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Kun Qu, Ph.D. - Publications

Affiliations: 
2010 Chemistry Indiana University, Bloomington, Bloomington, IN, United States 
Area:
systems biology, physical chemistry
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Li B, Li Y, Li K, Zhu L, Yu Q, Cai P, Fang J, Zhang W, Du P, Jiang C, Lin J, Qu K. APEC: an accesson-based method for single-cell chromatin accessibility analysis. Genome Biology. 21: 116. PMID 32398051 DOI: 10.1186/S13059-020-02034-Y  0.347
2020 Xie H, Zhang W, Zhang M, Akhtar T, Li Y, Yi W, Sun X, Zuo Z, Wei M, Fang X, Yao Z, Dong K, Zhong S, Liu Q, Shen Y, ... ... Qu K, et al. Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids. Science Advances. 6: eaay5247. PMID 32083182 DOI: 10.1126/Sciadv.Aay5247  0.321
2020 Du P, Cai P, Huang B, Jiang C, Wu Q, Li B, Qu K. SMAtool reveals sequences and structural principles of protein-RNA interaction. Biochemical and Biophysical Research Communications. PMID 32070491 DOI: 10.1016/J.Bbrc.2020.02.068  0.359
2019 Fang J, Ma Q, Chu C, Huang B, Li L, Cai P, Batista PJ, Tolentino KEM, Xu J, Li R, Du P, Qu K, Chang HY. PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications. Genome Biology. 20: 292. PMID 31862000 DOI: 10.1186/S13059-019-1880-3  0.374
2019 Cai P, Otten AB, Cheng B, Ishii MA, Zhang W, Huang B, Qu K, Sun BK. A genome-wide long noncoding RNA CRISPRi screen identifies as a novel regulator of epidermal homeostasis. Genome Research. PMID 31804951 DOI: 10.1101/Gr.251561.119  0.455
2019 Sun H, Liu L, Huang Q, Liu H, Huang M, Wang J, Wen H, Lin R, Qu K, Li K, Wei H, Xiao W, Sun R, Tian Z, Sun C. Accumulation of tumor-infiltrating CD49a+ NK cells correlates with poor prognosis for human hepatocellular carcinoma. Cancer Immunology Research. PMID 31311791 DOI: 10.1158/2326-6066.Cir-18-0757  0.308
2019 Ang CE, Ma Q, Wapinski OL, Fan S, Flynn RA, Lee QY, Coe B, Onoguchi M, Olmos VH, Do BT, Dukes-Rimsky L, Xu J, Tanabe K, Wang L, Elling U, ... ... Qu K, et al. The novel lncRNA is pro-neurogenic and mutated in human neurodevelopmental disorders. Elife. 8. PMID 30628890 DOI: 10.7554/Elife.41770  0.388
2019 Otten A, Cai P, Cheng B, Ishii M, Qu K, Sun B. 194 A CRISPR-interference screen identifies PRANCR and other novel long non-coding RNAs controlling human epidermis formation Journal of Investigative Dermatology. 139. DOI: 10.1016/J.Jid.2019.07.195  0.335
2019 Otten A, Cai P, Cheng B, Ishii MA, Qu K, Sun B. 332 A noncoding RNA CRISPR-interference screen identifies novel regulators and pathways of human epidermis formation Journal of Investigative Dermatology. 139. DOI: 10.1016/J.Jid.2019.03.408  0.363
2017 Bao X, Siprashvili Z, Zarnegar BJ, Shenoy RM, Rios EJ, Nady N, Qu K, Mah A, Webster DE, Rubin AJ, Wozniak GG, Tao S, Wysocka J, Khavari PA. CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-Renewing Somatic Tissue. Developmental Cell. PMID 28943242 DOI: 10.1016/J.Devcel.2017.08.021  0.363
2017 Pan W, Zhu S, Qu K, Meeth K, Cheng J, He K, Ma H, Liao Y, Wen X, Roden C, Tobiasova Z, Wei Z, Zhao J, Liu J, Zheng J, et al. The DNA Methylcytosine Dioxygenase Tet2 Sustains Immunosuppressive Function of Tumor-Infiltrating Myeloid Cells to Promote Melanoma Progression. Immunity. 47: 284-297.e5. PMID 28813659 DOI: 10.1016/J.Immuni.2017.07.020  0.309
2017 Qu K, Zaba LC, Satpathy AT, Giresi PG, Li R, Jin Y, Armstrong R, Jin C, Schmitt N, Rahbar Z, Ueno H, Greenleaf WJ, Kim YH, Chang HY. Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. Cancer Cell. PMID 28625481 DOI: 10.1016/J.Ccell.2017.05.008  0.323
2017 Wu G, Yuan M, Shen S, Ma X, Fang J, Zhu L, Sun L, Liu Z, He X, Huang, Li T, Li C, Wu J, Hu X, Li Z, ... ... Qu K, et al. Menin enhances c-Myc-mediated transcription to promote cancer progression. Nature Communications. 8: 15278. PMID 28474697 DOI: 10.1038/Ncomms15278  0.386
2016 Xu J, Spitale RC, Guan L, Flynn RA, Torre EA, Li R, Raber I, Qu K, Kern D, Knaggs HE, Chang HY, Chang AL. Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. Plos One. 11: e0165913. PMID 27829007 DOI: 10.1371/Journal.Pone.0165913  0.304
2016 Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY. An inducible long noncoding RNA amplifies DNA damage signaling. Nature Genetics. PMID 27668660 DOI: 10.1038/Ng.3673  0.337
2016 Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, et al. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. Cell Metabolism. PMID 27133132 DOI: 10.1016/J.Cmet.2016.04.002  0.361
2016 He C, Hu H, Wilson KD, Wu H, Feng J, Xia S, Churko J, Qu K, Chang HY, Wu JC. 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. PMID 26896382 DOI: 10.1161/Circgenetics.115.001264  0.369
2016 Su X, Guo L, Ding L, Qu K, Shen C. Induction of Viable but Nonculturable State in Rhodococcus and Transcriptome Analysis Using RNA-seq. Plos One. 11: e0147593. PMID 26808070 DOI: 10.1371/Journal.Pone.0147593  0.374
2016 Wan Y, Qu K, Ouyang Z, Chang HY. Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1361: 141-60. PMID 26483021 DOI: 10.1007/978-1-4939-3079-1_9  0.357
2015 Bao X, Rubin AJ, Qu K, Zhang J, Giresi PG, Chang HY, Khavari PA. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology. 16: 284. PMID 26683334 DOI: 10.1186/S13059-015-0840-9  0.328
2015 Sun BK, Boxer LD, Ransohoff JD, Siprashvili Z, Qu K, Lopez-Pajares V, Hollmig ST, Khavari PA. CALML5 is a ZNF750- and TINCR-induced protein that binds stratifin to regulate epidermal differentiation. Genes & Development. 29: 2225-30. PMID 26545810 DOI: 10.1101/Gad.267708.115  0.409
2015 Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY. Individuality and variation of personal regulomes in primary human T cells. Cell Systems. 1: 51-61. PMID 26251845 DOI: 10.1016/J.Cels.2015.06.003  0.341
2015 Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas BC, Siprashvili Z, Zarnegar BJ, Boxer LD, Rios EJ, Tao S, Kretz M, Khavari PA. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Developmental Cell. 32: 693-706. PMID 25805135 DOI: 10.1016/J.Devcel.2015.01.028  0.388
2015 Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Research. 43: 1859-68. PMID 25618847 DOI: 10.1093/Nar/Gkv010  0.335
2015 Roost C, Lynch SR, Batista PJ, Qu K, Chang HY, Kool ET. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. Journal of the American Chemical Society. 137: 2107-15. PMID 25611135 DOI: 10.1021/Ja513080V  0.331
2015 Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. Dissecting noncoding and pathogen RNA-protein interactomes. Rna (New York, N.Y.). 21: 135-43. PMID 25411354 DOI: 10.1261/Rna.047803.114  0.37
2014 Paik KJ, Qu K, Hsueh B, Torre EA, Flynn RA, Chung MT, Spencley A, Wang KC, Wu JC, Longaker MT, Chang HY, Wan DC. Abstract 158: Identification of BMP-Responsive Long Noncoding RNAs in Pluripotent Cells. Plastic and Reconstructive Surgery. 133: 174. PMID 25942268 DOI: 10.1097/01.Prs.0000444987.90678.B2  0.378
2014 Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 15: 707-19. PMID 25456834 DOI: 10.1016/J.Stem.2014.09.019  0.389
2014 Benitez CM, Qu K, Sugiyama T, Pauerstein PT, Liu Y, Tsai J, Gu X, Ghodasara A, Arda HE, Zhang J, Dekker JD, Tucker HO, Chang HY, Kim SK. An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development. Plos Genetics. 10: e1004645. PMID 25330008 DOI: 10.1371/Journal.Pgen.1004645  0.4
2014 Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, Chang HY. Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nature Biotechnology. 32: 933-40. PMID 24997788 DOI: 10.1038/Nbt.2943  0.36
2014 Yang YW, Flynn RA, Chen Y, Qu K, Wan B, Wang KC, Lei M, Chang HY. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. Elife. 3: e02046. PMID 24521543 DOI: 10.7554/Elife.02046  0.35
2014 Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 505: 706-9. PMID 24476892 DOI: 10.1038/Nature12946  0.385
2013 Wapinski OL, Vierbuchen T, Qu K, Lee QY, Chanda S, Fuentes DR, Giresi PG, Ng YH, Marro S, Neff NF, Drechsel D, Martynoga B, Castro DS, Webb AE, Südhof TC, et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell. 155: 621-35. PMID 24243019 DOI: 10.1016/J.Cell.2013.09.028  0.37
2013 Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Reports. 5: 3-12. PMID 24075995 DOI: 10.1016/J.Celrep.2013.09.003  0.379
2013 Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge RM, Chang HY. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife. 2: e00762. PMID 23898399 DOI: 10.7554/Elife.00762  0.321
2013 Wan Y, Qu K, Ouyang Z, Chang HY. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nature Protocols. 8: 849-69. PMID 23558785 DOI: 10.1038/Nprot.2013.045  0.364
2013 Bao X, Tang J, Lopez-Pajares V, Tao S, Qu K, Crabtree GR, Khavari PA. ACTL6a enforces the epidermal progenitor state by suppressing SWI/SNF-dependent induction of KLF4. Cell Stem Cell. 12: 193-203. PMID 23395444 DOI: 10.1016/J.Stem.2012.12.014  0.371
2013 Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231-5. PMID 23201690 DOI: 10.1038/Nature11661  0.42
2013 Chang AL, Bitter PH, Qu K, Lin M, Rapicavoli NA, Chang HY. Rejuvenation of gene expression pattern of aged human skin by broadband light treatment: a pilot study. The Journal of Investigative Dermatology. 133: 394-402. PMID 22931923 DOI: 10.1038/Jid.2012.287  0.318
2013 Yang YW, Flynn RA, Chen Y, Qu K, Wan B, Wang KC, Lei M, Chang HY. Author response: Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency Elife. DOI: 10.7554/Elife.02046.013  0.347
2013 Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M, Paul KA. Abstract LB-248: BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Cancer Research. 72. DOI: 10.1158/1538-7445.Am2013-Lb-248  0.454
2012 Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY. Genome-wide measurement of RNA folding energies. Molecular Cell. 48: 169-81. PMID 22981864 DOI: 10.1016/J.Molcel.2012.08.008  0.372
2012 Lee CS, Ungewickell A, Bhaduri A, Qu K, Webster DE, Armstrong R, Weng WK, Aros CJ, Mah A, Chen RO, Lin M, Sundram U, Chang HY, Kretz M, Kim YH, et al. Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. Blood. 120: 3288-97. PMID 22936659 DOI: 10.1182/Blood-2012-04-423061  0.44
2012 Zarnegar BJ, Webster DE, Lopez-Pajares V, Vander Stoep Hunt B, Qu K, Yan KJ, Berk DR, Sen GL, Khavari PA. Genomic profiling of a human organotypic model of AEC syndrome reveals ZNF750 as an essential downstream target of mutant TP63. American Journal of Human Genetics. 91: 435-43. PMID 22922031 DOI: 10.1016/J.Ajhg.2012.07.007  0.336
2012 Gomez-Ospina N, Chang AL, Qu K, Oro AE. Translocation affecting sonic hedgehog genes in basal-cell carcinoma. The New England Journal of Medicine. 366: 2233-4. PMID 22670922 DOI: 10.1056/Nejmc1115123  0.309
2012 Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M, Khavari PA. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Research. 22: 1006-14. PMID 22581800 DOI: 10.1101/Gr.140061.112  0.302
2012 Sen GL, Boxer LD, Webster DE, Bussat RT, Qu K, Zarnegar BJ, Johnston D, Siprashvili Z, Khavari PA. ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation. Developmental Cell. 22: 669-77. PMID 22364861 DOI: 10.1016/J.Devcel.2011.12.001  0.362
2012 Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes & Development. 26: 338-43. PMID 22302877 DOI: 10.1101/Gad.182121.111  0.432
2012 Wang P, McKnight KD, Wong DJ, Rodriguez RT, Sugiyama T, Gu X, Ghodasara A, Qu K, Chang HY, Kim SK. A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells. Stem Cells and Development. 21: 2273-87. PMID 22236333 DOI: 10.1089/Scd.2011.0416  0.362
2011 Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Molecular Cell. 44: 667-78. PMID 21963238 DOI: 10.1016/J.Molcel.2011.08.027  0.393
2011 Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M. Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. Cell Stem Cell. 9: 374-82. PMID 21962918 DOI: 10.1016/J.Stem.2011.09.002  0.375
2011 Kawahara TLA, Rapicavoli NA, Wu AR, Qu K, Quake SR, Chang HY. Dynamic chromatin localization of sirt6 shapes stress- and aging-related transcriptional networks Plos Genetics. 7. PMID 21738489 DOI: 10.1371/Journal.Pgen.1002153  0.346
2010 Qu K, Yesnik AM, Ortoleva PJ. Alternative splicing regulatory network reconstruction from exon array data Journal of Theoretical Biology. 263: 471-480. PMID 20043923 DOI: 10.1016/J.Jtbi.2009.12.025  0.579
2008 Qu K, Ortoleva P. Understanding stem cell differentiation through self-organization theory Journal of Theoretical Biology. 250: 606-620. PMID 18076908 DOI: 10.1016/J.Jtbi.2007.10.019  0.567
2007 Qu K, Haidar AA, Fan J, Ensman L, Tuncay K, Jolly M, Ortoleva P. Cancer onset and progression: A genome-wide, nonlinear dynamical systems perspective on onconetworks Journal of Theoretical Biology. 246: 234-244. PMID 17289080 DOI: 10.1016/J.Jtbi.2006.12.002  0.56
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