara, K. Qu, H. Chang, S. 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. L. Littlepage, A. Adler, H. Kouros-Mehr, G. Huang, J. Chou, S. Krig, O. Griffith, J. Korkola, K. Qu, D. Lawson, Q. Xue, M. Sternlicht, G. Dijkgraaf, P. Yaswen, H. Rugo, C. Sweeney, C. Collins, J. Gray, H. Chang, Z. Werb# “The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progression”, Cancer Discovery, 2012.
  9. G. Sen, L. Boxer, D. Webster, R. Bussat, K. Qu, B. Zarnegar, D. Johnston, Z. Siprashvili, P. Khavari# “ZNF750 Is a p63 Target Gene that Induces KLF4 to Drive Terminal Epidermal Differentiation”, Developmental Cell, 2012.
  10. M. Kretz*, D. Webster*, R. Flockhart, C. Lee, A. Zehnder, V. Lopez-Pajares, K. Qu, G. Zheng, J. Chow, G. Kim, J. Rinn, H. Chang, Z. Siprashvili, P. Khavari# “Suppression of progenitor differentiation requires the long noncoding RNA ANCR”, Genes & Development, 2012.


  1. C. Chu, K. Qu, F. Zhong, S. Artandi, H. 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. S. Marro, Z. Pang, N. Yang, M. Tsai, K. Qu, et al., M. 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. T. Kawahara, N. Rapicavoli, An. Wu, K. Qu, S. Quake, H. Chang# “Dynamic chromatin localization of Sirt6 shapes stress-and aging-related transcriptional networks”, PLoS Genet, 2011.
  4. Z. Chen, Z. Liu, W. Li, K. Qu, X. Deng, M. Varma, A. Fichera, A. Pigazzi, J. Garcia-Aguilar# “Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer”, Genes, Chromosomes and Cancer, 2011.


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