 Connection
John Rinn to Humans
This is a "connection" page, showing publications John Rinn has written about Humans.
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0.870 |
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Much C, Lasda EL, Pereira IT, Vallery TK, Ramirez D, Lewandowski JP, Dowell RD, Smallegan MJ, Rinn JL. The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation. Nat Commun. 2024 Aug 09; 15(1):6821.
Score: 0.024
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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.
Score: 0.020
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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.
Score: 0.019
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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.
Score: 0.019
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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.
Score: 0.018
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Rinn JL, Chang HY. Long Noncoding RNAs: Molecular Modalities to Organismal Functions. Annu Rev Biochem. 2020 06 20; 89:283-308.
Score: 0.018
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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.
Score: 0.017
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Raj A, Rinn JL. Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harb Perspect Biol. 2019 05 01; 11(5).
Score: 0.016
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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.
Score: 0.016
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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.
Score: 0.016
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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.
Score: 0.015
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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.
Score: 0.015
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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).
Score: 0.015
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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.
Score: 0.015
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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.
Score: 0.015
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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.
Score: 0.014
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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.
Score: 0.013
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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.
Score: 0.013
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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.
Score: 0.013
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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.
Score: 0.013
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Younger ST, Rinn JL. Silent pericentromeric repeats speak out. Proc Natl Acad Sci U S A. 2015 Dec 08; 112(49):15008-9.
Score: 0.013
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Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Res. 2015 Oct; 25(10):1456-65.
Score: 0.013
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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.
Score: 0.013
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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.
Score: 0.012
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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.
Score: 0.012
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Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science. 2014 Sep 12; 345(6202):1240-1.
Score: 0.012
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Younger ST, Rinn JL. 'Lnc'-ing enhancers to MYC regulation. Cell Res. 2014 Jun; 24(6):643-4.
Score: 0.012
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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.
Score: 0.012
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Rinn JL, Ule J. 'Oming in on RNA-protein interactions. Genome Biol. 2014 Jan 31; 15(1):401.
Score: 0.011
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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.
Score: 0.011
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Goff LA, Rinn JL. Poly-combing the genome for RNA. Nat Struct Mol Biol. 2013 Dec; 20(12):1344-6.
Score: 0.011
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Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 2012 Nov 26; 13(11):R107.
Score: 0.011
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Hacisuleyman E, Cabili MN, Rinn JL. A Keystone for ncRNA. Genome Biol. 2012 May 25; 13(5):315.
Score: 0.010
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Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012; 81:145-66.
Score: 0.010
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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.
Score: 0.010
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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.
Score: 0.010
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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.
Score: 0.010
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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.
Score: 0.010
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Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol. 2011 Jun; 22(4):359-65.
Score: 0.009
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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.
Score: 0.009
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Khavari DA, Sen GL, Rinn JL. DNA methylation and epigenetic control of cellular differentiation. Cell Cycle. 2010 Oct 01; 9(19):3880-3.
Score: 0.009
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Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Hum Mol Genet. 2010 Oct 15; 19(R2):R152-61.
Score: 0.009
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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.
Score: 0.009
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Kellis M, Rinn JL. Sequences to systems. Genome Biol. 2010; 11(5):303.
Score: 0.009
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Koziol MJ, Rinn JL. RNA traffic control of chromatin complexes. Curr Opin Genet Dev. 2010 Apr; 20(2):142-8.
Score: 0.009
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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.
Score: 0.008
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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.
Score: 0.008
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Khavari TA, Rinn J. Ras/Erk MAPK signaling in epidermal homeostasis and neoplasia. Cell Cycle. 2007 Dec 01; 6(23):2928-31.
Score: 0.007
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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.
Score: 0.007
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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.
Score: 0.007
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Rinn JL, Snyder M. Sexual dimorphism in mammalian gene expression. Trends Genet. 2005 May; 21(5):298-305.
Score: 0.006
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Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE. Biophysical characterization of high-confidence, small human proteins. Biophys Rep (N Y). 2024 Sep 11; 4(3):100167.
Score: 0.006
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Lee YH, Hass EP, Campodonico W, Lee YK, Lasda E, Shah JS, Rinn JL, Hwang T. Massively parallel dissection of RNA in RNA-protein interactions in vivo. Nucleic Acids Res. 2024 Jun 10; 52(10):e48.
Score: 0.006
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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.
Score: 0.006
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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).
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.005
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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).
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.004
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014 Jan 16; 505(7483):344-52.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.003
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 2011 Feb; 12(2):136-49.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.002
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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.
Score: 0.001
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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.
Score: 0.001
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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.
Score: 0.001
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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