Entire list of publications and citations is available from : Google Scholar:
* equal contributions, # co-corresponding authors
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- C. Jin, K. Qu# “Application of bioinformatics techniques in revealing the mechanisms of epigenetic regulation“, SCIENTIA, 2017.
- K. Qu, S. Garamszegi, F. Wu, et al, J. Mesirov# “Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace”, Nature Methods, 2016.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- M. Corley, A. Solem, K. Qu, H. Chang#, A. Laederach “Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark”, Nucleic Acids Research, 2015.
- 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.
- 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.
- 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)
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- O. Wapinski, T. Vierbuchen, K. Qu, et al., H. Chang, and M. Wernig# “Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons”, Cell, 2013.
- 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.
- N. Rapicavoli, K. Qu, et al., H. Chang# “A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics”, eLife, 2013.
- 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.
- 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)
- 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.
- 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.
- 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)
- Y. Wan, K. Qu, Z. Ouyang, et al., E. Segal, H. Chang# “Genome-wide measurement of RNA folding energies”, Molecular Cell, 2012. (Faculty 1000)
- A. Bhaduri, K. Qu, et al., and P. Khavari# “Rapid identification of nonhuman sequencing in high throughput sequencing datasets”, Bioinformatics, 2012. (Faculty 1000)
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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)
- 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)
- 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.
- 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.
- K. Qu, A. Yesnik, P. Ortoleva# “Alternative splicing regulatory network reconstruction from exon array data”, Journal of Theoretical Biology, 2010.
- K. Qu, P. Ortoleva# “Understanding stem cell differentiation through self-organization theory”, Journal of Theoretical Biology, 2008.
- 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.