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 Genetics. November 2017
Zarnegar BJ, Flynn RA, Shen Y, Do DT, Chang HY, Khavari PA.
Ultraefficient irCLIP platform for characterization of protein-RNA interactions.
Nature Methods. April 2016
Highlighted in Nature Methods, News and Views and Molecular Cell, Technology Preview
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. April 2016
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
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. February 2016
Highlighted in Nature Reviews, Molecular Cell Biology
Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, 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. December 2015
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. December 2015
Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M, Wesche D, Martin L, Ware C, Blish C, Chang HY, Reijo Pera RA, Wysocka J.
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
Nature. April 2015
Highlighted in The New York Times and Stanford News
Chi C, Zhang QC, Teixeira da Rocha S, Flynn RA, Bharadqaj M, Calabrese JM, Magnuson T, Heard E, Chang HY.
Systematic Discovery of Xist RNA Binding Proteins.
Cell. April 2015
Highlighted in Stanford News and Nature News & Views
Spitale RC*, Flynn RA*, Zhang QC*, Crisalli P, Lee B, Jung J, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY.
Structural imprints in vivo reveal mechanisms of RNA regulation.
Nature, March 2015
Highlighted in Nature News Feature, Nature Reviews Genetics,and Nature Methods
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. January 2015
Highlighted in Nature Reviews Genetics
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. October 2014
Spitale RC*, Crisalli P*, Flynn RA*, Torre EA, Kool ET, Chang HY.
RNA SHAPE analysis in living cells.
Nature Chemical Biology. November 2013
Highlighted in F1000 Prime, Nature Methods, and BioTechniques
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. January 2013
Highlighted in F1000 Prime
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 Biology. August 2012