Selected Publications After Independence
- 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.
- 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.
- 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.
- 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.
- 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.
- 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:
- 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.
- 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)
- 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)
- 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)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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)
- 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)
- 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)
- 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)
- 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
- 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)
- 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)
- K. Qu*, A. Yesnik, P. Ortoleva. “Alternative splicing regulatory network reconstruction from exon array data”, Journal of Theoretical Biology, 263: 471-480, 2010
- K. Qu*, P. Ortoleva, “Understanding stem cell differentiation through self-organization theory”, Journal of Theoretical Biology, 250(4): 606-20, 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, 246: 234-244, 2007