Publications

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, J.L. Rinn, Meissner A, Root DE, Hacohen N, Regev A. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses. Science 2009 Sep 3. [Epub ahead of print]

Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES*, Rinn J.L.* Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. PNAS. 2009 Jul 14;106(28):11667-72. Epub 2009 Jul 1.

Mitchell Guttman, Ido Amit, Manuel Garber, Courtney French, Michael F. Lin, David Feldser, Maite Hurate, Tarjei S. Mikkelsen, Or Zuk, Nir Hacohen, Bradley E. Bernstein , Manolis Kellis, Aviv Regev, John L. Rinn*, and Eric S. Lander* Chromatin signature reveals more than a thousand highly conserved, large non-coding RNAs in mammals. Nature, 2009 Mar 12;458(7235):223-7. Epub 2009 Feb 1.

Somervaille TC, Matheny CJ, Spencer GJ, Iwasaki M, Rinn J.L. Witten DM, Chang HY, Shurtleff SA, Downing JR, Cleary ML.Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell 2009 Feb 6;4(2):129-40.

lMace KA, Restivo TE, Rinn J.L., Paquet AC, Chang HY, Young DM, Boudreau NJ.HOXA3 modulates injury-induced mobilization and recruitment of bone marrow-derived cells. Stem Cells . 2009 Jul;27(7):1654-65.

J.L. Rinn, J.K. Wang, N. Allen, S.A. Brugmann, A. Mikels, H. Liu, T. Ridky, H.S. Stadler, R. Nusse, J.A. Helms, H.Y. Chang. (2008). A dermal HOX transcriptional program regulates site-specific epidermal fate. Genes and Development. 2008 1; 22(3):303-307

J.L. Rinn, J.K. Wang, H. Liu and H.Y. Chang. (2008) A Systems Biology Approach to Anatomic Diversity of Skin. J. of Invs Dermatology. 2008 128(4): p. 776-82.

W. Chang, R.F. Zaarour, S. Reck-Peterson, J.L. Rinn, R.H. Singer, M. Snyder, P. Novick, M.S. Mooseker (2008). Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body. RNA. 2008 14(3):491-502

M.A. Su, K. Giang, K. Zumer, H. Jiang, I. Oven, J.L. Rinn, J.J. DeVoss, K.P.A. Johannes, W. Lu, J. Gardner, A. Chang, P. Bubulya, H.Y. Chang, B. M. Peterlin, and M.S. Anderson. (2008) Mechanisms of a novel autoimmunity syndrome caused by a dominant mutation in Aire. JCI, May;118(5):1712-26.

T.A. Khavari and J.L. Rinn. (2007). Ras/Erk MAPK Signaling in Epidermal Homeostasis and Neoplasia. Cell Cycle. 2007 6(23):2928-31

J.L. Rinn, M. Kertesz, J. Wang, S. Brunghman, H. Goodnough, B. Wong, M. Cleary, J.A. Helms, E. Segal, H.Y. Chang. (2007) Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Non-Coding RNAs. Cell. 2007 29;129(7):1311-23.

F. Lan, P.E. Bayliss, J.L. Rinn, J.R. Whetstine, J.K. Wang, S. Chen, S. Iwase, T.M. Roberts, H.Y. Chang, and Y. Shi (2007). A histone H3 lysine 27 demethylase regulates animal posterior development. Nature. 2007 11;449(7163):689-94

H. O'Green, S.L. Squazzo, S. Iyengar, K. Blahink, J.L. Rinn, H.Y.Chang, R. Green and P.J. Farnham (2007) Genome Wide Analysis of KAP1 Binding Reveals Auto-regulation of KRAB-ZNFs. PLoS Genetics. 2007 1;3(6):e89

1J.L. Rinn, C. Bondre, H.B Gladstone, P.O. Brown and H.Y. Chang. (2006) Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs. PLoS Genetics. 2006 Jul;2(7):e119.

J. DeVoss, Y. Hou, L. Fong, R. Caspi, J.L. Rinn, H. Chang, M.S. Anderson. (2006) Spontaneous eye autoimmunity in aire-deficient mice controlled by a single antigen. J. Exp Medicine. 2006 203(12):2727-35

J.L. Rinn and M. Snyder. (2005) Sexual Dimorphisms In Mammalian Gene Expression. Trends In Genetics. 2005 21(5):298-305.

E.A. Feingold et al. (2004). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2005 306: 636-40.

P. Bertone, V. Stolc, T.E. Royce, J.S. Rozowsky, A.E. Urban, X. Zhu, J.L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, M. Gerstein and M. Snyder. (2004) Global Identification of novel transcribed regions in humans using high resolution genomic tiling arrays. Science. 2004 306(5705):2242-6.

J.L. Rinn, J.S. Rozowsky, I.J. Laurenzi, P. Petersen, K. Zon, W. Zhong, M. Gerstein, M. Snyder. (2004) The Molecular Differences Between Mammalian Sexes are Involved in Drug and Steroid Metabolism and Renal Function. Developmental Cell. 2004 6(6): 791-800.

G.Euskirchen, T.E. Royce, P. Bertone, R. Martone, J.L. Rinn, F.K. Nelson, F. Sayward, N.M. Luscombe, P. Miller, M. Gerstein, S. Weissman, and M. Snyder. (2004) CREB Binds to Multiople Loci on Human Chromosome 22. Molecular and Cellular Biology. 2004 9:3804-3814.

L. Zheng, G. Euskirchen, J.L. Rinn, R. Martone, P. Bertone, S. Hartman, T. Royce, K. Nelson, F. Sayward, N. Luscombe, J. Yang, J-L. Li, P. Miller, M. Gerstein, S. Weissman, and M. Snyder. (2004) Identification of Novel Functional Elements in the Human Genome. Cold Spring Harbor Reviews. Cold Spring Harb Symp Quant Biol. 2003 68:317-22

J.L. Rinn, G. Euskirchen, P. Bertone, R. Martone, N.M Luscombe, S. Hartman, P.M. Harrison, F.K. Nelson, P.M. Miller, M. Gerstein, S. Weissman, and M. Snyder. (2003). The Transcriptional Activity of Human Chromosome 22. Genes and Development. 2003 17(4):529-540.

R. Martone, G. Euskirchen, P. Bertone, S. Hartman, T.E. Royce, N.M. Luscombe, J.L. Rinn, F.K. Nelson, P. Miller, M. Gerstein, S. Weissman, M. Snyder. (2003) Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 100 (21) 12247-52.

J.L. Fitzakerly, K.V. Star, J.L. Rinn, and B.J. Elmquist. (2000). Expression of Shal Potassium Channel Subunits in the Adult and Developing Cochlear Nucleus of the Mouse. Hearing Research. 2000; 147: 31-35.