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Global analyses of the dynamics of mammalian microRNA metabolism.

Kingston ER, Bartel DP.

Genome Res. 2019 Nov;29(11):1777-1790. doi: 10.1101/gr.251421.119. Epub 2019 Sep 13.


m6A modification of a 3' UTR site reduces RME1 mRNA levels to promote meiosis.

Bushkin GG, Pincus D, Morgan JT, Richardson K, Lewis C, Chan SH, Bartel DP, Fink GR.

Nat Commun. 2019 Jul 30;10(1):3414. doi: 10.1038/s41467-019-11232-7.


Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns.

Kwasnieski JC, Orr-Weaver TL, Bartel DP.

Genome Res. 2019 Jul;29(7):1188-1197. doi: 10.1101/gr.242164.118. Epub 2019 Jun 24.


Excised linear introns regulate growth in yeast.

Morgan JT, Fink GR, Bartel DP.

Nature. 2019 Jan;565(7741):606-611. doi: 10.1038/s41586-018-0828-1. Epub 2019 Jan 16.


Genetic dissection of the miR-200-Zeb1 axis reveals its importance in tumor differentiation and invasion.

Title AC, Hong SJ, Pires ND, Hasenöhrl L, Godbersen S, Stokar-Regenscheit N, Bartel DP, Stoffel M.

Nat Commun. 2018 Nov 7;9(1):4671. doi: 10.1038/s41467-018-07130-z.


Predicting microRNA targeting efficacy in Drosophila.

Agarwal V, Subtelny AO, Thiru P, Ulitsky I, Bartel DP.

Genome Biol. 2018 Oct 4;19(1):152. doi: 10.1186/s13059-018-1504-3.


The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs.

Guenther UP, Weinberg DE, Zubradt MM, Tedeschi FA, Stawicki BN, Zagore LL, Brar GA, Licatalosi DD, Bartel DP, Weissman JS, Jankowsky E.

Nature. 2018 Jul;559(7712):130-134. doi: 10.1038/s41586-018-0258-0. Epub 2018 Jun 27.


A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain.

Kleaveland B, Shi CY, Stefano J, Bartel DP.

Cell. 2018 Jul 12;174(2):350-362.e17. doi: 10.1016/j.cell.2018.05.022. Epub 2018 Jun 7.


New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi.

Vyas VK, Bushkin GG, Bernstein DA, Getz MA, Sewastianik M, Barrasa MI, Bartel DP, Fink GR.

mSphere. 2018 Apr 25;3(2). pii: e00154-18. doi: 10.1128/mSphere.00154-18. Print 2018 Apr 25.


Metazoan MicroRNAs.

Bartel DP.

Cell. 2018 Mar 22;173(1):20-51. doi: 10.1016/j.cell.2018.03.006. Review.


A Seed Mismatch Enhances Argonaute2-Catalyzed Cleavage and Partially Rescues Severely Impaired Cleavage Found in Fish.

Chen GR, Sive H, Bartel DP.

Mol Cell. 2017 Dec 21;68(6):1095-1107.e5. doi: 10.1016/j.molcel.2017.11.032.


The influence of microRNAs and poly(A) tail length on endogenous mRNA-protein complexes.

Rissland OS, Subtelny AO, Wang M, Lugowski A, Nicholson B, Laver JD, Sidhu SS, Smibert CA, Lipshitz HD, Bartel DP.

Genome Biol. 2017 Oct 31;18(1):211. doi: 10.1186/s13059-017-1330-z.


Widespread Influence of 3'-End Structures on Mammalian mRNA Processing and Stability.

Wu X, Bartel DP.

Cell. 2017 May 18;169(5):905-917.e11. doi: 10.1016/j.cell.2017.04.036.


kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences.

Wu X, Bartel DP.

Nucleic Acids Res. 2017 Jul 3;45(W1):W534-W538. doi: 10.1093/nar/gkx323.


Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways.

Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schöndorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S.

Cell Syst. 2017 Feb 22;4(2):157-170.e14. doi: 10.1016/j.cels.2016.12.011. Epub 2017 Jan 25.


Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression.

Denzler R, McGeary SE, Title AC, Agarwal V, Bartel DP, Stoffel M.

Mol Cell. 2016 Nov 3;64(3):565-579. doi: 10.1016/j.molcel.2016.09.027. Epub 2016 Oct 27.


RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria.

Guo JU, Bartel DP.

Science. 2016 Sep 23;353(6306). pii: aaf5371.


mRNA poly(A)-tail changes specified by deadenylation broadly reshape translation in Drosophila oocytes and early embryos.

Eichhorn SW, Subtelny AO, Kronja I, Kwasnieski JC, Orr-Weaver TL, Bartel DP.

Elife. 2016 Jul 30;5. pii: e16955. doi: 10.7554/eLife.16955.


Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation.

Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP.

Cell Rep. 2016 Feb 23;14(7):1787-1799. doi: 10.1016/j.celrep.2016.01.043. Epub 2016 Feb 11.


The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes.

Fang W, Bartel DP.

Mol Cell. 2015 Oct 1;60(1):131-45. doi: 10.1016/j.molcel.2015.08.015. Epub 2015 Sep 24.


Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs.

Wong SF, Agarwal V, Mansfield JH, Denans N, Schwartz MG, Prosser HM, Pourquié O, Bartel DP, Tabin CJ, McGlinn E.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4884-93. doi: 10.1073/pnas.1512655112. Epub 2015 Aug 17.


Predicting effective microRNA target sites in mammalian mRNAs.

Agarwal V, Bell GW, Nam JW, Bartel DP.

Elife. 2015 Aug 12;4. doi: 10.7554/eLife.05005.


Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I.

Cell Rep. 2015 May 19;11(7):1110-22. doi: 10.1016/j.celrep.2015.04.023. Epub 2015 May 7.


Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation.

Koppstein D, Ashour J, Bartel DP.

Nucleic Acids Res. 2015 May 26;43(10):5052-64. doi: 10.1093/nar/gkv333. Epub 2015 Apr 21.


mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues.

Eichhorn SW, Guo H, McGeary SE, Rodriguez-Mias RA, Shin C, Baek D, Hsu SH, Ghoshal K, Villén J, Bartel DP.

Mol Cell. 2014 Oct 2;56(1):104-15. doi: 10.1016/j.molcel.2014.08.028. Epub 2014 Sep 25.


Expanded identification and characterization of mammalian circular RNAs.

Guo JU, Agarwal V, Guo H, Bartel DP.

Genome Biol. 2014 Jul 29;15(7):409. doi: 10.1186/s13059-014-0409-z.


Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition.

Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL.

Cell Rep. 2014 Jun 12;7(5):1495-1508. doi: 10.1016/j.celrep.2014.05.002. Epub 2014 May 29.


Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance.

Denzler R, Agarwal V, Stefano J, Bartel DP, Stoffel M.

Mol Cell. 2014 Jun 5;54(5):766-76. doi: 10.1016/j.molcel.2014.03.045. Epub 2014 May 1.


Global analyses of the effect of different cellular contexts on microRNA targeting.

Nam JW, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, Yildirim MA, Rodriguez A, Bartel DP.

Mol Cell. 2014 Mar 20;53(6):1031-1043. doi: 10.1016/j.molcel.2014.02.013. Epub 2014 Mar 13.


Poly(A)-tail profiling reveals an embryonic switch in translational control.

Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP.

Nature. 2014 Apr 3;508(7494):66-71. doi: 10.1038/nature13007. Epub 2014 Jan 29.


3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts.

Spies N, Burge CB, Bartel DP.

Genome Res. 2013 Dec;23(12):2078-90. doi: 10.1101/gr.156919.113. Epub 2013 Sep 26.


lincRNAs: genomics, evolution, and mechanisms.

Ulitsky I, Bartel DP.

Cell. 2013 Jul 3;154(1):26-46. doi: 10.1016/j.cell.2013.06.020. Review.


Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme.

Curtis EA, Bartel DP.

RNA. 2013 Aug;19(8):1116-28. doi: 10.1261/rna.037572.112. Epub 2013 Jun 24.


Stalled spliceosomes are a signal for RNAi-mediated genome defense.

Dumesic PA, Natarajan P, Chen C, Drinnenberg IA, Schiller BJ, Thompson J, Moresco JJ, Yates JR 3rd, Bartel DP, Madhani HD.

Cell. 2013 Feb 28;152(5):957-68. doi: 10.1016/j.cell.2013.01.046. Epub 2013 Feb 14.


Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing.

Auyeung VC, Ulitsky I, McGeary SE, Bartel DP.

Cell. 2013 Feb 14;152(4):844-58. doi: 10.1016/j.cell.2013.01.031.


Extensive alternative polyadenylation during zebrafish development.

Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP.

Genome Res. 2012 Oct;22(10):2054-66. doi: 10.1101/gr.139733.112. Epub 2012 Jun 21.


Structure of yeast Argonaute with guide RNA.

Nakanishi K, Weinberg DE, Bartel DP, Patel DJ.

Nature. 2012 Jun 20;486(7403):368-74. doi: 10.1038/nature11211.


Long noncoding RNAs in C. elegans.

Nam JW, Bartel DP.

Genome Res. 2012 Dec;22(12):2529-40. doi: 10.1101/gr.140475.112. Epub 2012 Jun 15.


Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos.

Nodine MD, Bartel DP.

Nature. 2012 Jan 22;482(7383):94-7. doi: 10.1038/nature10756.


Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.

Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP.

Cell. 2011 Dec 23;147(7):1537-50. doi: 10.1016/j.cell.2011.11.055. Erratum in: Cell. 2012 Oct 26;151(3):684-6.


Candida albicans Dicer (CaDcr1) is required for efficient ribosomal and spliceosomal RNA maturation.

Bernstein DA, Vyas VK, Weinberg DE, Drinnenberg IA, Bartel DP, Fink GR.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):523-8. doi: 10.1073/pnas.1118859109. Epub 2011 Dec 15.


MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes.

Rissland OS, Hong SJ, Bartel DP.

Mol Cell. 2011 Sep 16;43(6):993-1004. doi: 10.1016/j.molcel.2011.08.021.


Compatibility with killer explains the rise of RNAi-deficient fungi.

Drinnenberg IA, Fink GR, Bartel DP.

Science. 2011 Sep 16;333(6049):1592. doi: 10.1126/science.1209575.


Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.

Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP.

Nat Struct Mol Biol. 2011 Sep 11;18(10):1139-46. doi: 10.1038/nsmb.2115.


The structural basis of RNA-catalyzed RNA polymerization.

Shechner DM, Bartel DP.

Nat Struct Mol Biol. 2011 Aug 21;18(9):1036-42. doi: 10.1038/nsmb.2107.


The inside-out mechanism of Dicers from budding yeasts.

Weinberg DE, Nakanishi K, Patel DJ, Bartel DP.

Cell. 2011 Jul 22;146(2):262-76. doi: 10.1016/j.cell.2011.06.021.


Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs.

Schnall-Levin M, Rissland OS, Johnston WK, Perrimon N, Bartel DP, Berger B.

Genome Res. 2011 Sep;21(9):1395-403. doi: 10.1101/gr.121210.111. Epub 2011 Jun 17.


A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.

Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA.

Nat Struct Mol Biol. 2011 Jan;18(1):100-6. doi: 10.1038/nsmb.1945. Epub 2010 Dec 12.


MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis.

Nodine MD, Bartel DP.

Genes Dev. 2010 Dec 1;24(23):2678-92. doi: 10.1101/gad.1986710.


Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.

Jan CH, Friedman RC, Ruby JG, Bartel DP.

Nature. 2011 Jan 6;469(7328):97-101. doi: 10.1038/nature09616. Epub 2010 Nov 17.

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