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John Rinn

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentBiochemistry

    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. Long Y, Hwang T, Gooding AR, Goodrich KJ, Hanson SD, Vallery TK, Rinn JL, Cech TR. Evaluation of the RNA-dependence of PRC2 binding to chromatin in human pluripotent stem cells. bioRxiv. 2024 May 02. PMID: 37645830.
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    2. Normandin E, Triana S, Raju SS, Lan TCT, Lagerborg K, Rudy M, Adams GC, DeRuff KC, Logue J, Liu D, Strebinger D, Rao A, Messer KS, Sacks M, Adams RD, Janosko K, Kotliar D, Shah R, Crozier I, Rinn JL, Mel? M, Honko AN, Zhang F, Babadi M, Luban J, Bennett RS, Shalek AK, Barkas N, Lin AE, Hensley LE, Sabeti PC, Siddle KJ. Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses. Cell Genom. 2023 12 13; 3(12):100440. PMID: 38169842.
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    3. Delfosse K, Gerhardinger C, Rinn JL, Maass PG. High-throughput functional analysis of regulatory variants using a massively parallel reporter assay. STAR Protoc. 2023 Dec 15; 4(4):102731. PMID: 37980569.
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    4. Santus L, Sopena-Rios M, Garc?a-P?rez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Mel? M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun. 2023 06 30; 14(1):3866. PMID: 37391481.
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    5. Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. Elife. 2023 01 31; 12. PMID: 36719724.
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    6. Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023 06; 24(6):430-447. PMID: 36596869.
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    7. Jansson-Fritzberg LI, Sousa CI, Smallegan MJ, Song JJ, Gooding AR, Kasinath V, Rinn JL, Cech TR. DNMT1 inhibition by pUG-fold quadruplex RNA. RNA. 2023 03; 29(3):346-360. PMID: 36574982.
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    8. Lawrence J, Rinn JL. Editorial overview: The genome in space-time. Curr Opin Genet Dev. 2022 10; 76:101969. PMID: 35998472.
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    9. Barutcu AR, Elizalde G, Gonzalez AE, Soni K, Rinn JL, Wagers AJ, Almada AE. Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells. Skelet Muscle. 2022 08 15; 12(1):20. PMID: 35971133.
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    10. Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, L?cuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guig? R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3. PMID: 35474001.
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    11. Much C, Smallegan MJ, Hwang T, Hanson SD, Dumbovic G, Rinn JL. Evolutionary divergence of Firre localization and expression. RNA. 2022 06; 28(6):842-853. PMID: 35304421.
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    12. Carter TA, Singh M, Dumbovic G, Chobirko JD, Rinn JL, Feschotte C. Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. Elife. 2022 02 18; 11. PMID: 35179489.
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    13. Andergassen D, Rinn JL. From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet. 2022 04; 23(4):229-243. PMID: 34837040.
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    14. Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci. 2021 12; 1506(1):118-141. PMID: 34791665.
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    15. Andergassen D, Smith ZD, Kretzmer H, Rinn JL, Meissner A. Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages. Dev Cell. 2021 11 08; 56(21):2995-3005.e4. PMID: 34752748.
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    16. Haswell JR, Mattioli K, Gerhardinger C, Maass PG, Foster DJ, Peinado P, Wang X, Medina PP, Rinn JL, Slack FJ. Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PLoS One. 2021; 16(11):e0252848. PMID: 34731163.
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    17. Dumbovic G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Publisher Correction: Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun. 2021 Oct 21; 12(1):6189. PMID: 34675241.
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    18. Smallegan MJ, Shehata S, Spradlin SF, Swearingen A, Wheeler G, Das A, Corbet G, Nebenfuehr B, Ahrens D, Tauber D, Lennon S, Choi K, Huynh T, Wieser T, Schneider K, Bradshaw M, Basken J, Lai M, Read T, Hynes-Grace M, Timmons D, Demasi J, Rinn JL. Genome-wide binding analysis of 195 DNA binding proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation. PLoS One. 2021; 16(6):e0237055. PMID: 34166368.
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    19. Dumbovic G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun. 2021 06 03; 12(1):3308. PMID: 34083519.
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    20. Broadwell LJ, Smallegan MJ, Rigby KM, Navarro-Arriola JS, Montgomery RL, Rinn JL, Leinwand LA. Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart. J Biol Chem. 2021 Jan-Jun; 296:100694. PMID: 33895132.
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    21. Teo AKK, Nguyen L, Gupta MK, Lau HH, Loo LSW, Jackson N, Lim CS, Mallard W, Gritsenko MA, Rinn JL, Smith RD, Qian WJ, Kulkarni RN. Defective insulin receptor signaling in hPSCs skews pluripotency and negatively perturbs neural differentiation. J Biol Chem. 2021 Jan-Jun; 296:100495. PMID: 33667549.
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    22. Harman CCD, Bailis W, Zhao J, Hill L, Qu R, Jackson RP, Shyer JA, Steach HR, Kluger Y, Goff LA, Rinn JL, Williams A, Henao-Mejia J, Flavell RA. An in vivo screen of noncoding loci reveals that Daedalus is a gatekeeper of an Ikaros-dependent checkpoint during haematopoiesis. Proc Natl Acad Sci U S A. 2021 01 19; 118(3). PMID: 33446502.
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    23. Ruan X, Li P, Ma Y, Jiang CF, Chen Y, Shi Y, Gupta N, Seifuddin F, Pirooznia M, Ohnishi Y, Yoneda N, Nishiwaki M, Dumbovic G, Rinn JL, Higuchi Y, Kawai K, Suemizu H, Cao H. Identification of human long noncoding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis. J Clin Invest. 2021 01 04; 131(1). PMID: 33048844.
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    24. Fang H, Bonora G, Lewandowski JP, Thakur J, Filippova GN, Henikoff S, Shendure J, Duan Z, Rinn JL, Deng X, Noble WS, Disteche CM. Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nat Commun. 2020 11 27; 11(1):6053. PMID: 33247132.
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    25. Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet. 2020 12; 52(12):1333-1345. PMID: 33230299.
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    26. Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MR, Adams GC, Adams R, Rinn JL, Mel? M, Schaffner SF, Nolan GP, Barnes KG, Hensley LE, McIlwain DR, Shalek AK, Sabeti PC, Bennett RS. Single-Cell Profiling of Ebola Virus Disease In?Vivo Reveals Viral and Host Dynamics. Cell. 2020 11 25; 183(5):1383-1401.e19. PMID: 33159858.
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    27. Lewandowski JP, Dumbovic G, Watson AR, Hwang T, Jacobs-Palmer E, Chang N, Much C, Turner KM, Kirby C, Rubinstein ND, Groff AF, Liapis SC, Gerhardinger C, Bester A, Pandolfi PP, Clohessy JG, Hoekstra HE, Sauvageau M, Rinn JL. The Tug1 lncRNA locus is essential for male fertility. Genome Biol. 2020 09 07; 21(1):237. PMID: 32894169.
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    28. Mattioli K, Oliveros W, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, Mel? M. Cis and trans effects differentially contribute to the evolution of promoters and enhancers. Genome Biol. 2020 08 20; 21(1):210. PMID: 32819422.
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    29. Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, L?cuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guig? R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. PMID: 32728249.
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    30. Long Y, Hwang T, Gooding AR, Goodrich KJ, Rinn JL, Cech TR. RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nat Genet. 2020 09; 52(9):931-938. PMID: 32632336.
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    31. Rinn JL, Chang HY. Long Noncoding RNAs: Molecular Modalities to Organismal Functions. Annu Rev Biochem. 2020 06 20; 89:283-308. PMID: 32569523.
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    32. Holmes ZE, Hamilton DJ, Hwang T, Parsonnet NV, Rinn JL, Wuttke DS, Batey RT. The Sox2 transcription factor binds RNA. Nat Commun. 2020 04 14; 11(1):1805. PMID: 32286318.
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    33. Friesen M, Warren CR, Yu H, Toyohara T, Ding Q, Florido MHC, Sayre C, Pope BD, Goff LA, Rinn JL, Cowan CA. Mitoregulin Controls ?-Oxidation in Human and Mouse Adipocytes. Stem Cell Reports. 2020 04 14; 14(4):590-602. PMID: 32243843.
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    34. Bourges C, Groff AF, Burren OS, Gerhardinger C, Mattioli K, Hutchinson A, Hu T, Anand T, Epping MW, Wallace C, Smith KG, Rinn JL, Lee JC. Resolving mechanisms of immune-mediated disease in primary CD4 T cells. EMBO Mol Med. 2020 05 08; 12(5):e12112. PMID: 32239644.
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    35. Andergassen D, Smith ZD, Lewandowski JP, Gerhardinger C, Meissner A, Rinn JL. In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation. Elife. 2019 11 18; 8. PMID: 31738164.
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    36. Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun. 2019 11 13; 10(1):5137. PMID: 31723143.
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    37. Smallegan MJ, Rinn JL. Linking long noncoding RNA to drug resistance. Proc Natl Acad Sci U S A. 2019 10 29; 116(44):21963-21965. PMID: 31601736.
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    38. Groff AF, Resetkova N, DiDomenico F, Sakkas D, Penzias A, Rinn JL, Eggan K. RNA-seq as a tool for evaluating human embryo competence. Genome Res. 2019 10; 29(10):1705-1718. PMID: 31548358.
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    39. Barutcu AR, Blencowe BJ, Rinn JL. Differential contribution of steady-state RNA and active transcription in chromatin organization. EMBO Rep. 2019 10 04; 20(10):e48068. PMID: 31448565.
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    40. Rowland TJ, Dumbovic G, Hass EP, Rinn JL, Cech TR. Single-cell imaging reveals unexpected heterogeneity of telomerase reverse transcriptase expression across human cancer cell lines. Proc Natl Acad Sci U S A. 2019 09 10; 116(37):18488-18497. PMID: 31451652.
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    41. Raj A, Rinn JL. Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harb Perspect Biol. 2019 05 01; 11(5). PMID: 31043413.
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    42. Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Mel? M, Rinn JL. High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Res. 2019 03; 29(3):344-355. PMID: 30683753.
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    43. Groff AF, Barutcu AR, Lewandowski JP, Rinn JL. Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biol. 2018 12 11; 19(1):219. PMID: 30537984.
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    44. Elling R, Robinson EK, Shapleigh B, Liapis SC, Covarrubias S, Katzman S, Groff AF, Jiang Z, Agarwal S, Motwani M, Chan J, Sharma S, Hennessy EJ, FitzGerald GA, McManus MT, Rinn JL, Fitzgerald KA, Carpenter S. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Rep. 2018 11 06; 25(6):1511-1524.e6. PMID: 30404006.
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    45. Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C. Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Syst. 2018 09 26; 7(3):258-268.e3. PMID: 30195438.
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    46. Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. J Cell Biol. 2019 01 07; 218(1):27-38. PMID: 30181316.
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    47. Maass PG, Weise A, Rittscher K, Lichtenwald J, Barutcu AR, Liehr T, Aydin A, Wefeld-Neuenfeld Y, P?lsler L, Tinschert S, Rinn JL, Luft FC, B?hring S. Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome. EMBO J. 2018 08 01; 37(15). PMID: 29921581.
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    48. 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 04 19; 173(3):649-664.e20. PMID: 29677511.
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    49. 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 04 13; 9(1):1444. PMID: 29654311.
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    50. Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell. 2018 04 05; 70(1):188-189. PMID: 29625035.
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    51. 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 04 05; 22(4):575-588.e7. PMID: 29625070.
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    52. Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Mol Cell. 2018 03 15; 69(6):1039-1045.e3. PMID: 29526697.
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    53. 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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    54. 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 02; 50(2):250-258. PMID: 29358654.
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    55. 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 03 15; 37(6). PMID: 29335281.
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    56. Maass PG, Barutcu AR, Shechner DM, Weiner CL, Mel? M, Rinn JL. Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nat Struct Mol Biol. 2018 02; 25(2):176-184. PMID: 29343869.
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    57. 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 12 14; 6. PMID: 29239719.
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    58. 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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    59. 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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    60. Del?s 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 09 06; 6. PMID: 28875933.
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    61. 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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    62. 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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    63. Mel? 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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    64. Caballero IS, Honko AN, Gire SK, Winnicki SM, Mel? 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.
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    65. 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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    66. 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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    67. Mel? 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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    68. 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.
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    69. 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.
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    70. 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.
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    71. 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.
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    72. 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.
      View in: PubMed
    73. 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.
      View in: PubMed
    74. 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.
      View in: PubMed
    75. 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.
      View in: PubMed
    76. 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.
      View in: PubMed
    77. 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.
      View in: PubMed
    78. Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Res. 2015 Oct; 25(10):1456-65. PMID: 26430155.
      View in: PubMed
    79. 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.
      View in: PubMed
    80. 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.
      View in: PubMed
    81. 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.
      View in: PubMed
    82. 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.
      View in: PubMed
    83. 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.
      View in: PubMed
    84. 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.
      View in: PubMed
    85. 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.
      View in: PubMed
    86. 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.
      View in: PubMed
    87. 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.
      View in: PubMed
    88. 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.
      View in: PubMed
    89. Mattick JS, Rinn JL. Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol. 2015 Jan; 22(1):5-7. PMID: 25565026.
      View in: PubMed
    90. 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.
      View in: PubMed
    91. 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.
      View in: PubMed
    92. Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science. 2014 Sep 12; 345(6202):1240-1. PMID: 25214588.
      View in: PubMed
    93. Rinn JL. lncRNAs: linking RNA to chromatin. Cold Spring Harb Perspect Biol. 2014 Aug 01; 6(8). PMID: 25085913.
      View in: PubMed
    94. 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.
      View in: PubMed
    95. Younger ST, Rinn JL. 'Lnc'-ing enhancers to MYC regulation. Cell Res. 2014 Jun; 24(6):643-4. PMID: 24777251.
      View in: PubMed
    96. 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.
      View in: PubMed
    97. Rinn JL, Ule J. 'Oming in on RNA-protein interactions. Genome Biol. 2014 Jan 31; 15(1):401. PMID: 24485348.
      View in: PubMed
    98. 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.
      View in: PubMed
    99. Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014 Jan 16; 505(7483):344-52. PMID: 24429633.
      View in: PubMed
    100. 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.
      View in: PubMed
    101. 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.
      View in: PubMed
    102. Goff LA, Rinn JL. Poly-combing the genome for RNA. Nat Struct Mol Biol. 2013 Dec; 20(12):1344-6. PMID: 24304912.
      View in: PubMed
    103. 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'Al? 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.
      View in: PubMed
    104. 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.
      View in: PubMed
    105. 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.
      View in: PubMed
    106. 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.
      View in: PubMed
    107. 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.
      View in: PubMed
    108. Henao-Mejia J, Williams A, Goff LA, Staron M, Licona-Lim?n 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.
      View in: PubMed
    109. 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.
      View in: PubMed
    110. 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.
      View in: PubMed
    111. 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.
      View in: PubMed
    112. Mar?n-B?jar O, Marchese FP, Athie A, S?nchez Y, Gonz?lez J, Segura V, Huang L, Moreno I, Navarro A, Monz? M, Garc?a-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.
      View in: PubMed
    113. 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.
      View in: PubMed
    114. 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.
      View in: PubMed
    115. 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.
      View in: PubMed
    116. 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.
      View in: PubMed
    117. 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.
      View in: PubMed
    118. 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.
      View in: PubMed
    119. Hacisuleyman E, Cabili MN, Rinn JL. A Keystone for ncRNA. Genome Biol. 2012 May 25; 13(5):315. PMID: 22632630.
      View in: PubMed
    120. 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.
      View in: PubMed
    121. Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012 Feb 15; 482(7385):339-46. PMID: 22337053.
      View in: PubMed
    122. 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.
      View in: PubMed
    123. 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.
      View in: PubMed
    124. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012; 81:145-66. PMID: 22663078.
      View in: PubMed
    125. 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.
      View in: PubMed
    126. 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.
      View in: PubMed
    127. 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.
      View in: PubMed
    128. 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.
      View in: PubMed
    129. 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.
      View in: PubMed
    130. 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.
      View in: PubMed
    131. 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.
      View in: PubMed
    132. 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.
      View in: PubMed
    133. 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.
      View in: PubMed
    134. Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol. 2011 Jun; 22(4):359-65. PMID: 21333748.
      View in: PubMed
    135. Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 2011 Feb; 12(2):136-49. PMID: 21245830.
      View in: PubMed
    136. 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.
      View in: PubMed
    137. 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.
      View in: PubMed
    138. 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.
      View in: PubMed
    139. Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Hum Mol Genet. 2010 Oct 15; 19(R2):R152-61. PMID: 20729297.
      View in: PubMed
    140. 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.
      View in: PubMed
    141. 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.
      View in: PubMed
    142. Kellis M, Rinn JL. Sequences to systems. Genome Biol. 2010; 11(5):303. PMID: 20500907.
      View in: PubMed
    143. 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.
      View in: PubMed
    144. 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.
      View in: PubMed
    145. Koziol MJ, Rinn JL. RNA traffic control of chromatin complexes. Curr Opin Genet Dev. 2010 Apr; 20(2):142-8. PMID: 20362426.
      View in: PubMed
    146. 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.
      View in: PubMed
    147. 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.
      View in: PubMed
    148. 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.
      View in: PubMed
    149. 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.
      View in: PubMed
    150. 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.
      View in: PubMed
    151. 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.
      View in: PubMed
    152. 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.
      View in: PubMed
    153. 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.
      View in: PubMed
    154. 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.
      View in: PubMed
    155. 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.
      View in: PubMed
    156. 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.
      View in: PubMed
    157. Khavari TA, Rinn J. Ras/Erk MAPK signaling in epidermal homeostasis and neoplasia. Cell Cycle. 2007 Dec 01; 6(23):2928-31. PMID: 18000402.
      View in: PubMed
    158. 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.
      View in: PubMed
    159. 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.
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    160. 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.
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    161. 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.
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    162. Rinn JL, Snyder M. Sexual dimorphism in mammalian gene expression. Trends Genet. 2005 May; 21(5):298-305. PMID: 15851067.
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    163. 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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    164. 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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    165. 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.
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    166. 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.
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    167. 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.
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    168. 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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    169. 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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