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Ryan Alexander Flynn, M.D., Ph.D.

Other Positions

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  1. F30CA189514 (FLYNN, RYAN ALEXANDER) Sep 30, 2014 - Sep 29, 2016
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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 05 06; 50(8):4329-4339. PMID: 35438783; PMCID: PMC9071496.
    Citations:    Fields:    Translation:Cells
  2. Shivaprasad S, Weng KF, Ooi YS, Belk J, Carette JE, Flynn R, Sarnow P. Loquacious modulates flaviviral RNA replication in mosquito cells. PLoS Pathog. 2022 04; 18(4):e1010163. PMID: 35482886; PMCID: PMC9089905.
    Citations:    Fields:    Translation:AnimalsCells
  3. Thangavelu G, Zaiken MC, Mohamed FA, Flynn R, Du J, Rhee SY, Riddle MJ, Aguilar EG, Panoskaltsis-Mortari A, Sanders ME, Blazar BR. Targeting the Retinoid X Receptor Pathway Prevents and Ameliorates Murine Chronic Graft-Versus-Host Disease. Front Immunol. 2022; 13:765319. PMID: 35359939; PMCID: PMC8963714.
    Citations:    Fields:    Translation:HumansAnimalsCells
  4. Levy RB, Mousa HM, Lightbourn CO, Shiuey EJ, Latoni D, Duffort S, Flynn R, Du J, Barreras H, Zaiken M, Paz K, Blazar BR, Perez VL. Analyses and Correlation of Pathologic and Ocular Cutaneous Changes in Murine Graft versus Host Disease. Int J Mol Sci. 2021 Dec 24; 23(1). PMID: 35008621; PMCID: PMC8745722.
    Citations:    Fields:    Translation:Animals
  5. 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, Pa?ca AM, Pa?ca 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 12; 13(622):eabg2919. PMID: 34851695; PMCID: PMC9067636.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  6. 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 11 18; 49(20):11868-11882. PMID: 34634799; PMCID: PMC8599799.
    Citations: 1     Fields:    Translation:HumansCells
  7. 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 09 17; 2(3):100762. PMID: 34485935; PMCID: PMC8406031.
    Citations:    Fields:    Translation:HumansCells
  8. 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 06 10; 184(12):3109-3124.e22. PMID: 34004145; PMCID: PMC9097497.
    Citations: 54     Fields:    Translation:HumansAnimalsCells
  9. 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 04 29; 184(9):2394-2411.e16. PMID: 33743211; PMCID: PMC7951565.
    Citations: 40     Fields:    Translation:HumansAnimalsCells
  10. 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 12; 588(7839):670-675. PMID: 33238290.
    Citations: 87     Fields:    Translation:HumansCells
  11. 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 11 25; 9. PMID: 33236985.
    Citations: 5     Fields:    Translation:AnimalsCells
  12. 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 12 03; 80(5):903-914.e8. PMID: 33242392.
    Citations: 5     Fields:    Translation:HumansCells
  13. Flynn RA, Belk JA, Qi Y, Yasumoto Y, Schmitz CO, Mumbach MR, Limaye A, Wei J, Alfajaro MM, Parker KR, Chang HY, Horvath TL, Carette JE, Bertozzi C, Wilen CB, Satpathy AT. Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection. bioRxiv. 2020 Oct 06. PMID: 33052334; PMCID: PMC7553159.
  14. 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 07 27; 48(13):7279-7297. PMID: 32463448.
    Citations: 2     Fields:    Translation:HumansCells
  15. Salahudeen AA, Choi SS, Rustagi A, Zhu J, de la O SM, Flynn RA, Margalef-Català M, Santos AJM, Ju J, Batish A, van Unen V, 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 long-term human distal lung organoid cultures. bioRxiv. 2020 Jul 27. PMID: 32743583.
    Citations: 2     
  16. Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, 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. 2020 04; 22(4):372-379. PMID: 32231306; PMCID: PMC7185069.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  17. 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 rRNA processing and haematopoiesis. Nature. 2020 03; 579(7798):291-296. PMID: 32103174.
    Citations: 25     Fields:    Translation:HumansCells
  18. Thangavelu G, Du J, Paz KG, Loschi M, Zaiken MC, Flynn R, Taylor PA, Kirchmeier AK, Panoskaltsis-Mortari A, Luznik L, MacDonald KP, Hill GR, Maillard I, Munn DH, Serody JS, Murphy WJ, Miklos D, Cutler CS, Koreth J, Antin JH, Soiffer RJ, Ritz J, Dahlberg C, Miller AT, Blazar BR. Inhibition of inositol kinase B controls acute and chronic graft-versus-host disease. Blood. 2020 01 02; 135(1):28-40. PMID: 31697815; PMCID: PMC6940197.
    Citations: 7     Fields:    Translation:Animals
  19. Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nat Commun. 2019 12 13; 10(1):5712. PMID: 31836708.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  20. 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 12; 4(12):2369-2382. PMID: 31384002; PMCID: PMC6879806.
    Citations: 39     Fields:    Translation:HumansCells
  21. Sinha RK, Flynn R, Zaiken M, Paz K, Gavin AL, Nemazee D, Fernández JA, Xu X, Griffin JH, Blazar BR. Activated protein C ameliorates chronic graft-versus-host disease by PAR1-dependent biased cell signaling on T cells. Blood. 2019 08 29; 134(9):776-781. PMID: 31243040; PMCID: PMC6716074.
    Citations: 2     Fields:    Translation:AnimalsCells
  22. 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 06; 16(6):489-492. PMID: 31133759; PMCID: PMC6638558.
    Citations: 34     Fields:    Translation:AnimalsCells
  23. Paz K, Flynn R, Du J, Tannheimer S, Johnson AJ, Dong S, Stark AK, Okkenhaug K, Panoskaltsis-Mortari A, Sage PT, Sharpe AH, Luznik L, Ritz J, Soiffer RJ, Cutler CS, Koreth J, Antin JH, Miklos DB, MacDonald KP, Hill GR, Maillard I, Serody JS, Murphy WJ, Munn DH, Feser C, Zaiken M, Vanhaesebroeck B, Turka LA, Byrd JC, Blazar BR. Targeting PI3Kd function for amelioration of murine chronic graft-versus-host disease. Am J Transplant. 2019 06; 19(6):1820-1830. PMID: 30748099.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  24. 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 01 10; 8. PMID: 30628890.
    Citations: 21     Fields:    Translation:HumansCells
  25. Verghese DA, Chun N, Paz K, Fribourg M, Woodruff TM, Flynn R, Hu Y, Xiong H, Zhang W, Yi Z, Du J, Blazar BR, Heeger PS. C5aR1 regulates T follicular helper differentiation and chronic graft-versus-host disease bronchiolitis obliterans. JCI Insight. 2018 12 20; 3(24). PMID: 30568034; PMCID: PMC6338317.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  26. Paz K, Flynn R, Du J, Qi J, Luznik L, Maillard I, MacDonald KP, Hill GR, Serody JS, Murphy WJ, Sage PT, Sharpe AH, Miklos D, Cutler CS, Koreth J, Antin JH, Soiffer RJ, Ritz J, Bradner JE, Melnick AM, Blazar BR. Small-molecule BCL6 inhibitor effectively treats mice with nonsclerodermatous chronic graft-versus-host disease. Blood. 2019 01 03; 133(1):94-99. PMID: 30279226.
    Citations: 12     Fields:    Translation:AnimalsCells
  27. Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR. Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. 2018 10; 562(7725):150. PMID: 29973715.
    Citations: 4     Fields:    
  28. Radojcic V, Paz K, Chung J, Du J, Perkey ET, Flynn R, Ivcevic S, Zaiken M, Friedman A, Yan M, Pletneva MA, Sarantopoulos S, Siebel CW, Blazar BR, Maillard I. Notch signaling mediated by Delta-like ligands 1 and 4 controls the pathogenesis of chronic GVHD in mice. Blood. 2018 11 15; 132(20):2188-2200. PMID: 30181175; PMCID: PMC6238189.
    Citations: 15     Fields:    Translation:AnimalsCells
  29. 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 02 01; 554(7690):112-117. PMID: 29364875.
    Citations: 52     Fields:    Translation:HumansAnimalsCells
  30. Du J, Flynn R, Paz K, Ren HG, Ogata Y, Zhang Q, Gafken PR, Storer BE, Roy NH, Burkhardt JK, Mathews W, Tolar J, Lee SJ, Blazar BR, Paczesny S. Murine chronic graft-versus-host disease proteome profiling discovers CCL15 as a novel biomarker in patients. Blood. 2018 04 12; 131(15):1743-1754. PMID: 29348127; PMCID: PMC5897867.
    Citations: 12     Fields:    Translation:HumansAnimals
  31. 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 Cent Sci. 2017 Nov 22; 3(11):1143-1155. PMID: 29202016; PMCID: PMC5704294.
    Citations: 62     
  32. 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. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet. 2017 Nov; 49(11):1602-1612. PMID: 28945252; PMCID: PMC5805393.
    Citations: 183     Fields:    Translation:HumansCells
  33. Forcade E, Paz K, Flynn R, Griesenauer B, Amet T, Li W, Liu L, Bakoyannis G, Jiang D, Chu HW, Lobera M, Yang J, Wilkes DS, Du J, Gartlan K, Hill GR, MacDonald KP, Espada EL, Blanco P, Serody JS, Koreth J, Cutler CS, Antin JH, Soiffer RJ, Ritz J, Paczesny S, Blazar BR. An activated Th17-prone T cell subset involved in chronic graft-versus-host disease sensitive to pharmacological inhibition. JCI Insight. 2017 Jun 15; 2(12). PMID: 28614794.
    Citations: 31     Fields:    
  34. 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 01; 169(6):1051-1065.e18. PMID: 28575669.
    Citations: 144     Fields:    Translation:AnimalsCells
  35. Du J, Paz K, Thangavelu G, Schneidawind D, Baker J, Flynn R, Duramad O, Feser C, Panoskaltsis-Mortari A, Negrin RS, Blazar BR. Invariant natural killer T cells ameliorate murine chronic GVHD by expanding donor regulatory T cells. Blood. 2017 06 08; 129(23):3121-3125. PMID: 28416503; PMCID: PMC5465838.
    Citations: 32     Fields:    Translation:HumansAnimalsCells
  36. 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 04; 56(13):1811-1814. PMID: 28319368.
    Citations: 4     Fields:    Translation:HumansCells
  37. Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY. Comparison of SHAPE reagents for mapping RNA structures inside living cells. RNA. 2017 02; 23(2):169-174. PMID: 27879433; PMCID: PMC5238792.
    Citations: 36     Fields:    Translation:AnimalsCells
  38. 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; 11(11):e0165913. PMID: 27829007; PMCID: PMC5102383.
    Citations: 3     Fields:    Translation:HumansCells
  39. 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. Nat Genet. 2016 11; 48(11):1370-1376. PMID: 27668660.
    Citations: 104     Fields:    Translation:HumansAnimalsCells
  40. Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods. 2016 Nov; 13(11):919-922. PMID: 27643841; PMCID: PMC5501173.
    Citations: 372     Fields:    Translation:HumansAnimalsCells
  41. Weiss JM, Chen W, Nyuydzefe MS, Trzeciak A, Flynn R, Tonra JR, Marusic S, Blazar BR, Waksal SD, Zanin-Zhorov A. ROCK2 signaling is required to induce a subset of T follicular helper cells through opposing effects on STATs in autoimmune settings. Sci Signal. 2016 07 19; 9(437):ra73. PMID: 27436361.
    Citations: 24     Fields:    Translation:HumansAnimalsCells
  42. Zanin-Zhorov A, Flynn R, Waksal SD, Blazar BR. Isoform-specific targeting of ROCK proteins in immune cells. Small GTPases. 2016 07 02; 7(3):173-7. PMID: 27254302.
    Citations: 12     Fields:    Translation:HumansAnimals
  43. 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. 2016 May 19; 165(5):1267-1279. PMID: 27180905.
    Citations: 243     Fields:    Translation:HumansAnimalsCells
  44. 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 May 10; 7(19):28169-82. PMID: 27058758.
    Citations: 30     Fields:    Translation:HumansCells
  45. Li W, Liu L, Gomez A, Zhang J, Ramadan A, Zhang Q, Choi SW, Zhang P, Greenson JK, Liu C, Jiang D, Virts E, Kelich SL, Chu HW, Flynn R, Blazar BR, Hanenberg H, Hanash S, Paczesny S. Proteomics analysis reveals a Th17-prone cell population in presymptomatic graft-versus-host disease. JCI Insight. 2016 May 05; 1(6). PMID: 27195312.
    Citations: 24     Fields:    
  46. Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA. irCLIP platform for efficient characterization of protein-RNA interactions. Nat Methods. 2016 06; 13(6):489-92. PMID: 27111506; PMCID: PMC5477425.
    Citations: 98     Fields:    Translation:HumansCells
  47. 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. Mol Cell. 2016 Apr 07; 62(1):34-46. PMID: 27058786; PMCID: PMC4836061.
    Citations: 40     Fields:    Translation:HumansAnimalsCells
  48. Flynn R, Paz K, Du J, Reichenbach DK, Taylor PA, Panoskaltsis-Mortari A, Vulic A, Luznik L, MacDonald KK, Hill GR, Nyuydzefe MS, Weiss JM, Chen W, Trzeciak A, Serody JS, Aguilar EG, Murphy WJ, Maillard I, Munn D, Koreth J, Cutler CS, Antin JH, Ritz J, Waksal SD, Zanin-Zhorov A, Blazar BR. Targeted Rho-associated kinase 2 inhibition suppresses murine and human chronic GVHD through a Stat3-dependent mechanism. Blood. 2016 04 28; 127(17):2144-54. PMID: 26983850; PMCID: PMC4850869.
    Citations: 75     Fields:    Translation:HumansAnimalsCells
  49. 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. Nat Struct Mol Biol. 2016 Mar; 23(3):231-8. PMID: 26878240; PMCID: PMC4982704.
    Citations: 42     Fields:    Translation:HumansAnimalsCells
  50. Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR. Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. 2016 May 05; 533(7601):130. PMID: 26789242.
    Citations:    Fields:    
  51. Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb; 11(2):273-90. PMID: 26766114.
    Citations: 54     Fields:    Translation:Cells
  52. Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Rigo FW, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR. DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. 2015 Dec 24; 528(7583):517-22. PMID: 26675721; PMCID: PMC4762670.
    Citations: 79     Fields:    Translation:HumansAnimalsCells
  53. Furlan SN, Watkins B, Tkachev V, Flynn R, Cooley S, Ramakrishnan S, Singh K, Giver C, Hamby K, Stempora L, Garrett A, Chen J, Betz KM, Ziegler CG, Tharp GK, Bosinger SE, Promislow DE, Miller JS, Waller EK, Blazar BR, Kean LS. Transcriptome analysis of GVHD reveals aurora kinase A as a targetable pathway for disease prevention. Sci Transl Med. 2015 Nov 25; 7(315):315ra191. PMID: 26606970.
    Citations: 35     Fields:    Translation:HumansCells
  54. 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 03; 17(6):675-688. PMID: 26607380.
    Citations: 98     Fields:    Translation:HumansCells
  55. Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015 Nov 12; 527(7577):264. PMID: 26416736.
    Citations: 5     Fields:    
  56. Zeiser R, Burchert A, Lengerke C, Verbeek M, Maas-Bauer K, Metzelder SK, Spoerl S, Ditschkowski M, Ecsedi M, Sockel K, Ayuk F, Ajib S, de Fontbrune FS, Na IK, Penter L, Holtick U, Wolf D, Schuler E, Meyer E, Apostolova P, Bertz H, Marks R, Lübbert M, Wäsch R, Scheid C, Stölzel F, Ordemann R, Bug G, Kobbe G, Negrin R, Brune M, Spyridonidis A, Schmitt-Gräff A, van der Velden W, Huls G, Mielke S, Grigoleit GU, Kuball J, Flynn R, Ihorst G, Du J, Blazar BR, Arnold R, Kröger N, Passweg J, Halter J, Socié G, Beelen D, Peschel C, Neubauer A, Finke J, Duyster J, von Bubnoff N. Ruxolitinib in corticosteroid-refractory graft-versus-host disease after allogeneic stem cell transplantation: a multicenter survey. Leukemia. 2015 Oct; 29(10):2062-8. PMID: 26228813; PMCID: PMC4854652.
    Citations: 173     Fields:    Translation:HumansAnimals
  57. Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M, Wesche DJ, Martin L, Ware CB, Blish CA, Chang HY, Pera RA, Wysocka J. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 2015 Jun 11; 522(7555):221-5. PMID: 25896322.
    Citations: 236     Fields:    Translation:HumansCells
  58. Flynn R, Allen JL, Luznik L, MacDonald KP, Paz K, Alexander KA, Vulic A, Du J, Panoskaltsis-Mortari A, Taylor PA, Poe JC, Serody JS, Murphy WJ, Hill GR, Maillard I, Koreth J, Cutler CS, Soiffer RJ, Antin JH, Ritz J, Chao NJ, Clynes RA, Sarantopoulos S, Blazar BR. Targeting Syk-activated B cells in murine and human chronic graft-versus-host disease. Blood. 2015 Jun 25; 125(26):4085-94. PMID: 25852057; PMCID: PMC4481596.
    Citations: 54     Fields:    Translation:HumansAnimalsCells
  59. 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 09; 161(2):404-16. PMID: 25843628.
    Citations: 445     Fields:    Translation:HumansAnimalsCells
  60. Veenstra RG, Flynn R, Kreymborg K, McDonald-Hyman C, Saha A, Taylor PA, Osborn MJ, Panoskaltsis-Mortari A, Schmitt-Graeff A, Lieberknecht E, Murphy WJ, Serody JS, Munn DH, Freeman GJ, Allison JP, Mak TW, van den Brink M, Zeiser R, Blazar BR. B7-H3 expression in donor T cells and host cells negatively regulates acute graft-versus-host disease lethality. Blood. 2015 05 21; 125(21):3335-46. PMID: 25814530; PMCID: PMC4440885.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  61. 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. PMID: 25799993.
    Citations: 309     Fields:    Translation:AnimalsCells
  62. Blazar BR, Flynn R, Lee R, Marcucci G, Caliguiri MA, Heeger PS. Strategies to inhibit alloantibody production in alloprimed murine recipients of hematopoietic stem cell grafts. Am J Transplant. 2015 Apr; 15(4):931-41. PMID: 25762193.
    Citations:    Fields:    Translation:AnimalsCells
  63. Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 2015 Feb 12; 518(7538):249-53. PMID: 25470060.
    Citations: 123     Fields:    Translation:HumansCells
  64. 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. 2015 Jan; 21(1):135-43. PMID: 25411354.
    Citations: 47     Fields:    Translation:HumansCells
  65. Hechinger AK, Smith BA, Flynn R, Hanke K, McDonald-Hyman C, Taylor PA, Pfeifer D, Hackanson B, Leonhardt F, Prinz G, Dierbach H, Schmitt-Graeff A, Kovarik J, Blazar BR, Zeiser R. Therapeutic activity of multiple common ?-chain cytokine inhibition in acute and chronic GVHD. Blood. 2015 Jan 15; 125(3):570-80. PMID: 25352130; PMCID: PMC4296017.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  66. 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. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 2014 Dec 04; 15(6):707-19. PMID: 25456834.
    Citations: 478     Fields:    Translation:HumansAnimalsCells
  67. Dubovsky JA, Flynn R, Du J, Harrington BK, Zhong Y, Kaffenberger B, Yang C, Towns WH, Lehman A, Johnson AJ, Muthusamy N, Devine SM, Jaglowski S, Serody JS, Murphy WJ, Munn DH, Luznik L, Hill GR, Wong HK, MacDonald KK, Maillard I, Koreth J, Elias L, Cutler C, Soiffer RJ, Antin JH, Ritz J, Panoskaltsis-Mortari A, Byrd JC, Blazar BR. Ibrutinib treatment ameliorates murine chronic graft-versus-host disease. J Clin Invest. 2014 Nov; 124(11):4867-76. PMID: 25271622; PMCID: PMC4347242.
    Citations: 86     Fields:    Translation:Animals
  68. Alexander KA, Flynn R, Lineburg KE, Kuns RD, Teal BE, Olver SD, Lor M, Raffelt NC, Koyama M, Leveque L, Le Texier L, Melino M, Markey KA, Varelias A, Engwerda C, Serody JS, Janela B, Ginhoux F, Clouston AD, Blazar BR, Hill GR, MacDonald KP. CSF-1-dependant donor-derived macrophages mediate chronic graft-versus-host disease. J Clin Invest. 2014 Oct; 124(10):4266-80. PMID: 25157821; PMCID: PMC4191032.
    Citations: 77     Fields:    Translation:AnimalsCells
  69. Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdiscip Rev RNA. 2014 Nov-Dec; 5(6):867-81. PMID: 25132067.
    Citations: 28     Fields:    Translation:Cells
  70. Flynn RA, Chang HY. Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell. 2014 Jun 05; 14(6):752-61. PMID: 24905165.
    Citations: 255     Fields:    Translation:HumansAnimalsCells
  71. 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. Plast Reconstr Surg. 2014 Mar; 133(3 Suppl):174. PMID: 25942268.
    Citations: 1     Fields:    
  72. 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. PMID: 24521543.
    Citations: 102     Fields:    Translation:AnimalsCells
  73. 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. PMID: 24476892.
    Citations: 259     Fields:    Translation:HumansCells
  74. 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. PMID: 23295233.
    Citations: 3     Fields:    Translation:HumansCells
  75. 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. PMID: 23201690; PMCID: PMC3674581.
    Citations: 439     Fields:    Translation:HumansCells
  76. 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. PMID: 23178934.
    Citations: 192     Fields:    Translation:HumansAnimalsCells
  77. 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.
    Citations: 130     Fields:    Translation:HumansCells
  78. Veenstra RG, Taylor PA, Zhou Q, Panoskaltsis-Mortari A, Hirashima M, Flynn R, Liu D, Anderson AC, Strom TB, Kuchroo VK, Blazar BR. Contrasting acute graft-versus-host disease effects of Tim-3/galectin-9 pathway blockade dependent upon the presence of donor regulatory T cells. Blood. 2012 Jul 19; 120(3):682-90. PMID: 22677125; PMCID: PMC3401220.
    Citations: 28     Fields:    Translation:AnimalsCells
  79. Liu Y, Flynn R, Yang W, Kim Y, Wu X. SU-E-T-606: Optimal Emission Angle Selection in Rotating Shield Brachytherapy. Med Phys. 2012 Jun; 39(6Part19):3845. PMID: 28517084.
    Citations:    Fields:    
  80. Yang W, Kim Y, Liu Y, Wu X, Flynn R. SU-E-T-547: Rotating Shield Brachytherapy (RSBT) for Cervical Cancer. Med Phys. 2012 Jun; 39(6Part18):3831. PMID: 28518488.
    Citations:    Fields:    
  81. Flynn RA, Chang HY. Active chromatin and noncoding RNAs: an intimate relationship. Curr Opin Genet Dev. 2012 Apr; 22(2):172-8. PMID: 22154525.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  82. Srinivasan M, Flynn R, Price A, Ranger A, Browning JL, Taylor PA, Ritz J, Antin JH, Murphy WJ, Luznik L, Shlomchik MJ, Panoskaltsis-Mortari A, Blazar BR. Donor B-cell alloantibody deposition and germinal center formation are required for the development of murine chronic GVHD and bronchiolitis obliterans. Blood. 2012 Feb 09; 119(6):1570-80. PMID: 22072556; PMCID: PMC3286218.
    Citations: 124     Fields:    Translation:HumansAnimalsCells
  83. Flynn RA, Almada AE, Zamudio JR, Sharp PA. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10460-5. PMID: 21670248.
    Citations: 110     Fields:    Translation:AnimalsCells
  84. 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. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011 Apr 07; 472(7341):120-4. PMID: 21423168.
    Citations: 1013     Fields:    Translation:HumansAnimalsCells
  85. Dronadula N, Du L, Flynn R, Buckler J, Kho J, Jiang Z, Tanaka S, Dichek DA. Construction of a novel expression cassette for increasing transgene expression in vivo in endothelial cells of large blood vessels. Gene Ther. 2011 May; 18(5):501-8. PMID: 21179172.
    Citations: 10     Fields:    Translation:AnimalsCells
  86. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann 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.
    Citations: 1137     Fields:    Translation:HumansAnimalsCells
  87. 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; 6(7):1227-37. PMID: 20461251.
    Citations: 25     Fields:    Translation:HumansCells
  88. 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.
    Citations: 749     Fields:    Translation:HumansAnimalsCells
  89. Seila AC, Calabrese JM, 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.
    Citations: 501     Fields:    Translation:HumansAnimalsCells
  90. 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 U S A. 2007 Jul 31; 104(31):12867-72. PMID: 17646646; PMCID: PMC1937558.
    Citations: 190     Fields:    Translation:HumansAnimalsCells
  91. 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.
    Citations: 6     Fields:    Translation:Humans
  92. Kosslyn SM, Flynn RA, Amsterdam JB, Wang G. Components of high-level vision: a cognitive neuroscience analysis and accounts of neurological syndromes. Cognition. 1990 Mar; 34(3):203-77. PMID: 2183962.
    Citations: 6     Fields:    Translation:HumansAnimals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.