Publications

2011

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS. The reality of pervasive transcription. PLoS Biol. 2011 Jul;9(7):e1000625. Epub 2011 Jul 12.

Broadbent K, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC*, Rinn JL*. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 2011 Jun 20;12(6):R56. [Epub ahead of print]

Rinn JL, Huarte M.To repress or not to repress: This is the guardian's question. Trends Cell Biol. 2011 Jun;21(6):344-53. Epub 2011 May 19.

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol (2011) Mar 16;12(3)

Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol (2011) Epub Feb 17.

Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis.Nat Rev Genet (2011) Feb;12(2):136-49.

2010

S. Loewer, M. Guttman, Y.H. Loh, M. Garber, K. Thomas, I.H. Park 1, M. Curran, S. Agarwal, P. Manos, S. Datta, E.S. Lander, T. Schlaeger, G.Q. Daley* and J.L. Rinn*. Large intergenic non-coding RNAs as novel regulators of induced pluripotent cell survival. Nature Genetics. (2010), Epub Nov 7.

.M. Huarte, M. Guttman, D. Feldser, M. Garber, A.M. Khalil, O. Zuk, I Amit, A. Regev, E.S. Lander, T. Jacks and J.L. Rinn. A large iintergenic noncoding RNA induced by p53 mediates global gene repression in the p53 transcriptional response. Cell. (2010), Aug 6;142(3):409-19.

M. Huarte and J.L. Rinn. Large non-coding RNAs: missing links in cancer? (2010). Hum Mol Genet. Oct 15;19(R2):R152-61. Epub 2010 Aug 20.

M. Kertesz, Y. Wan, E. Mazor, J.L. Rinn, R.C. Nutter, H.Y. Chang, E. Segal. Genome-wide measurement of RNA secondary structure in yeast Nature. 2010 Sep 2;467(7311):103-7.

.D.A. Khavari, G.L. Sen, J.L. Rinn. DNA methylation and epigenetic control of cellular differentiation. Cell Cycle. 2010 Oct 1;9(19):3880-3. Epub 2010 Oct 20.

H. Zhu, S. Shah, N. Shyh-Chang, G. Shinoda, W.S. Einhorn, S.R. Viswanathan, A. Takeuchi, C. Grasemann, J.L. Rinn, M.F. Lopez, J.N. Hirschhorn, M.R Palmert & G. Q. Daley. Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies (2010). Nature Genetics.

M. Kellis, J.L. Rinn J.L. Sequences to Systems (2010). Genome Biol. May 25;11(5):303.

M. Guttman*, M. Garber*, J.Z. Levin, J.Donaghey, J. Robinson, X. Adiconis, L. Fan, M. Koziol, A. Gnirke, C. Nusbaum, J.L. Rinn, E.S. Lander, and A. Regev. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs (2010). Nature Biotechnology. May;28(5):503-10. Epub May 2.

N.L. Vastenhouw, Y. Zhang, I.G. Woods, F. Imam, A. Regev, X.S. Liu*, J.L. Rinn* and A.F. Schier*. Chromatin signature of embryonic pluripotency is established during genome activation (2010). Nature. Apr 8;464(7290):922-6. Epub 2010 Mar 24.

M.J. Koziol and J.L. Rinn. RNA traffic control of chromatin complexes (2010). Current Opinions in Genetics and Development. Apr;20(2):142-8. Epub 2010 Mar 31.

R.A. Gupta, N. Shah, K.C. Wang, J. Kim, H.M. Horlings, D.J.Wong, M.Tsai, T. Hung1, P. Argani, J.L. Rinn, Y. Wang, P. Brzoska, B. Kong, R. Li, R.B. West, M.J. van de Vijver, S. Sukumar and H.Y. Chang. Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis (2010). Nature. Apr 15;464(7291):1071-6.

2009

I. Amit, M. Garber, N. Chevrier, A.P. Leite, Y. Donner, T. Eisenhaure, M. Guttman, J.K. Grenier, W. Li, O. Zuk, L.A. Schubert, B. Birditt, T. Shay, A. Goren, X. Zhang, Z. Smith, R. Deering, R.C. McDonald, M. Cabili, B.E. Bernstein, J.L. Rinn, A. Meissner, D.E. Root, N. Hacohen, A. Regev. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses (2009). Science. 2009 Oct 9;326(5950):257-63. Epub 2009 Sep 3.

A.M. Khalil*, M. Guttman*, M. Huarte, M. Garber, A. Raj, D. Rivera, K. Thomas, A. Presser, B. Bernsteina,d, A. Oudenaarden, A. Regev, E.S. Lander* and J.L. Rinn*. Many Mammalian Large Intergenic Non coding RNAs Associate with Chromatin Modifying Complexes (2009). PNAS. Jul 14;106(28):11667-72. Epub 2009 Jul 1.

M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Hurate, T.S. Mikkelsen, O. Zuk, N. Hacohen, B.E. Bernstein , M. Kellis, A. Regev, J.L. Rinn*, E.S. Lander*. Chromatin signature reveals more than a thousand highly conserved, large non-coding RNAs in mammals (2009) Nature. Mar 12;458(7235):223-7

T.C. Somervaille, C.J. Matheny, G.J. Spencer, M. Iwasaki, J.L. Rinn, D.M. Witten, H.Y. Chang, S.A. Shurtleff, J.R. Downing, M.L. Cleary. Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells (2009). Cell Stem Cell. Feb 6;4(2):129-40.

Mace 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 (2009). Stem Cells. 2009 Jul;27(7):1654-65.

2003-2008

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. Feb 1; 22(3):303-307

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. Mar;14(3):491-502.

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. Apr; 28(4):776-82.

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.

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. Jun 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. Oct 11;449(7163):689-94 (online 9/12/08).

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

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. Jun 1;3(6):e89

J.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. Nov 27;203(12):2727-35

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

E.A. Feingold et al (2004). The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 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 Dec 24;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 6 (6): 791-800.

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 17 (4):529-540.

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

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 9:3804-3814.

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. 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 147: 31-35.