Kun QU,Ph.D.

Professor, School of Life Science

University of Science and Technology of China (USTC)

443 Huangshang Road, Hefei City, Anhui, 230027, P. R. China

Email: qukun@ustc.edu.cn

Homepage: http://qulab.ustc.edu.cn/

Education:

2004-2010:Ph.D., Physical Chemistry, Indiana University, USA

1999-2004:B.S., Chemical Physics, USTC, China

Research Experience:

2016-Pre:Professor, School of Life Science, USTC, China

2014-2016:Director of Bioinformatics, School of Medicine, Stanford University

2012-2014:Sr. Bioinformatics Scientist, School of Medicine, Stanford University

2010-2011:Bioinformatician, School of Medicine, Stanford University, USA

2009-2010:Bioinformatics Specialist, City of Hope Cancer Center, USA

Honors and Awards: 

2007-2008:ORISE Fellowship

Research Fields of Interests: 

1. Personalized medicine, personalized tumor regulome

2. Bioinformatics, computational biology, and development of cloud-based software for big data in life science

3. Transcription factor, lncRNA and epigenetic modification in gene regulation

Selected Publications

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, bby056–bby056, 2018.

2. 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.

3. K. Qu*, S. Garamszegi*, F. Wu*, et al, J. Mesirov “Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace”, Nature Methods, 2016, Jan 18. doi: 10.1038/nmeth.3732.

4. K. Qu*, L. Zaba*, P. Giresi, et al, H. Chang “Individuality and dynamics of personal regulomes in human T cells”, Cell Systems, 1:51-61, 2015 (Previewed in Cell System)

5. Y. Wan*, K. Qu*, Q. Zhang, R. Flynn, O. Manor, Z. Ouyang, J. Zhang, R. Spitale, M. Snyder, E. Segaland H. Chang “Landscape and variation of RNA secondary structure across the human transcriptome” Nature, 505:706-9, 2014 (Highlighted in Nature News & Views)

6. 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)

7. 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

8. 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

9. 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

10. O. Wapinski*, T. Vierbuchen*, K. Qu, et al., H. Chang, and M. Wernig “Hierarchical mechanisms for transcription factor-mediated reprogramming of fibroblasts to neurons” Cell, 155(3), 2013

11. 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

12. 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

13. 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

14. 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)

15. R. Flockhart, D. Webster, K. Qu, et al., P. Khavari “BRAF^V600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration” Genome Research, 22(6):1006-14, 2012 (Highlighted inNature Reviews Cancer)

16. 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)

17. A. Bhaduri, K. Qu, et al., and P. Khavari. “Rapid Identification of Nonhuman Sequencing in High Throughput Sequencing Data Sets” Bioinformatics, 28(8):1174-5, 2012 (Faculty 1000)

18. N. Gomez-Ospina, A. Chang, K. Qu, A. Oro. “Translocation Affecting Sonic Hedgehog Gene associated with Basal Cell Carcinomas” The New England Journal of Medicine, 366:2233-2234, 2012

19. C. Chu, K. Qu, F. Zhong, S. Artandi, H. Chang. “Genomic maps of lincRNA 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)

20. 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)

21. K. Qu, A. Yesnik, P. Ortoleva. “Alternative splicing regulatory network reconstruction from exon array data” Journal of Theoretical Biology, 263: 471-480, 2010

22. K. Qu, P. Ortoleva, “Understanding stem cell differentiation through self-organization” Journal of Theoretical Biology, 250(4): 606-20, 2008

23. 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

Google Scholar: http://scholar.google.com/citations?hl=en&user=2CdOi4EAAAAJ

Job Opportunities:

We are seeking highly motivated undergraduates, graduate students, and post-doctoral fellows to join our research team. Applicants with expertise in bioinformatics, computer science, immunology, and molecular and cellular biology are particularly welcome. Please contact Dr. QU Kun directly with your CV and a description of your previous research experience.