Kun Qu

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Kun Qu

Publications by authors named "Kun Qu"

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55Publications

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CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue.

Dev Cell 2017 10 21;43(2):227-239.e5. Epub 2017 Sep 21.

Program in Epithelial Biology, Stanford University, 269 Campus Drive, Room 2145, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA. Electronic address:

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October 2017

The DNA Methylcytosine Dioxygenase Tet2 Sustains Immunosuppressive Function of Tumor-Infiltrating Myeloid Cells to Promote Melanoma Progression.

Immunity 2017 08;47(2):284-297.e5

Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale Cancer Center, Yale Cooperative Center of Excellence in Hematology, Yale University, New Haven, CT 06520, USA. Electronic address:

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August 2017

Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing.

PLoS One 2016 9;11(11):e0165913. Epub 2016 Nov 9.

Department of Dermatology, Stanford University School of Medicine, Redwood City, California, United States of America.

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July 2017

Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors.

Cancer Cell 2017 07 15;32(1):27-41.e4. Epub 2017 Jun 15.

Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA 94305-5168, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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July 2017

Menin enhances c-Myc-mediated transcription to promote cancer progression.

Nat Commun 2017 May 5;8:15278. Epub 2017 May 5.

CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui 230027, China.

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May 2017

An inducible long noncoding RNA amplifies DNA damage signaling.

Nat Genet 2016 11 26;48(11):1370-1376. Epub 2016 Sep 26.

Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.

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November 2016

Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing.

Methods Mol Biol 2016 ;1361:141-60

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.

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August 2016

Induction of Viable but Nonculturable State in Rhodococcus and Transcriptome Analysis Using RNA-seq.

PLoS One 2016 25;11(1):e0147593. Epub 2016 Jan 25.

Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.

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July 2016

Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function.

Cell Metab 2016 05 28;23(5):909-20. Epub 2016 Apr 28.

Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine (Oncology Division), Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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May 2016

Systematic Characterization of Long Noncoding RNAs Reveals the Contrasting Coordination of Cis- and Trans-Molecular Regulation in Human Fetal and Adult Hearts.

Circ Cardiovasc Genet 2016 Apr 19;9(2):110-8. Epub 2016 Feb 19.

From the Stanford Cardiovascular Institute (C.H., K.D.W., H.W., J.C., J.C.W.), Division of Cardiology, Department of Medicine (C.H., H.W., J.C., J.C.W.), Department of Pathology (K.D.W.), and Program in Epithelial Biology (K.Q., H.Y.C.), Stanford University, CA; and School of Basic Medical Science (C.H., H.H., S.X.) and International School of Software (J.F.), Wuhan University, Wuhan, China.

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April 2016

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.

Genome Biol 2015 Dec 18;16:284. Epub 2015 Dec 18.

Program in Epithelial Biology, Stanford University, 269 Campus Drive, Stanford, CA, 94305, USA.

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December 2015

CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation.

Genes Dev 2015 Nov;29(21):2225-30

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA; Veterans Affairs Healthcare System, Palo Alto, California 94304, USA.

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November 2015

Individuality and variation of personal regulomes in primary human T cells.

Cell Syst 2015 Jul;1(1):51-61

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.

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July 2015

A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation.

Dev Cell 2015 Mar;32(6):693-706

Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA. Electronic address:

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March 2015

Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification.

J Am Chem Soc 2015 Feb 2;137(5):2107-15. Epub 2015 Feb 2.

Department of Chemistry, ‡Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University , Stanford, California 94305, United States.

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February 2015

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark.

Nucleic Acids Res 2015 Feb 23;43(3):1859-68. Epub 2015 Jan 23.

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 37599, USA Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA

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February 2015

Dissecting noncoding and pathogen RNA-protein interactomes.

RNA 2015 Jan 19;21(1):135-43. Epub 2014 Nov 19.

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA

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January 2015

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.

Cell Stem Cell 2014 Dec 16;15(6):707-19. Epub 2014 Oct 16.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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December 2014

An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.

PLoS Genet 2014 Oct 16;10(10):e1004645. Epub 2014 Oct 16.

Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America; Department of Medicine (Oncology Division), Stanford University School of Medicine, Stanford, California, United States of America.

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October 2014

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.

Nat Biotechnol 2014 Sep 6;32(9):933-940. Epub 2014 Jul 6.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford CA 94305, USA.

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September 2014

An improved integration method in serial femtosecond crystallography.

Acta Crystallogr D Biol Crystallogr 2014 May 26;70(Pt 5):1202-11. Epub 2014 Apr 26.

Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

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May 2014

Abstract 158: Identification of BMP-Responsive Long Noncoding RNAs in Pluripotent Cells.

Plast Reconstr Surg 2014 Mar;133(3 Suppl):174

1Hagey Laboratory for Pediatric Regenerative Medicine, Department of Surgery, Plastic and Reconstructive Surgery Division, Stanford, CA, 2Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford, CA, 3Department of Dermatology, Stanford, CA, 4Department of Radiology and Department of Medicine, Division of Cardiology, Stanford, CA.

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March 2014

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency.

Elife 2014 Feb 12;3:e02046. Epub 2014 Feb 12.

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.

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February 2014

Landscape and variation of RNA secondary structure across the human transcriptome.

Nature 2014 Jan;505(7485):706-9

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.

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January 2014

Targeted disruption of Hotair leads to homeotic transformation and gene derepression.

Cell Rep 2013 Oct 26;5(1):3-12. Epub 2013 Sep 26.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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October 2013

Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons.

Cell 2013 Oct 24;155(3):621-35. Epub 2013 Oct 24.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Program in Cancer Biology, Stanford University, Stanford, CA 94305, USA.

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October 2013

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics.

Elife 2013 Jul 23;2:e00762. Epub 2013 Jul 23.

Program in Epithelial Biology , Howard Hughes Medical Institute, Stanford University School of Medicine , Stanford , United States.

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July 2013

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing.

Nat Protoc 2013 May 4;8(5):849-69. Epub 2013 Apr 4.

Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.

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May 2013

Rejuvenation of gene expression pattern of aged human skin by broadband light treatment: a pilot study.

J Invest Dermatol 2013 Feb 30;133(2):394-402. Epub 2012 Aug 30.

Department of Dermatology, Stanford University School of Medicine, Redwood City, California 94063, USA.

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February 2013

ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4.

Cell Stem Cell 2013 Feb;12(2):193-203

Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.

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February 2013

Genome-wide measurement of RNA folding energies.

Mol Cell 2012 Oct 13;48(2):169-81. Epub 2012 Sep 13.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.

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October 2012

Genomic profiling of a human organotypic model of AEC syndrome reveals ZNF750 as an essential downstream target of mutant TP63.

Am J Hum Genet 2012 Sep 23;91(3):435-43. Epub 2012 Aug 23.

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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September 2012

A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells.

Stem Cells Dev 2012 Aug 29;21(12):2273-87. Epub 2012 Feb 29.

Department of Developmental Biology, Stanford University School of Medicine, Stanford, Califorina, USA.

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August 2012

BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration.

Genome Res 2012 Jun 11;22(6):1006-14. Epub 2012 May 11.

Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA.

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June 2012

Rapid identification of non-human sequences in high-throughput sequencing datasets.

Bioinformatics 2012 Apr 28;28(8):1174-5. Epub 2012 Feb 28.

Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA.

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April 2012

ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation.

Dev Cell 2012 Mar 23;22(3):669-77. Epub 2012 Feb 23.

Department of Medicine/Cellular and Molecular Medicine, University of California-San Diego School of Medicine, La Jolla, CA 92093, USA.

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March 2012

The structural basis of the response regulator DrRRA from Deinococcus radiodurans.

Biochem Biophys Res Commun 2012 Jan 29;417(4):1206-12. Epub 2011 Dec 29.

Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.

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January 2012

Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.

Mol Cell 2011 Nov 29;44(4):667-78. Epub 2011 Sep 29.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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November 2011

Direct lineage conversion of terminally differentiated hepatocytes to functional neurons.

Cell Stem Cell 2011 Oct 29;9(4):374-82. Epub 2011 Sep 29.

Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, CA 94305, USA.

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October 2011

Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer.

Genes Chromosomes Cancer 2011 Sep 16;50(9):689-99. Epub 2011 May 16.

Department of Surgery, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.

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September 2011

Dynamic chromatin localization of Sirt6 shapes stress- and aging-related transcriptional networks.

PLoS Genet 2011 Jun 30;7(6):e1002153. Epub 2011 Jun 30.

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, United States of America.

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June 2011

Alternative splicing regulatory network reconstruction from exon array data.

J Theor Biol 2010 Apr 5;263(4):471-80. Epub 2010 Jan 5.

Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.

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April 2010

Hydrogen sulfide is a mediator of cerebral ischemic damage.

Stroke 2006 Mar 26;37(3):889-93. Epub 2006 Jan 26.

Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore.

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March 2006

Transfer of noise into signal through one-way coupled chemical oscillators.

Chemphyschem 2005 Jan;6(1):58-61

Department of Chemical Physics, University of Science and Technology of China Hefei, Anhui, 230026, People's Republic of China.

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January 2005