Daneshvar K, Ardehali MB, Klein IA, Kratkiewicz AJ, Zhou C, Mahpour A, Cook BM, Li­­ W, Pondick JV, Moran SP, Young RA, Kingston RE, Mullen AC. (2019).  lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. bioRxiv



Chan Z, Molinie B, Daneshvar K., Pondick JV, Wang J, Wittenberghe NO, Xing Y, Giallourakis CC, Mullen AC. (2017). Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs. Cell Reports. 20, 2262-2276.  Pubmed



Chen JY, Newcomb B, Zhou C, Pondick JV, Ghoshal S, York SR, Motola DL, Coant N, Yi JK, Mao C, Tanabe KK, Bronova I, Berdyshev EV, Fuchs BC, Hannun Y, Chung RT, Mullen AC. (2017). Tricyclic Antidepressants Promote Ceramide Accumulation to Regulate Collagen Production in Human Hepatic Stellate Cells. Scientific Reports. 7, 44867.  Pubmed



Mullen AC and Wrana JL. (2017). TGF-beta family signaling in embryonic and somatic stem cell renewal and differentiation.  Cold Spring Harbor Perspectives in Biology. Jan 20;:a022186–33.  Pubmed



Daneshvar K, Pondick JV, Kim, BM, Zhou C, York SR, Macklin JA, Abualteen A, Bo T, Sigova, AA, Marcho, C, Tremblay, KD, Mager J, Choi MY, Mullen AC. (2016). DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells. Cell Reports. 17, 353-365.  Pubmed



Zhou C, York SR, Chen JY, Pondick J, Motola, D, Chung, RA, Mullen AC. (2016). Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins. Genome Medicine. 8, 31. PMCID PMC4804564.  Pubmed



Molinie B, Wang J, Lim K-S, Hillebrand R, ‎ Lu Z-X, Van Wittenberghe N, Howard BD, Daneshvar K, Mullen AC, Dedon P, Xing Y, Giallourakis CC. (2016). m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveals the census and complexity of the m6A epitranscriptome. Nat Methods.13, 692-8.  Pubmed



Batista, PJ, Molinie, B, Wang, J, Qu, K, Zhang, J, Li, L, Bouley, D M, Lujan, E, Haddad, B, Daneshvar, K, Carter, AC, Flynn, RA, Zhou, C, Lim, K-S, Dedon, P, Wernig, M, Mullen, AC, Xing, Y, Giallourakis, CC, Chang, HY. (2014). m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 15, 707-719.



Sigova, AA, Mullen, AC *, Moline, B, Gupta, S, Orlando, DA, Guenther, MG, Alamada, AE, Lin C, Sharp, PA, Giallourakis, CC, Young, RA (2013). Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells.  Proceedings of the National Academy of Sciences USA 110, 2876-81. * co-first author.  Pubmed



Mullen, AC, Orlando, DA, Newman, JJ, Loven, J, Kumar, RM, Bilodeau, ., Reddy, J, Guenther, MG, DeKoter, RP, and Young, RA (2011). Master transcription factors determine cell-type-specific responses to TGF-beta signaling. Cell 147, 565-576.  Pubmed



Pearce, E. L., Mullen, A. C., Martins, G. A., Krawczyk, C. M., Hutchins, A. S., Zediak, V. P., Banica, M., DiCioccio, C. B., Gross, D. A., Mao, C., Shen, H., Cereb, N., Yang, S. Y., Lindsten, T., Rossant, J., Hunter, C. A., and Reiner, S. L. (2003). Control of effector CD8+ T cell function by the transcription factor Eomesodermin. Science 302, 1041-1043.



Mullen, A. C., Hutchins, A. S., High, F. A., Lee, H. W., Sykes, K. J., Chodosh, L. A., and Reiner, S. L. (2002). Hlx is induced by and genetically interacts with T-bet to promote heritable TH1 gene induction. Nature Immunology 3, 652-658.



Hutchins, A. S., Mullen, A. C., Lee, H. W., Sykes, K. J., High, F. A., Hendrich, B. D., Bird, A. P., and Reiner, S. L. (2002). Gene silencing quantitatively controls the function of a developmental trans-activator. Mol Cell 10, 81-91.



Mullen, A. C., High, F. A., Hutchins, A. S., Lee, H. W., Villarino, A. V., Livingston, D. M., Kung, A. L., Cereb, N., Yao, T. P., Yang, S. Y., and Reiner, S. L. (2001). Role of T-bet in commitment of TH1 cells before IL-12-dependent selection. Science 292, 1907-1910.



Mullen, A. C., Hutchins, A. S., Villarino, A. V., Lee, H. W., High, F. A., Cereb, N., Yang, S. Y., Hua, X., and Reiner, S. L. (2001). Cell cycle controlling the silencing and functioning of mammalian activators. Curr Biol 11, 1695-1699.


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