66. Xie Y*, Chai P*, Till NA, Hemberger H, Lebedenko CG, Porat J, Watkins CP, Caldwell RM, George BM, Perr J, Bertozzi CR, Garcia BA#, Flynn RA#. The modified RNA base acp3U is an attachment site for N-glycans in glycoRNA. Cell 2024. PMID: 39173631.

65. Kageler L, Perr J, Flynn RA#. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chemical Biology. 2024 PMID: 38772372 Review.

64. Zheng R, Dunlap M, Bobkov GOM, Gonzalez-Figueroa C, Patel KJ, Lyu J, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Le Roux CA, Bartels MD, Vuong A, Flynn RA, Chang HY, Van Nostrand EL, Xiao X, Cheng C. hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing. Molecular Cell. 2024 PMID: 38815579.

63. Hristov P, Flynn RA#. Imaging glycosylated RNAs at the subcellular scale. Nature Biotechnology. 2023 PMID: 37872411 Review.

62. Peltan EL, Riley NM, Flynn RA, Roberts DS, Bertozzi CR. Galectin-3 does not interact with RNA directly. Glycobiology. 2024 PMID: 37815932.

61. Aryan F, Detrés D, Luo CC, Kim SX, Shah AN, Bartusel M, Flynn RA, Calo E. Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing. Molecular Cell. 2023 PMID: 37979585.

60. Chai P, Lebedenko CG, Flynn RA#. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet. 2023 Apr 17. doi: 10.1146/annurev-genom-101722-101224. Online ahead of print. PMID: 37068783 Review.

59. Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Co-transcriptional genome surveillance by HUSH is coupled to termination machinery. Mol Cell. 2023 May 18;83(10):1623-1639.e8. doi: 10.1016/j.molcel.2023.04.014. Epub 2023 May 9. PMID: 37164018.

58. Miao W, Porter DF, Lopez-Pajares V, Siprashvili Z, Meyers RM, Bai Y, Nguyen DT, Ko LA, Zarnegar BJ, Ferguson ID, Mills MM, Jilly-Rehak CE, Wu CG, Yang YY, Meyers JM, Hong AW, Reynolds DL, Ramanathan M, Tao S, Jiang S, Flynn RA, Wang Y, Nolan GP, Khavari PA. Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation. Cell. 2023 Jan 5;186(1):80-97.e26. doi: 10.1016/j.cell.2022.12.004. PMID: 36608661.

57. Leon KE, Khalid MM, Flynn RA, Fontaine KA, Nguyen TT, Kumar GR, Simoneau CR, Tomar S, Jimenez-Morales D, Dunlap M, Kaye J, Shah PS, Finkbeiner S, Krogan NJ, Bertozzi C, Carette JE, Ott M. Nuclear accumulation of host transcripts during Zika Virus Infection. PLoS Pathog. 2023 Jan 5;19(1):e1011070. doi: 10.1371/journal.ppat.1011070. eCollection 2023 Jan. PMID: 36603024.

56. Watkins CP, Flynn RA#. A (cross)link in the chains. Nat Chem. 2023 Jan;15(1):5-6. doi: 10.1038/s41557-022-01116-7. PMID: 36609645 Review.

55. Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, Shi PY, Bartenschlager R, Puschnik AS, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T, Carette JE. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science. 2022 Oct 7;378(6615):eabn5648. doi: 10.1126/science.abn5648. Epub 2022 Oct 7. PMID: 36074821.

54. England WE, Wang J, Chen S, Baldi P, Flynn RA#, Spitale RC#. An atlas of posttranslational modifications on RNA binding proteins. Nucleic Acids Res. 2022 May 6;50(8):4329-4339. doi: 10.1093/nar/gkac243. PMID: 35438783.

53. Pluvinage JV, Sun J, Claes C, Flynn RA, Haney MS, Iram T, Meng X, Lindemann R, Riley NM, Danhash E, Chadarevian JP, Tapp E, Gate D, Kondapavulur S, Cobos I, Chetty S, Pașca AM, Pașca SP, Berry-Kravis E, Bertozzi CR, Blurton-Jones M, Wyss-Coray T. The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C. Sci Transl Med. 2021 Dec. PMID: 34851695.

52. Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Res. 2021 Nov. PMID: 34634799.

51. Corley M, Flynn RA, Blue SM, Yee BA, Chang HY, Yeo GW. fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins. STAR Protoc. 2021 Aug. PMID: 34485935.

50. Flynn RA*,#, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR#. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell. 2021 Jun PMID: 34004145.

49. Flynn RA#,*, Belk JA*, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, Carette JE, Bertozzi CR, Wilen CB#, Satpathy AT#. Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell. 2021 Apr PMID: 33743211.

48. Corley M, Flynn RA, Lee B, Blue SM, Chang HY, Yeo GW. Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces. Mol Cell. 2020 PMID: 33242392.

47. Salahudeen AA, Choi SS, Rustagi A, Zhu J, van Unen V, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, Usui T, Zheng GXY, Edwards CE, Wagar LE, Luca V, Anchang B, Nagendran M, Nguyen K, Hart DJ, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Harbury PB, Glenn JS, Garcia KC, Davis MM, Baric RS, Sabatti C, Amieva MR, Blish CA, Desai TJ, Kuo CJ. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature. 2020 Nov PMID: 33238290.

46. Zaro BW, Noh JJ, Mascetti VL, Demeter J, George B, Zukowska M, Gulati GS, Sinha R, Flynn RA, Banuelos A, Zhang A, Wilkinson AC, Jackson P, Weissman IL. Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells. Elife. 2020 Nov PMID: 33236985.

45. Johnson AG, Flynn RA, Lapointe CP, Ooi YS, Zhao ML, Richards CM, Qiao W, Yamada SB, Couthouis J, Gitler AD, Carette JE, Puglisi JD. A memory of eS25 loss drives resistance phenotypes. Nucleic Acids Res. 2020 Jul. PMID: 32463448.

44. Santoriello S*, Sporrij A*, Yang S, Flynn RA, Henriques T, Dorjsuren B, Greig EC, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol. April 2020 PMID: 32231306.

43. Shao Z*, Flynn RA*, Crowe JL*, Zhu Y*, Liang J, Jiang W, Aryan F, Aoude P, Bertozzi CR, Estes VM, Lee BJ, Bhagat G, Zha S, Calo E. DNA-PKcs has KU dependent function in ribosomal RNA processing and hematopoiesis. Nature. 2020 March. PMID: 32103174.

42. Ooi YS*, Majzoub K*, Flynn RA*#, Mata MA, Diep J, Li JK, van Buuren N, Rumachik N, Johnson AG, Puschnik AS, Marceau CD, Mlera L, Grabowski JM, Kirkegaard K, Bloom ME, Sarnow P, Bertozzi CR, Carette JE#. An RNA-centric dissection of host complexes controlling flavivirus infection. Nat Microbiol. 2019 Aug. PMID: 31384002.

41. Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY. HiChIRP reveals RNA-associated chromosome conformation. Nat Methods. 2019 Jun. PMID: 31133759.

40. 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, Penninger JM, Zhao Y, Qu K, Eichler EE, Srivastava A, Wernig M, Chang HY. The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders. Elife. 2019 Jan. PMID: 30628890.

39. Calo E, Gu B, Bowen ME, Aryan F, Zalc A, Liang J, Flynn RA, Swigut T, Chang HY, Attardi LD, Wysocka J. Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. Nature. 2018 Feb. PMID: 29364875.

38. Tomlin FM*, Gerling-Driessen UIM*, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS Central Science 2017. PMID: 29202016.

37. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Nat Genet. 2017 Nov. PMID: 28945252.

36. Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M. The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell. 2017 Jun 1. PMID: 28575669.

35. Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC. Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts. Biochemistry. 2017 Apr 4. PMID: 28319368.

34. Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. Comparison of SHAPE Reagents for Mapping RNA Structures Inside Living Cells. RNA. 2016 Nov 22. PMID: 27879433 Review.

33. 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. 2016 Nov 9. doi: 10.1371/journal.pone.0165913. PMID: 27829007.

32. Schmitt AM*, Garcia JT*, Hung T*, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Kenzelmann Broz D, Guo S, Attardi LD, Chen JK, Chang HY. An inducible long noncoding RNA guides DNA damage signaling. Nature Genetics. 2016 Sep 26. doi: 10.1038/ng.3673. PMID: 27668660.

31. Mumbach MR*, Rubin AJ*, Flynn RA*, Khavari PA Greenleaf WJ, Chang HY. HiChIP: Efficient and sensitive analysis of protein-directed genome architecture. Nature Methods. 2016 Sep 19. doi: 10.1038/nmeth.3999. PMID: 27643841.

30. Lu Z*, Zhang QC*, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. May 2016. PMID: 27180905.

29. Zarnegar BJ, Flynn RA, Shen Y, Do DT, Chang HY, Khavari PA. Ultraefficient irCLIP platform for characterization of protein-RNA interactions. Nature Methods. 2016 Apr 25. doi: 10.1038/nmeth.3840. PMID: 27111506.

28. Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Molecular Cell. 2016 Apr 7;62(1):34-46. doi: 10.1016/j.molcel.2016.03.013. PMID: 27058786.

27. Oh S*, Flynn RA*, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget. 2016 Apr 5. doi: 10.18632/oncotarget.8612. PMID: 27058758.

26. Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY. 7SK-BAF axis controls pervasive transcription at enhancers. Nature Structural and Molecular Biology. 2016 Feb 15. doi: 10.1038/nsmb.3176. PMID: 26878240.

25. Flynn RA*, Zhang QC*, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14. PMID: 26766114.

24. Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R. Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. Cell Stem Cell. 2015 Dec 3;17(6):675-88. doi: 10.1016/j.stem.2015.09.017. Epub 2015 Oct 22. PMID: 26607380.

23. Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M, Wesche DJ, Martin L, Ware CB, Blish CA, Chang HY, Reijo Pera RA, Wysocka J. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 2015 Apr 20. doi: 10.1038/nature14308. PMID: 25896322.

22. Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY. Systematic discovery of xist RNA binding proteins. Cell. 2015 Apr 9;161(2):404-16. doi: 10.1016/j.cell.2015.03.025. Epub 2015 Apr 2. PMID: 25843628.

21. Spitale RC*, Flynn RA*, Zhang QC*, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015 Mar 26;519(7544):486-90. doi: 10.1038/nature14263. Epub 2015 Mar 18. PMID: 25799993.

20. Calo E*, Flynn RA*, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 2014 Nov 24. PMID: 25470060.

19. 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, Wernig M, Mullen AC, Xing Y, Giallourakis CC, Chang HY. m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells. Cell Stem Cell. 2014 Oct 16. PMID: 25456834.

18. 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. 2014 Nov 19. PMID: 25411354.

17. Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdiscip Rev RNA. 2014 Nov;5(6):867-81. doi: 10.1002/wrna.1253. PMID: 25132067.

16. Flynn RA, Chang HY. Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell. 2014 Jun 5;14(6):752-61. doi: 10.1016/j.stem.2014.05.014. PMID: 24905165.

15. 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. 2014 Feb 12;3:e02046. doi: 10.7554/eLife.02046. PMID: 24521543.

14. 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. 2014 Jan 30;505(7485):706-9. doi: 10.1038/nature12946. PMID: 24476892.

13. Hyun JS, Montoro DT, Lo DD, Flynn RA, Wong V, Chung MT, Longaker MT, Wan DC. The seed and the soil: optimizing stem cells and their environment for tissue regeneration. Ann Plast Surg. 2013 Feb;70(2):235-9. doi: 10.1097/SAP.0b013e31826a18fb. PMID: 23295233.

12. 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, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013 Jan 10;493(7431):231-5. doi: 10.1038/nature11661. PMID: 23201690.

11. Spitale RC*, Crisalli P*, Flynn RA*, Torre EA, Kool ET, Chang HY. RNA SHAPE analysis in living cells. Nat Chem Biol. 2013 Jan;9(1):18-20. doi: 10.1038/nchembio.1131. PMID: 23178934.

10. Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, Tibshirani R, Chang HY, van de Rijn M, West RB. Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol. 2012 Aug 28;13(8):R75. PMID: 22929540.

9. Flynn RA, Chang HY. Active Chromatin and noncoding RNAs: an intimate relationship. Curr Opin Genet Dev. 2012 Apr;22(2):172-8. PMID:22154525.

8. Flynn RA*, Almada AE*, Zamudio JR, Sharp PA. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent substrates for the RNA exosome. Proc Natl Acad Sci USA. 2011 Jun 28;108(26):10460-5. PMID:21670248.

7. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. Long noncoding RNA connects chromosomal structure to active chromatin domain and gene expression. Nature. 2011 Apr 7;472(7341):120-4. PMID:21423168.

6. Rada-Iglesias A, Bajpai R, Swigut T, Burgmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011 Feb 10;470(7333):279-83. PMID:21160473.

5. Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM, Flynn RA, Cavenee WK, Furnari FB, White FM. Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth. Mol Biosyst. 2010 Jul 15;6(7):1227-37. PMID: 20461251.

4. Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA. c-Myc regulates transcriptional pause release. Cell. 2010 Apr 30;141(3):432-45. PMID: 20434984.

3. Seila AC, Calabrese M, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA. Divergent transcription from active promoters. Science. 2008 Dec 19;322(5909):1849-51. PMID: 19056940.

2. Huang PH, Mukasa A, Bonavia R, Flynn RA, Brewer ZE, Cavenee WK, Furnari FB, White FM., Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci USA. 2007 Jul 31;104(31):12867-72. PMID: 17646646.

1. Tuli R, Flynn RA, Brill KL, Sabol JL, Usuki KY, Rosenberg AL., Diagnosis, treatment, and management of breast cancer in previously augmented women. Breast J. 2006 Jul-Aug;12(4):343-8. PMID: 16848844.

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