Selected Publications After Independence

  1. J. Fang*, Q. Ma*, C. Chu, B. Huang, L. Li, P. Cai, Pedro J. Batista, Karen Erisse Martin 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, In Press, 2019.
  2. 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, In Press, 2019.
  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, In Press, 2019.
  4. 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, 8:e41770, 2019.
  5. 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#, and C. Sun# “Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC”, Cancer Research, CAN-19-0630, 2019.
  6. 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, 403–417, 2019.
  7. 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, VOL.0,NO.0, 2019.
  8. Z. Zuo, Y. Jin, W. Zhang, Y. Lu, B. Li & K. Qu# “ATAC-pipe: general analysis of genome-wide chromatin accessibility”, Briefings in Bioinformatics, bby056–bby056, 2018.
  9. 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, 47, 227–239, 2017.
  10. 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, 47, 284–297, 2017.
  11. 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, 32, 1-15, 2017.
  12. 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, 8, 15278, 2017.
  13. C. Jin , K. Qu# Application of bioinformatics techniques in revealing the mechanisms of epigenetic regulation  SCIENTIA SINICA Vitae 47(1), 116-124 , 2017.

Selected Publications Before Independence (21 out of 40)

Entire list of publications is available from Google Scholar:

  1. K. Qu, S. Garamszegi, F. Wu, et al, J. Mesirov “Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace”, Nature Methods, 13, 245-247, 2016.
  2. K. Qu, L. Zaba, P. Giresi, et al, H. Chang “Individuality and variation of personal regulomes in primary human T cells”, Cell Systems, 1:51-61, 2015 (Previewed in Cell System)
  3. V. Lopez-Pajares, K. Qu, et al, P. Khavari “A LncRNA-MAF/MAFB transcription factor network regulates epidermal differentiation”, Developmental Cell, 32(6), 693-706, 2015 (Cover Article, Previewed in Developmental Cell)
  4. Y. Wan, K. Qu, Q. Zhang, R. Flynn, O. Manor, Z. Ouyang, J. Zhang, R. Spitale, M. Snyder, E. Segal and H. Chang “Landscape and variation of RNA secondary structure across the human transcriptome”, Nature, 505:706-9, 2014 (Highlighted in Nature News & Views)
  5. C. Benitez, K. Qu, et al, S. Kim “An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development”, PLoS Genetics, Oct. 16, 2014
  6. 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, 32:933-940, 2014
  7. 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, 15(6), 707-719, 2014
  8. O. Wapinski, T. Vierbuchen, K. Qu, et al., H. Chang, and M. Wernig “Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons”, Cell, 155(3), 2013
  9. Y. Wan, K. Qu, Z. Ouyang, and H. Chang “Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing”, Nature Protocols, 8(5):849-69, 2013
  10. N. Rapicavoli, K. Qu, et al., H. Chang “A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics”, eLife, July 23, 2013
  11. 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, 12(2):193-203, 2013
  12. 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, 493(7431):231-5, 2013 (Faculty 1000
  13. 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, 22(6):1006-14, 2012 (Highlighted in Nature Reviews Cancer)
  14. Y. Wan, K. Qu, Z. Ouyang, et al., E. Segal, H. Chang. “Genome-wide measurement of RNA folding energies”, Molecular Cell, 48:1-13, 2012 (Faculty 1000)
  15. A. Bhaduri, K. Qu, et al., and P. Khavari. “Rapid identification of nonhuman sequencing in high throughput sequencing datasets”, Bioinformatics, 28(8):1174-5, 2012 (Faculty 1000)
  16. N. Gomez-Ospina, A. Chang, K. Qu, A. Oro. “Translocation affecting sonic hedgehog gene in basal cell carcinomas”, The New England Journal of Medicine, 366:2233-2234, 2012
  17. C. Chu, K. Qu, F. Zhong, S. Artandi, H. Chang. “Genomic maps of lncRNA occupancy reveal principles of RNA-chromatin interactions”, Molecular Cell, 44(4), 667-678, 2011 (Cover Article, Highlighted in Nature Reviews Genetics and Nature Methods, Faculty 1000)
  18. 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, 9(4) 374-382, 2011 (Cover Article, Faculty 1000, and Highlighted in Nature Biotechnology)
  19. K. Qu, A. Yesnik, P. Ortoleva. “Alternative splicing regulatory network reconstruction from exon array data”, Journal of Theoretical Biology, 263: 471-480, 2010
  20. K. Qu, P. Ortoleva, “Understanding stem cell differentiation through self-organization theory”, Journal of Theoretical Biology, 250(4): 606-20, 2008
  21. 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, 246: 234-244, 2007