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.