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John Rinn
John Rinn
Verified email at colorado.edu - Homepage
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ...
Nature protocols 7 (3), 562-578, 2012
127322012
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
RA Gupta, N Shah, KC Wang, J Kim, HM Horlings, DJ Wong, MC Tsai, ...
nature 464 (7291), 1071-1076, 2010
57122010
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
JL Rinn, M Kertesz, JK Wang, SL Squazzo, X Xu, SA Brugmann, ...
cell 129 (7), 1311-1323, 2007
49722007
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
C Trapnell, D Cacchiarelli, J Grimsby, P Pokharel, S Li, M Morse, ...
Nature biotechnology 32 (4), 381-386, 2014
48892014
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
M Guttman, I Amit, M Garber, C French, MF Lin, D Feldser, M Huarte, ...
Nature 458 (7235), 223-227, 2009
47612009
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
M Guttman, I Amit, M Garber, C French, MF Lin, D Feldser, M Huarte, ...
Nature 458 (7235), 223-227, 2009
47612009
Genome regulation by long noncoding RNAs
JL Rinn, HY Chang
Annual review of biochemistry 81, 145-166, 2012
43172012
Differential analysis of gene regulation at transcript resolution with RNA-seq
C Trapnell, DG Hendrickson, M Sauvageau, L Goff, JL Rinn, L Pachter
Nature biotechnology 31 (1), 46-53, 2013
37802013
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
MN Cabili, C Trapnell, L Goff, M Koziol, B Tazon-Vega, A Regev, JL Rinn
Genes & development 25 (18), 1915-1927, 2011
37022011
The multilayered complexity of ceRNA crosstalk and competition
Y Tay, J Rinn, PP Pandolfi
Nature 505 (7483), 344-352, 2014
33822014
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
AM Khalil, M Guttman, M Huarte, M Garber, A Raj, D Rivea Morales, ...
Proceedings of the National Academy of Sciences 106 (28), 11667-11672, 2009
32572009
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response
M Huarte, M Guttman, D Feldser, M Garber, MJ Koziol, ...
Cell 142 (3), 409-419, 2010
23852010
Modular regulatory principles of large non-coding RNAs
M Guttman, JL Rinn
Nature 482 (7385), 339-346, 2012
23662012
The ENCODE (ENCyclopedia of DNA elements) project
EA Feingold, PJ Good, MS Guyer, S Kamholz, L Liefer, K Wetterstrand, ...
Science 306 (5696), 636-640, 2004
23522004
lincRNAs act in the circuitry controlling pluripotency and differentiation
M Guttman, J Donaghey, BW Carey, M Garber, JK Grenier, G Munson, ...
Nature 477 (7364), 295-300, 2011
21522011
Improving RNA-Seq expression estimates by correcting for fragment bias
A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter
Genome biology 12, 1-14, 2011
14792011
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
M Guttman, M Garber, JZ Levin, J Donaghey, J Robinson, X Adiconis, ...
Nature biotechnology 28 (5), 503-510, 2010
14612010
Global identification of human transcribed sequences with genome tiling arrays
P Bertone, V Stolc, TE Royce, JS Rozowsky, AE Urban, X Zhu, JL Rinn, ...
Science 306 (5705), 2242-2246, 2004
13232004
Expanded encyclopaedias of DNA elements in the human and mouse genomes
JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ...
Nature 583 (7818), 699-710, 2020
11362020
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells
S Loewer, MN Cabili, M Guttman, YH Loh, K Thomas, IH Park, M Garber, ...
Nature genetics 42 (12), 1113-1117, 2010
10762010
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