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John Rinn

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentChemistry & Biochemistry

    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Bester AC, Lee JD, Chavez A, Lee YR, Nachmani D, Vora S, Victor J, Sauvageau M, Monteleone E, Rinn JL, Provero P, Church GM, Clohessy JG, Pandolfi PP. An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell. 2018 Apr 19; 173(3):649-664.e20. PMID: 29677511.
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    2. Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat Commun. 2018 Apr 13; 9(1):1444. PMID: 29654311.
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    3. Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell. 2018 Apr 05; 70(1):188-189. PMID: 29625035.
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    4. Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 2018 Apr 05; 22(4):575-588.e7. PMID: 29625070.
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    5. Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell. 2018 Mar 15; 69(6):1039-1045.e3. PMID: 29526697.
      View in: PubMed
    6. Wolff RA, Wang-Gillam A, Alvarez H, Tiriac H, Engle D, Hou S, Groff AF, San Lucas A, Bernard V, Allenson K, Castillo J, Kim D, Mulu F, Huang J, Stephens B, Wistuba II, Katz M, Varadhachary G, Park Y, Hicks J, Chinnaiyan A, Scampavia L, Spicer T, Gerhardinger C, Maitra A, Tuveson D, Rinn J, Lizee G, Yee C, Levine AJ. Dynamic changes during the treatment of pancreatic cancer. Oncotarget. 2018 Mar 13; 9(19):14764-14790. PMID: 29599906.
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    7. Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet. 2018 Feb; 50(2):250-258. PMID: 29358654.
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    8. Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL. High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 2018 Mar 15; 37(6). PMID: 29335281.
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    9. Maass PG, Barutcu AR, Shechner DM, Weiner CL, Melé M, Rinn JL. Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nat Struct Mol Biol. 2018 Feb; 25(2):176-184. PMID: 29343869.
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    10. Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY. Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. Elife. 2017 Dec 14; 6. PMID: 29239719.
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    11. Younger ST, Rinn JL. p53 regulates enhancer accessibility and activity in response to DNA damage. Nucleic Acids Res. 2017 Sep 29; 45(17):9889-9900. PMID: 28973438.
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    12. Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, Hughes C, Fonseca-Pereira D, Veiga-Fernandes H, Raj A, Kambayashi T, Brodsky IE, O'Shea JJ, Wherry EJ, Goff LA, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. Immunity. 2017 09 19; 47(3):435-449.e8. PMID: 28930659.
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    13. Delás MJ, Sabin LR, Dolzhenko E, Knott SR, Munera Maravilla E, Jackson BT, Wild SA, Kovacevic T, Stork EM, Zhou M, Erard N, Lee E, Kelley DR, Roth M, Barbosa IA, Zuber J, Rinn JL, Smith AD, Hannon GJ. lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. Elife. 2017 Sep 06; 6. PMID: 28875933.
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    14. Mello SS, Sinow C, Raj N, Mazur PK, Bieging-Rolett K, Broz DK, Imam JFC, Vogel H, Wood LD, Sage J, Hirose T, Nakagawa S, Rinn J, Attardi LD. Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes Dev. 2017 06 01; 31(11):1095-1108. PMID: 28698299.
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    15. Henry WS, Hendrickson DG, Beca F, Glass B, Lindahl-Allen M, He L, Ji Z, Struhl K, Beck AH, Rinn JL, Toker A. LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer. Oncotarget. 2016 Dec 13; 7(50):81981-81994. PMID: 27626181.
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    16. Melé M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res. 2017 01; 27(1):27-37. PMID: 27927715.
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    17. Caballero IS, Honko AN, Gire SK, Winnicki SM, Melé M, Gerhardinger C, Lin AE, Rinn JL, Sabeti PC, Hensley LE, Connor JH. In vivo Ebola virus infection leads to a strong innate response in circulating immune cells. BMC Genomics. 2016 09 05; 17:707. PMID: 27595844; PMCID: PMC5011782.
    18. Kotzin JJ, Spencer SP, McCright SJ, Kumar DBU, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CCD, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature. 2016 09 08; 537(7619):239-243. PMID: 27525555.
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    19. Groff AF, Sanchez-Gomez DB, Soruco MML, Gerhardinger C, Barutcu AR, Li E, Elcavage L, Plana O, Sanchez LV, Lee JC, Sauvageau M, Rinn JL. In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. Cell Rep. 2016 08 23; 16(8):2178-2186. PMID: 27524623.
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    20. Melé M, Rinn JL. "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. Mol Cell. 2016 06 02; 62(5):657-64. PMID: 27259198.
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    21. Kelley DR, Snoek J, Rinn JL. Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res. 2016 07; 26(7):990-9. PMID: 27197224; PMCID: PMC4937568.
    22. Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL. A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proc Natl Acad Sci U S A. 2016 May 10; 113(19):5364-9. PMID: 27078102; PMCID: PMC4868469 [Available on 11/10/16].
    23. Hacisuleyman E, Shukla CJ, Weiner CL, Rinn JL. Function and evolution of local repeats in the Firre locus. Nat Commun. 2016 Mar 24; 7:11021. PMID: 27009974; PMCID: PMC4820808.
    24. Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nat Commun. 2016 Mar 15; 7:10982. PMID: 26975529; PMCID: PMC4796315.
    25. G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biol. 2016 Feb 16; 17:28. PMID: 26883116; PMCID: PMC4756407.
    26. Stojic L, Niemczyk M, Orjalo A, Ito Y, Ruijter AE, Uribe-Lewis S, Joseph N, Weston S, Menon S, Odom DT, Rinn J, Gergely F, Murrell A. Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions. Nat Commun. 2016 Feb 02; 7:10406. PMID: 26832224; PMCID: PMC4740813.
    27. Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10; 528(7581):218-24. PMID: 26659182.
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    28. Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G. Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution. Neuron. 2015 Dec 02; 88(5):861-877. PMID: 26637795.
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    29. Younger ST, Rinn JL. Silent pericentromeric repeats speak out. Proc Natl Acad Sci U S A. 2015 Dec 08; 112(49):15008-9. PMID: 26582791; PMCID: PMC4679049.
    30. Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 2015 Nov; 33(11):1173-81. PMID: 26501951; PMCID: PMC4847940.
    31. Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Res. 2015 Oct; 25(10):1456-65. PMID: 26430155; PMCID: PMC4579330.
    32. Ng SY, Soh BS, Rodriguez-Muela N, Hendrickson DG, Price F, Rinn JL, Rubin LL. Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy. Cell Stem Cell. 2015 Nov 05; 17(5):569-84. PMID: 26321202; PMCID: PMC4839185 [Available on 11/05/16].
    33. Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell. 2015 Jul 16; 162(2):412-424. PMID: 26186193; PMCID: PMC4511597.
    34. Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics. 2015 Jun 13; 16:454. PMID: 26070627; PMCID: PMC4465157.
    35. Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M, Plana O, Li E, Gerhardinger C, Tomassy GS, Arlotta P, Rinn JL. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):6855-62. PMID: 26034286; PMCID: PMC4460505.
    36. Shechner DM, Hacisuleyman E, Younger ST, Rinn JL. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods. 2015 Jul; 12(7):664-70. PMID: 26030444; PMCID: PMC4821475.
    37. Lai KM, Gong G, Atanasio A, Rojas J, Quispe J, Posca J, White D, Huang M, Fedorova D, Grant C, Miloscio L, Droguett G, Poueymirou WT, Auerbach W, Yancopoulos GD, Frendewey D, Rinn J, Valenzuela DM. Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs. PLoS One. 2015; 10(4):e0125522. PMID: 25909911; PMCID: PMC4409293.
    38. Younger ST, Kenzelmann-Broz D, Jung H, Attardi LD, Rinn JL. Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage. Nucleic Acids Res. 2015 May 19; 43(9):4447-62. PMID: 25883152; PMCID: PMC4482066.
    39. Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015 May; 47(5):469-78. PMID: 25822089; PMCID: PMC4414868.
    40. Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 2015 Jan 29; 16:20. PMID: 25630241; PMCID: PMC4369099.
    41. Dunagin M, Cabili MN, Rinn J, Raj A. Visualization of lncRNA by single-molecule fluorescence in situ hybridization. Methods Mol Biol. 2015; 1262:3-19. PMID: 25555572.
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    42. Mattick JS, Rinn JL. Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol. 2015 Jan; 22(1):5-7. PMID: 25565026.
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    43. Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron. 2015 Jan 21; 85(2):275-288. PMID: 25556833; PMCID: PMC4430475.
    44. Kelley DR, Hendrickson DG, Tenen D, Rinn JL. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biol. 2014 Dec 03; 15(12):537. PMID: 25572935; PMCID: PMC4272801.
    45. Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science. 2014 Sep 12; 345(6202):1240-1. PMID: 25214588; PMCID: PMC4186717.
    46. Rinn JL. lncRNAs: linking RNA to chromatin. Cold Spring Harb Perspect Biol. 2014 Aug 01; 6(8). PMID: 25085913; PMCID: PMC4107985.
    47. Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat Neurosci. 2014 Aug; 17(8):1046-54. PMID: 24997765; PMCID: PMC4188416.
    48. Younger ST, Rinn JL. 'Lnc'-ing enhancers to MYC regulation. Cell Res. 2014 Jun; 24(6):643-4. PMID: 24777251; PMCID: PMC4042177.
    49. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014 Apr; 32(4):381-386. PMID: 24658644; PMCID: PMC4122333.
    50. Rinn JL, Ule J. 'Oming in on RNA-protein interactions. Genome Biol. 2014 Jan 31; 15(1):401. PMID: 24485348.
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    51. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014 Feb; 21(2):198-206. PMID: 24463464; PMCID: PMC3950333.
    52. Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014 Jan 16; 505(7483):344-52. PMID: 24429633; PMCID: PMC4113481.
    53. Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biol. 2014 Jan 07; 15(1):R3. PMID: 24393486; PMCID: PMC4053792.
    54. Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013 Dec 31; 2:e01749. PMID: 24381249; PMCID: PMC3874104.
    55. Goff LA, Rinn JL. Poly-combing the genome for RNA. Nat Struct Mol Biol. 2013 Dec; 20(12):1344-6. PMID: 24304912.
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    56. Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013 Nov 21; 503(7476):371-6. PMID: 24107992; PMCID: PMC3870304.
    57. Maamar H, Cabili MN, Rinn J, Raj A. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev. 2013 Jun 01; 27(11):1260-71. PMID: 23723417; PMCID: PMC3690399.
    58. Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E. Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development. 2013 Jul; 140(13):2828-34. PMID: 23698349; PMCID: PMC3678345.
    59. Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763; PMCID: PMC3709577.
    60. Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biol. 2013 Apr 25; 14(4):113. PMID: 23651518; PMCID: PMC3663092.
    61. Henao-Mejia J, Williams A, Goff LA, Staron M, Licona-Limón P, Kaech SM, Nakayama M, Rinn JL, Flavell RA. The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis. Immunity. 2013 May 23; 38(5):984-97. PMID: 23623381; PMCID: PMC3738211.
    62. Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL, Lander ES, Schaffner SF, Sabeti PC. Identifying recent adaptations in large-scale genomic data. Cell. 2013 Feb 14; 152(4):703-13. PMID: 23415221.
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    63. Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A. 2013 Feb 26; 110(9):3387-92. PMID: 23401553; PMCID: PMC3587215.
    64. Yoon JH, Abdelmohsen K, Kim J, Yang X, Martindale JL, Tominaga-Yamanaka K, White EJ, Orjalo AV, Rinn JL, Kreft SG, Wilson GM, Gorospe M. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. Nat Commun. 2013; 4:2939. PMID: 24326307.
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    65. Marín-Béjar O, Marchese FP, Athie A, Sánchez Y, González J, Segura V, Huang L, Moreno I, Navarro A, Monzó M, García-Foncillas J, Rinn JL, Guo S, Huarte M. Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol. 2013; 14(9):R104. PMID: 24070194; PMCID: PMC4053822.
    66. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013 Jan; 31(1):46-53. PMID: 23222703; PMCID: PMC3869392.
    67. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013 Jan 10; 493(7431):231-5. PMID: 23201690.
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    68. Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 2012 Nov 26; 13(11):R107. PMID: 23181609; PMCID: PMC3580499.
    69. Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol. 2013 Jan; 9(1):59-64. PMID: 23160002; PMCID: PMC3625679.
    70. Siprashvili Z, Webster DE, Kretz M, Johnston D, Rinn JL, Chang HY, Khavari PA. Identification of proteins binding coding and non-coding human RNAs using protein microarrays. BMC Genomics. 2012 Nov 16; 13:633. PMID: 23157412; PMCID: PMC3562209.
    71. Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA. 2012 Nov-Dec; 3(6):759-78. PMID: 22991327; PMCID: PMC3472101.
    72. Hacisuleyman E, Cabili MN, Rinn JL. A Keystone for ncRNA. Genome Biol. 2012 May 25; 13(5):315. PMID: 22632630; PMCID: PMC3446285.
    73. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 01; 7(3):562-78. PMID: 22383036; PMCID: PMC3334321.
    74. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012 Feb 15; 482(7385):339-46. PMID: 22337053; PMCID: PMC4197003.
    75. Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev. 2012 Feb 15; 26(4):338-43. PMID: 22302877; PMCID: PMC3289881.
    76. Ahfeldt T, Schinzel RT, Lee YK, Hendrickson D, Kaplan A, Lum DH, Camahort R, Xia F, Shay J, Rhee EP, Clish CB, Deo RC, Shen T, Lau FH, Cowley A, Mowrer G, Al-Siddiqi H, Nahrendorf M, Musunuru K, Gerszten RE, Rinn JL, Cowan CA. Programming human pluripotent stem cells into white and brown adipocytes. Nat Cell Biol. 2012 Jan 15; 14(2):209-19. PMID: 22246346; PMCID: PMC3385947.
    77. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012; 81:145-66. PMID: 22663078; PMCID: PMC3858397.
    78. Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL, Walhout AJ. Genomics in 2011: challenges and opportunities. Genome Biol. 2011 Dec 28; 12(12):137. PMID: 22204305; PMCID: PMC3334607.
    79. Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 2012 Mar; 22(3):577-91. PMID: 22110045; PMCID: PMC3290793.
    80. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol. 2011 Nov 13; 30(1):99-104. PMID: 22081020; PMCID: PMC3710462.
    81. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15; 25(18):1915-27. PMID: 21890647; PMCID: PMC3185964.
    82. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011 Aug 28; 477(7364):295-300. PMID: 21874018; PMCID: PMC3175327.
    83. 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; discussion e1001102. PMID: 21765801; PMCID: PMC3134446.
    84. Broadbent KM, 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. PMID: 21689454; PMCID: PMC3218844.
    85. 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. PMID: 21601459.
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    86. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 2011; 12(3):R22. PMID: 21410973; PMCID: PMC3129672.
    87. Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol. 2011 Jun; 22(4):359-65. PMID: 21333748; PMCID: PMC3184770.
    88. Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 2011 Feb; 12(2):136-49. PMID: 21245830; PMCID: PMC4081495.
    89. Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, Rinn JL. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet. 2010 Dec; 42(12):1113-7. PMID: 21057500; PMCID: PMC3040650.
    90. Khavari DA, Sen GL, Rinn JL. DNA methylation and epigenetic control of cellular differentiation. Cell Cycle. 2010 Oct 01; 9(19):3880-3. PMID: 20890116.
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    91. Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010 Sep 02; 467(7311):103-7. PMID: 20811459; PMCID: PMC3847670.
    92. Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Hum Mol Genet. 2010 Oct 15; 19(R2):R152-61. PMID: 20729297; PMCID: PMC2953740.
    93. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 2010 Aug 06; 142(3):409-19. PMID: 20673990; PMCID: PMC2956184.
    94. Zhu H, Shah S, Shyh-Chang N, Shinoda G, Einhorn WS, Viswanathan SR, Takeuchi A, Grasemann C, Rinn JL, Lopez MF, Hirschhorn JN, Palmert MR, Daley GQ. Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies. Nat Genet. 2010 Jul; 42(7):626-30. PMID: 20512147; PMCID: PMC3069638.
    95. Kellis M, Rinn JL. Sequences to systems. Genome Biol. 2010; 11(5):303. PMID: 20500907; PMCID: PMC2898084.
    96. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010 May; 28(5):503-10. PMID: 20436462; PMCID: PMC2868100.
    97. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010 Apr 15; 464(7291):1071-6. PMID: 20393566.
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    98. Koziol MJ, Rinn JL. RNA traffic control of chromatin complexes. Curr Opin Genet Dev. 2010 Apr; 20(2):142-8. PMID: 20362426; PMCID: PMC2895502.
    99. Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, Liu XS, Rinn J, Schier AF. Chromatin signature of embryonic pluripotency is established during genome activation. Nature. 2010 Apr 08; 464(7290):922-6. PMID: 20336069; PMCID: PMC2874748.
    100. 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, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009 Oct 09; 326(5950):257-63. PMID: 19729616; PMCID: PMC2879337.
    101. Mace KA, Restivo TE, Rinn JL, 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. PMID: 19544454; PMCID: PMC2733377.
    102. 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 JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14; 106(28):11667-72. PMID: 19571010; PMCID: PMC2704857.
    103. Somervaille TC, Matheny CJ, Spencer GJ, Iwasaki M, Rinn JL, 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 06; 4(2):129-40. PMID: 19200802; PMCID: PMC2670853.
    104. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009 Mar 12; 458(7235):223-7. PMID: 19182780; PMCID: PMC2754849.
    105. Su MA, Giang K, Zumer K, Jiang H, Oven I, Rinn JL, Devoss JJ, Johannes KP, Lu W, Gardner J, Chang A, Bubulya P, Chang HY, Peterlin BM, Anderson MS. Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire. J Clin Invest. 2008 May; 118(5):1712-26. PMID: 18414681; PMCID: PMC2293336.
    106. Rinn JL, Wang JK, Liu H, Montgomery K, van de Rijn M, Chang HY. A systems biology approach to anatomic diversity of skin. J Invest Dermatol. 2008 Apr; 128(4):776-82. PMID: 18337710.
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    107. Rinn JL, Wang JK, Allen N, Brugmann SA, Mikels AJ, Liu H, Ridky TW, Stadler HS, Nusse R, Helms JA, Chang HY. A dermal HOX transcriptional program regulates site-specific epidermal fate. Genes Dev. 2008 Feb 01; 22(3):303-7. PMID: 18245445; PMCID: PMC2216690.
    108. Chang W, Zaarour RF, Reck-Peterson S, Rinn J, Singer RH, Snyder M, Novick P, Mooseker MS. 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 Mar; 14(3):491-502. PMID: 18218704; PMCID: PMC2248268.
    109. Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, Iwase S, Alpatov R, Issaeva I, Canaani E, Roberts TM, Chang HY, Shi Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature. 2007 Oct 11; 449(7163):689-94. PMID: 17851529.
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    110. Khavari TA, Rinn J. Ras/Erk MAPK signaling in epidermal homeostasis and neoplasia. Cell Cycle. 2007 Dec 01; 6(23):2928-31. PMID: 18000402.
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    111. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007 Jun 29; 129(7):1311-23. PMID: 17604720; PMCID: PMC2084369.
    112. O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 2007 Jun; 3(6):e89. PMID: 17542650; PMCID: PMC1885280.
    113. DeVoss J, Hou Y, Johannes K, Lu W, Liou GI, Rinn J, Chang H, Caspi RR, Caspi R, Fong L, Anderson MS. Spontaneous autoimmunity prevented by thymic expression of a single self-antigen. J Exp Med. 2006 Nov 27; 203(12):2727-35. PMID: 17116738; PMCID: PMC2118158.
    114. Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY. Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet. 2006 Jul; 2(7):e119. PMID: 16895450; PMCID: PMC1523235.
    115. Rinn JL, Snyder M. Sexual dimorphism in mammalian gene expression. Trends Genet. 2005 May; 21(5):298-305. PMID: 15851067.
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    116. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science. 2004 Dec 24; 306(5705):2242-6. PMID: 15539566.
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    117. Rinn JL, Rozowsky JS, Laurenzi IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M. Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell. 2004 Jun; 6(6):791-800. PMID: 15177028.
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    118. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May; 24(9):3804-14. PMID: 15082775; PMCID: PMC387762.
    119. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12247-52. PMID: 14527995; PMCID: PMC218744.
    120. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. The transcriptional activity of human Chromosome 22. Genes Dev. 2003 Feb 15; 17(4):529-40. PMID: 12600945; PMCID: PMC195998.
    121. Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, Snyder M. Identification of novel functional elements in the human genome. Cold Spring Harb Symp Quant Biol. 2003; 68:317-22. PMID: 15338632.
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    122. Fitzakerley JL, Star KV, Rinn JL, Elmquist BJ. Expression of Shal potassium channel subunits in the adult and developing cochlear nucleus of the mouse. Hear Res. 2000 Sep; 147(1-2):31-45. PMID: 10962171.
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