John Rinn, Ph.D. - Publications

Affiliations: 
2004 Yale University, New Haven, CT 

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Year Citation  Score
2019 Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Melé M, Rinn JL. High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity. Genome Research. PMID 30683753 DOI: 10.1101/gr.242222.118  0.52
2018 Groff AF, Barutcu AR, Lewandowski JP, Rinn JL. Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biology. 19: 219. PMID 30537984 DOI: 10.1186/s13059-018-1589-8  0.52
2018 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, et al. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Reports. 25: 1511-1524.e6. PMID 30404006 DOI: 10.1016/j.celrep.2018.10.027  0.44
2018 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 Systems. PMID 30195438 DOI: 10.1016/j.cels.2018.07.006  0.6
2018 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. 173: 649-664.e20. PMID 29677511 DOI: 10.1016/j.cell.2018.03.052  0.6
2018 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, ... ... Rinn JL, et al. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 22: 575-588.e7. PMID 29625070 DOI: 10.1016/j.stem.2018.03.012  0.6
2018 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, ... ... Rinn J, et al. Dynamic changes during the treatment of pancreatic cancer. Oncotarget. 9: 14764-14790. PMID 29599906 DOI: 10.18632/oncotarget.24483  0.52
2017 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, ... ... Rinn JL, et al. Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. Immunity. 47: 435-449.e8. PMID 28930659 DOI: 10.1016/j.immuni.2017.08.012  0.68
2016 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. PMID 27626181 DOI: 10.18632/oncotarget.11962  0.6
2016 Kotzin JJ, Spencer SP, McCright SJ, Kumar DB, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CC, Virtue AT, Zhu S, Bailis W, Stein J, ... ... Rinn JL, et al. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature. PMID 27525555 DOI: 10.1038/nature19346  0.68
2016 Groff AF, Sanchez-Gomez DB, Soruco MM, 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 Reports. PMID 27524623 DOI: 10.1016/j.celrep.2016.07.050  1
2016 Hacisuleyman E, Shukla CJ, Weiner CL, Rinn JL. Function and evolution of local repeats in the Firre locus. Nature Communications. 7: 11021. PMID 27009974 DOI: 10.1038/ncomms11021  1
2016 G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biology. 17: 28. PMID 26883116 DOI: 10.1186/s13059-016-0878-3  1
2015 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, ... ... Rinn J, et al. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 528: 218-224. PMID 26659182 DOI: 10.1038/nature15749  0.88
2015 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. 88: 861-77. PMID 26637795 DOI: 10.1016/j.neuron.2015.09.045  1
2015 Younger ST, Rinn JL. Silent pericentromeric repeats speak out. Proceedings of the National Academy of Sciences of the United States of America. PMID 26582791 DOI: 10.1073/pnas.1520341112  1
2015 Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Research. 25: 1456-65. PMID 26430155 DOI: 10.1101/gr.191122.115  1
2015 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. PMID 26321202 DOI: 10.1016/j.stem.2015.08.003  0.6
2015 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, et al. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell. 162: 412-424. PMID 26186193 DOI: 10.1016/j.cell.2015.06.016  1
2015 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, et al. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. PMID 26034286 DOI: 10.1073/pnas.1411263112  1
2015 Shechner DM, Hacisuleyman E, Younger ST, Rinn JL. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nature Methods. 12: 664-70. PMID 26030444 DOI: 10.1038/nmeth.3433  1
2015 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, ... ... Rinn J, et al. Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs. Plos One. 10: e0125522. PMID 25909911 DOI: 10.1371/journal.pone.0125522  1
2015 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 Research. 43: 4447-62. PMID 25883152 DOI: 10.1093/nar/gkv284  1
2015 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, et al. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nature Genetics. 47: 469-78. PMID 25822089 DOI: 10.1038/ng.3258  1
2015 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 Biology. 16: 20. PMID 25630241 DOI: 10.1186/s13059-015-0586-4  1
2015 Mattick JS, Rinn JL. Discovery and annotation of long noncoding RNAs. Nature Structural & Molecular Biology. 22: 5-7. PMID 25565026 DOI: 10.1038/nsmb.2942  1
2015 Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Brown JR, Hrvatin S, Rinn JL, Arlotta P. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron. 85: 275-88. PMID 25556833 DOI: 10.1016/j.neuron.2014.12.024  1
2015 Dunagin M, Cabili MN, Rinn J, Raj A. Visualization of lncRNA by single-molecule fluorescence in situ hybridization. Methods in Molecular Biology (Clifton, N.J.). 1262: 3-19. PMID 25555572 DOI: 10.1007/978-1-4939-2253-6_1  1
2015 Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 518: 355-9. PMID 25533951 DOI: 10.1038/nature13990  1
2015 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. 16. DOI: 10.1186/s12864-015-1603-4  1
2014 Kelley DR, Hendrickson DG, Tenen D, Rinn JL. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biology. 15: 537. PMID 25572935 DOI: 10.1186/s13059-014-0537-5  0.6
2014 Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science (New York, N.Y.). 345: 1240-1. PMID 25214588 DOI: 10.1126/science.1252966  1
2014 Rinn JL. lncRNAs: linking RNA to chromatin. Cold Spring Harbor Perspectives in Biology. 6. PMID 25085913 DOI: 10.1101/cshperspect.a018614  1
2014 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. Nature Neuroscience. 17: 1046-54. PMID 24997765 DOI: 10.1038/nn.3757  1
2014 Younger ST, Rinn JL. 'Lnc'-ing enhancers to MYC regulation. Cell Research. 24: 643-4. PMID 24777251 DOI: 10.1038/cr.2014.54  1
2014 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. Nature Biotechnology. 32: 381-6. PMID 24658644 DOI: 10.1038/nbt.2859  1
2014 Rinn JL, Ule J. 'Oming in on RNA-protein interactions. Genome Biology. 15: 401. PMID 24485348 DOI: 10.1186/gb4158  1
2014 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, ... ... Rinn JL, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nature Structural & Molecular Biology. 21: 198-206. PMID 24463464 DOI: 10.1038/nsmb.2764  1
2014 Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 505: 344-52. PMID 24429633 DOI: 10.1038/nature12986  1
2014 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 Biology. 15: R3. PMID 24393486 DOI: 10.1186/gb-2014-15-1-r3  1
2013 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, ... ... Rinn JL, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2: e01749. PMID 24381249 DOI: 10.7554/eLife.01749  1
2013 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. Nature Communications. 4: 2939. PMID 24326307 DOI: 10.1038/ncomms3939  1
2013 Goff LA, Rinn JL. Poly-combing the genome for RNA. Nature Structural & Molecular Biology. 20: 1344-6. PMID 24304912 DOI: 10.1038/nsmb.2728  1
2013 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, ... ... Rinn JL, et al. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 503: 371-6. PMID 24107992 DOI: 10.1038/nature12598  1
2013 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 Biology. 14: R104. PMID 24070194 DOI: 10.1186/gb-2013-14-9-r104  1
2013 Maamar H, Cabili MN, Rinn J, Raj A. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes & Development. 27: 1260-71. PMID 23723417 DOI: 10.1101/gad.217018.113  1
2013 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 (Cambridge, England). 140: 2828-34. PMID 23698349 DOI: 10.1242/dev.098343  1
2013 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, ... ... Rinn J, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/j.cell.2013.04.037  1
2013 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 Biology. 14: 113. PMID 23651518 DOI: 10.1186/gb-2013-14-4-113  1
2013 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. 38: 984-97. PMID 23623381 DOI: 10.1016/j.immuni.2013.02.021  0.6
2013 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, et al. Identifying recent adaptations in large-scale genomic data. Cell. 152: 703-13. PMID 23415221 DOI: 10.1016/j.cell.2013.01.035  1
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 3387-92. PMID 23401553 DOI: 10.1073/pnas.1222643110  1
2013 Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 31: 46-53. PMID 23222703 DOI: 10.1038/nbt.2450  1
2013 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, ... ... Rinn JL, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 493: 231-5. PMID 23201690 DOI: 10.1038/nature11661  1
2013 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. Nature Chemical Biology. 9: 59-64. PMID 23160002 DOI: 10.1038/nchembio.1120  1
2012 Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biology. 13: R107. PMID 23181609 DOI: 10.1186/gb-2012-13-11-r107  1
2012 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. 13: 633. PMID 23157412 DOI: 10.1186/1471-2164-13-633  1
2012 Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. Wiley Interdisciplinary Reviews. Rna. 3: 759-78. PMID 22991327 DOI: 10.1002/wrna.1134  1
2012 Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annual Review of Biochemistry. 81: 145-66. PMID 22663078 DOI: 10.1146/annurev-biochem-051410-092902  1
2012 Hacisuleyman E, Cabili MN, Rinn JL. A Keystone for ncRNA. Genome Biology. 13: 315. PMID 22632630 DOI: 10.1186/gb-2012-13-5-315  1
2012 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. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/nprot.2012.016  1
2012 Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 482: 339-46. PMID 22337053 DOI: 10.1038/nature10887  1
2012 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 & Development. 26: 338-43. PMID 22302877 DOI: 10.1101/gad.182121.111  1
2012 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, ... ... Rinn JL, et al. Programming human pluripotent stem cells into white and brown adipocytes. Nature Cell Biology. 14: 209-19. PMID 22246346 DOI: 10.1038/ncb2411  1
2012 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 Research. 22: 577-91. PMID 22110045 DOI: 10.1101/gr.133009.111  1
2012 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. Nature Biotechnology. 30: 99-104. PMID 22081020 DOI: 10.1038/nbt.2024  1
2011 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 Biology. 12: 137. PMID 22204305 DOI: 10.1186/gb-2011-12-12-137  1
2011 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 & Development. 25: 1915-27. PMID 21890647 DOI: 10.1101/gad.17446611  1
2011 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, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 477: 295-300. PMID 21874018 DOI: 10.1038/nature10398  1
2011 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, et al. The reality of pervasive transcription. Plos Biology. 9: e1000625; discussion. PMID 21765801 DOI: 10.1371/journal.pbio.1000625  1
2011 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 Biology. 12: R56. PMID 21689454 DOI: 10.1186/gb-2011-12-6-r56  1
2011 Rinn JL, Huarte M. To repress or not to repress: this is the guardian's question. Trends in Cell Biology. 21: 344-53. PMID 21601459 DOI: 10.1016/j.tcb.2011.04.002  1
2011 Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology. 12: R22. PMID 21410973 DOI: 10.1186/gb-2011-12-3-r22  1
2011 Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Seminars in Cell & Developmental Biology. 22: 359-65. PMID 21333748 DOI: 10.1016/j.semcdb.2011.02.016  1
2011 Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis. Nature Reviews. Genetics. 12: 136-49. PMID 21245830 DOI: 10.1038/nrg2904  1
2010 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, et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genetics. 42: 1113-7. PMID 21057500 DOI: 10.1038/ng.710  1
2010 Khavari DA, Sen GL, Rinn JL. DNA methylation and epigenetic control of cellular differentiation. Cell Cycle (Georgetown, Tex.). 9: 3880-3. PMID 20890116 DOI: 10.4161/cc.9.19.13385  1
2010 Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature. 467: 103-7. PMID 20811459 DOI: 10.1038/nature09322  1
2010 Huarte M, Rinn JL. Large non-coding RNAs: missing links in cancer? Human Molecular Genetics. 19: R152-61. PMID 20729297 DOI: 10.1093/hmg/ddq353  1
2010 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. 142: 409-19. PMID 20673990 DOI: 10.1016/j.cell.2010.06.040  1
2010 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. Nature Genetics. 42: 626-30. PMID 20512147 DOI: 10.1038/ng.593  1
2010 Kellis M, Rinn JL. Sequences to systems. Genome Biology. 11: 303. PMID 20500907 DOI: 10.1186/gb-2010-11-5-303  1
2010 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. Nature Biotechnology. 28: 503-10. PMID 20436462 DOI: 10.1038/nbt.1633  1
2010 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, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 464: 1071-6. PMID 20393566 DOI: 10.1038/nature08975  1
2010 Koziol MJ, Rinn JL. RNA traffic control of chromatin complexes. Current Opinion in Genetics & Development. 20: 142-8. PMID 20362426 DOI: 10.1016/j.gde.2010.03.003  1
2010 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. 464: 922-6. PMID 20336069 DOI: 10.1038/nature08866  1
2009 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, ... ... Rinn JL, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (New York, N.Y.). 326: 257-63. PMID 19729616 DOI: 10.1126/science.1179050  1
2009 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. Proceedings of the National Academy of Sciences of the United States of America. 106: 11667-72. PMID 19571010 DOI: 10.1073/pnas.0904715106  1
2009 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 (Dayton, Ohio). 27: 1654-65. PMID 19544454 DOI: 10.1002/stem.90  1
2009 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. 4: 129-40. PMID 19200802 DOI: 10.1016/j.stem.2008.11.015  1
2009 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, ... ... Rinn JL, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458: 223-7. PMID 19182780 DOI: 10.1038/nature07672  1
2008 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. The Journal of Clinical Investigation. 118: 1712-26. PMID 18414681 DOI: 10.1172/JCI34523  1
2008 Rinn JL, Wang JK, Liu H, Montgomery K, van de Rijn M, Chang HY. A systems biology approach to anatomic diversity of skin. The Journal of Investigative Dermatology. 128: 776-82. PMID 18337710 DOI: 10.1038/sj.jid.5700986  1
2008 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 & Development. 22: 303-7. PMID 18245445 DOI: 10.1101/gad.1610508  1
2008 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 (New York, N.Y.). 14: 491-502. PMID 18218704 DOI: 10.1261/rna.665008  1
2007 Khavari TA, Rinn J. Ras/Erk MAPK signaling in epidermal homeostasis and neoplasia. Cell Cycle (Georgetown, Tex.). 6: 2928-31. PMID 18000402  1
2007 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. 449: 689-94. PMID 17851529 DOI: 10.1038/nature06192  1
2007 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. 129: 1311-23. PMID 17604720 DOI: 10.1016/j.cell.2007.05.022  1
2007 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 Genetics. 3: e89. PMID 17542650 DOI: 10.1371/journal.pgen.0030089  1
2007 Sayward FG, Yang J, Nelson FK, Euskirchen G, Urban AE, Bertone P, Rinn J, Weissman S, Gerstein M, Snyder M, Miller PL. Design issues in implementing a portable Sample Tracking and Analysis Research Support (STARS) system for PCR based microarray research 2006 Ieee Conference On Information Sciences and Systems, Ciss 2006 - Proceedings. 1578-1598. DOI: 10.1109/CISS.2006.286390  1
2006 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. The Journal of Experimental Medicine. 203: 2727-35. PMID 17116738 DOI: 10.1084/jem.20061864  1
2006 Rinn JL, Bondre C, Gladstone HB, Brown PO, Chang HY. Anatomic demarcation by positional variation in fibroblast gene expression programs. Plos Genetics. 2: e119. PMID 16895450 DOI: 10.1371/journal.pgen.0020119  1
2005 Rinn JL, Snyder M. Sexual dimorphism in mammalian gene expression. Trends in Genetics : Tig. 21: 298-305. PMID 15851067 DOI: 10.1016/j.tig.2005.03.005  1
2004 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 (New York, N.Y.). 306: 2242-6. PMID 15539566 DOI: 10.1126/science.1103388  1
2004 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. Developmental Cell. 6: 791-800. PMID 15177028 DOI: 10.1016/j.devcel.2004.05.005  1
2004 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. Molecular and Cellular Biology. 24: 3804-14. PMID 15082775 DOI: 10.1128/MCB.24.9.3804-3814.2004  1
2003 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, et al. Identification of novel functional elements in the human genome. Cold Spring Harbor Symposia On Quantitative Biology. 68: 317-22. PMID 15338632  1
2003 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. Proceedings of the National Academy of Sciences of the United States of America. 100: 12247-52. PMID 14527995 DOI: 10.1073/pnas.2135255100  1
2003 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 & Development. 17: 529-40. PMID 12600945 DOI: 10.1101/gad.1055203  1
2000 Fitzakerley JL, Star KV, Rinn JL, Elmquist BJ. Expression of Shal potassium channel subunits in the adult and developing cochlear nucleus of the mouse. Hearing Research. 147: 31-45. PMID 10962171 DOI: 10.1016/S0378-5955(00)00118-0  1
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2018 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, et al. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nature Genetics. PMID 29358654 DOI: 10.1038/s41588-017-0034-3  0.28
2019 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 Research. 29: 1705-1718. PMID 31548358 DOI: 10.1101/gr.252981.119  0.24
2019 Barutcu AR, Blencowe BJ, Rinn JL. Differential contribution of steady-state RNA and active transcription in chromatin organization. Embo Reports. e48068. PMID 31448565 DOI: 10.15252/embr.201948068  0.24
2018 Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. The Journal of Cell Biology. PMID 30181316 DOI: 10.1083/jcb.201806052  0.24
2018 Maass PG, Weise A, Rittscher K, Lichtenwald J, Barutcu AR, Liehr T, Aydin A, Wefeld-Neuenfeld Y, Pölsler L, Tinschert S, Rinn JL, Luft FC, Bähring S. Reorganization of chromosomal interactions in the 2q37-deletion syndrome. The Embo Journal. PMID 29921581 DOI: 10.15252/embj.201696257  0.24
2018 Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nature Communications. 9: 1444. PMID 29654311 DOI: 10.1038/s41467-018-03614-0  0.24
2018 Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Molecular Cell. 70: 188-189. PMID 29625035 DOI: 10.1016/j.molcel.2018.03.021  0.24
2018 Maass PG, Barutcu AR, Weiner CL, Rinn JL. Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Molecular Cell. PMID 29526697 DOI: 10.1016/j.molcel.2018.02.007  0.24
2018 Maass PG, Barutcu AR, Shechner DM, Weiner CL, Melé M, Rinn JL. Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Nature Structural & Molecular Biology. PMID 29343869 DOI: 10.1038/s41594-017-0015-3  0.24
2018 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. The Embo Journal. PMID 29335281 DOI: 10.15252/embj.201798452  0.2
2017 Younger ST, Rinn JL. p53 regulates enhancer accessibility and activity in response to DNA damage. Nucleic Acids Research. 45: 9889-9900. PMID 28973438 DOI: 10.1093/nar/gkx577  0.2
2016 Melé M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Research. PMID 27927715 DOI: 10.1101/gr.214205.116  0.2
2016 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. Nature Communications. 7: 10982. PMID 26975529 DOI: 10.1038/ncomms10982  0.2
2016 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. Nature Communications. 7: 10406. PMID 26832224 DOI: 10.1038/ncomms10406  0.2
2017 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 ISA, ... ... Rinn JL, et al. lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. Elife. 6. PMID 28875933 DOI: 10.7554/eLife.25607  0.16
2016 Kelley DR, Snoek J, Rinn J. Basset: Learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Research. PMID 27197224 DOI: 10.1101/gr.200535.115  0.16
2016 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 27078102 DOI: 10.1073/pnas.1602886113  0.16
2019 Raj A, Rinn JL. Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harbor Perspectives in Biology. 11. PMID 31043413 DOI: 10.1101/cshperspect.a032094  0.04
2015 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. Nature Biotechnology. PMID 26501951 DOI: 10.1038/nbt.3388  0.04
2019 Smallegan MJ, Rinn JL. Linking long noncoding RNA to drug resistance. Proceedings of the National Academy of Sciences of the United States of America. PMID 31601736 DOI: 10.1073/pnas.1915690116  0.01
2019 Rowland TJ, Dumbović G, Hass EP, Rinn JL, Cech TR. Single-cell imaging reveals unexpected heterogeneity of telomerase reverse transcriptase expression across human cancer cell lines. Proceedings of the National Academy of Sciences of the United States of America. PMID 31451652 DOI: 10.1073/pnas.1908275116  0.01
2017 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. 6. PMID 29239719 DOI: 10.7554/eLife.29224  0.01
2017 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 & Development. PMID 28698299 DOI: 10.1101/gad.284661.116  0.01
2016 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. 17: 707. PMID 27595844 DOI: 10.1186/s12864-016-3060-0  0.01
2016 Melé M, Rinn JL. "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. Molecular Cell. 62: 657-64. PMID 27259198 DOI: 10.1016/j.molcel.2016.05.011  0.01
2015 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. 16: 454. PMID 26070627 DOI: 10.1186/s12864-015-1603-4  0.01
2015 Kristen AV, Rinn J, Hegenbart U, Lindenmaier D, Merkle C, Röcken C, Hardt S, Giannitsis E, Katus HA. Improvement of risk assessment in systemic light-chain amyloidosis using human placental growth factor. Clinical Research in Cardiology : Official Journal of the German Cardiac Society. 104: 250-7. PMID 25331161 DOI: 10.1007/s00392-014-0779-y  0.01
2008 Memmel T, Geyer F, Rinn J, Reiterer H. A zoom-based specification tool for corporate user interface development McCsis'08 - Iadis Multi Conference On Computer Science and Information Systems; Proceedings of Interfaces and Human Computer Interaction 2008. 368-370.  0.01
2008 Memmel T, Geyer F, Rinn J, Reiterer H. Tool-support for interdisciplinary and collaborative user interface specification McCsis'08 - Iadis Multi Conference On Computer Science and Information Systems; Proceedings of Interfaces and Human Computer Interaction 2008. 51-60.  0.01
2006 Rinn JP, Schwella N, Wollmer E, Jaques G, Heinzel-Gutenbrunner M, Strassmann G, Gross MW, Movassaghi K, Neubauer A, Ritter M. Local irradiation prior to stem cell harvest has no influence on CD34+ yield: a quantitative analysis. Annals of Hematology. 85: 38-44. PMID 16012838 DOI: 10.1007/s00277-005-1078-5  0.01
2006 De Rijk G, Bajko M, Cornelis M, Fessia P, Miles J, Modena M, Molinari G, Rinn J, Savary F, Vlogaert J. Electrical integrity tests during production of the LHC dipoles Ieee Transactions On Applied Superconductivity. 16: 200-203. DOI: 10.1109/TASC.2006.870501  0.01
2005 De Rijk G, Bajko M, Cornelis M, Durante M, Fessia P, Miles J, Modena M, Molinari G, Rinn J, Savary F, Schirm K, Simon F, Tommasini D, Tortschanoff T, Vlogaert J. Status report on the LHC main magnet production Ieee Transactions On Applied Superconductivity. 15: 1078-1083. DOI: 10.1109/TASC.2005.849500  0.01
2003 Modena M, Bajko M, Cornelis M, Fessia P, Miles J, Pugnat P, Rinn J, De Rijk G, Savary F, Siemko A, Todesco E, Vlogaert J. Status of the LHC Main Dipole pre-series production Proceedings of the Ieee Particle Accelerator Conference. 3: 1942-1944.  0.01
1965 Rinn JL. Structure of phenomenal domains. Psychological Review. 72: 445-66. PMID 5322171 DOI: 10.1037/h0022795  0.01
1963 RINN JL. Group behavior descriptions: an nonmetric multidimensional analysis. Journal of Abnormal and Social Psychology. 67: 173-6. PMID 13973999 DOI: 10.1037/h0045632  0.01
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