2024 |
|||
Xiang, K., J. Ly, D.P. Bartel. 2024. Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos. Dev Cell 59:1–17.
|
|||
2023 |
|||
Wang, P.Y. and D.P. Bartel. 2023. The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. biorxiv https://doi.org/10.1101/2023.10.15.562437
|
Shi, C.Y., L.E. Elcavage, R.R. Chivukula, J. Stefano, B. Kleaveland, D.P. Bartel. 2023. ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development. Genome Res 33:1482–1496.
|
||
Wang, P.Y. and D.P. Bartel. 2023. A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data. BMC Bioinform 24:195.
|
|||
2022 |
|||
Kingston, E.R., L.W. Blodgett, D.P. Bartel. 2022. Endogenous transcripts direct microRNA degradation in Drosophila, and this targeted degradation is required for proper embryonic development. Mol Cell 82:1-13.
|
|||
Hallacli, E., C. Kayatekin, S. Nazeen, X.H. Wang, Z. Sheinkopf, S. Sathyakumar, S. Sarkar, X. Jiang, X. Dong, R. Di Maio, W. Wang, M.T. Keeney, D. Felsky, J. Sandoe, A. Vahdatshoar, N.D. Udeshi, D.R. Mani, S.A. Carr, S. Lindquist, P.L. De Jager, D.P. Bartel, C.L. Myers, J.T. Greenamyre, M.B. Feany, S.R. Sunyaev, C.Y. Chung, V. Khurana. 2022. The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 185:2035–2056.
|
|||
Eisen, T.J., J.J. Li, D.P. Bartel. 2022. The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation. RNA 28:808–831.
|
|||
McGeary, S.E., N. Bisaria, T.M. Pham, P.Y. Wang, D.P. Bartel. 2022. MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position. eLife 11:e69803.
|
|||
2021 |
|||
Yang, J.Y., W. Fang, F. Miranda-Sanchez, J.M. Brown, K.M. Kauffman, C.M. Acevero, D.P. Bartel, M.F. Polz, L. Kelly. 2017. Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Syst 12:771–779.
|
|||
Xiang, K. and D.P. Bartel. 2021. The molecular basis of coupling between poly(A)-tail length and translational efficiency. eLife 10:e66493.
|
|||
Kingston, E.R. and D.P. Bartel. 2021. Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2′-O-methylation. RNA 27:710–724.
|
|||
2020 |
|||
Shi, C.Y., E.R. Kingston, B. Kleaveland, D.H. Lin, M.W. Stubna, D.P. Bartel. 2020. The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. Science 370:eabc9359.
|
|||
Briskin, D., P.Y. Wang, D.P. Bartel. 2020. The biochemical basis for the cooperative action of microRNAs. Proc Natl Acad Sci 117:17764-17774.
|
|||
Getz, M.A., D.E. Weinberg, I.A. Drinnenberg, G.R. Fink, D.P. Bartel. 2020. Xrn1p acts at multiple steps in the budding-yeast RNAi pathway to enhance the efficiency of silencing. Nucleic Acids Res 48:7404-7420.
|
|||
Fang, W. and D.P. Bartel. 2020. MicroRNA clustering assists processing of suboptimal microRNA hairpins through the action of the ERH protein. Mol Cell 78:289-302.
|
|||
Eisen, T.J., S.W. Eichhorn, A.O. Subtelny, D.P. Bartel. 2020. MicroRNAs cause accelerated decay of short-tailed target mRNAs. Mol Cell 77:775-785.
|
|||
Eisen, T.J., S.W. Eichhorn, A.O. Subtelny, K.S. Lin, S.E. McGeary, S. Gupta, D.P. Bartel. 2020. The dynamics of cytoplasmic mRNA metabolism. Mol Cell 77:786-799.
|
|||
2019 |
|||
McGeary, S.E., K.S. Lin, C.Y. Shi, T.M. Pham, N. Bisaria, G.M. Kelley, D.P. Bartel. 2019. The biochemical basis of microRNA targeting efficacy. Science 366:eaav1741. transcript references
|
|||
Kingston, E.R. and D.P. Bartel. 2019. Global analyses of the dynamics of mammalian microRNA metabolism. Genome Res 29:1777-90.
|
|||
Bushkin, G.G., D. Pincus, J.T. Morgan, K. Richardson, C. Lewis, S.H. Chan, D.P. Bartel, G.R. Fink. 2019. m6A modification of a 3′ UTR site reduces RME1 mRNA levels to promote meiosis. Nat Commun 10(1):3414.
|
|||
Kwasnieski, J.C., T.L. Orr-Weaver, D.P. Bartel. 2019. Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns. Genome Res 29:1188-97.
|
|||
Morgan, J.T., G.R. Fink, D.P. Bartel. 2019. Excised linear introns regulate growth in yeast. Nature 565:606-11.
|
|||
2018 |
|||
Title, A.C., S.J. Hong, N.D. Pires, L. Hasenöhrl, S. Godbersen, N. Stokar-Regenscheit, D.P. Bartel, M. Stoffel. 2018. Genetic dissection of the miR-200-Zeb1 axis reveals its importance in tumor differentiation and invasion. Nat Commun 9(1):4671.
|
|||
Agarwal, V., A.O. Subtelny, P. Thiru, I. Ulitsky, D.P. Bartel. 2018. Predicting microRNA targeting efficacy in Drosophila. Genome Biol 19:152.
|
|||
Guenther, U.P., D.E. Weinberg, M.M. Zubradt, F.A. Tedeschi, B.N. Stawicki, L.L. Zagore, G.A. Brar, D.D. Licatalosi, D.P. Bartel, J.S. Weissman, E. Jankowsky. 2018. The helicase Ded1p controls use of near-cognate translation initiation codons in 5′ UTRs. Nature 559:130-4.
|
|||
Kleaveland, B., C.Y. Shi, J. Stefano, D.P. Bartel. 2018. A network of noncoding regulatory RNAs acts in the mammalian brain. Cell 174:350-62.
|
|||
Vyas, V.K., G.G. Bushkin, D.A. Bernstein, M.A. Getz, M. Sewastianik, M.I. Barrasa, D.P. Bartel, G.R. Fink. 2018. New CRISPR mutagenesis strategies reveal variation in repair mechanisms among fungi. mSphere 3(2):e00154-18.
|
|||
Bartel, D.P. 2018. Metazoan microRNAs. Cell 173:20-51. (Review)
|
|||
2017 |
|||
Chen, G.R., H. Sive, D.P. Bartel. 2017. A seed mismatch enhances Argonaute2-catalyzed cleavage and partially rescues severely impaired cleavage found in fish. Mol Cell 68:1095-1107.
|
|||
Rissland, O.S., A.O. Subtelny, M. Wang, A. Lugowski, B. Nicholson, J.D. Laver, S.S. Sidhu, C.A. Smibert, H.D. Lipshitz, D.P. Bartel. 2017. The influence of microRNAs and poly(A) tail length on endogenous mRNA–protein complexes. Genome Biol 18:211.
|
|||
Wu, X. and D.P. Bartel. 2017. Widespread influence of 3′-end structures on mammalian mRNA processing and stability. Cell 169:905–917.
|
|||
Wu, X. and D.P. Bartel. 2017. kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences. Nucleic Acids Res W1:gkx323. Webserver
|
|||
Khurana, V., J. Peng, C.Y. Chung, P.K. Auluck, S. Fanning, D.F. Tardiff , T. Bartels, M. Koeva, S.W. Eichhorn, H. Benyamini, Y. Lou, A. Nutter-Upham, V. Baru, Y. Freyzon, N. Tuncbag, M. Costanzo, B.J. San Luis, D.C. Schöndorf, M.I. Barrasa, S. Ehsani, N. Sanjana, Q. Zhong, T. Gasser, D.P. Bartel, M. Vidal, M. Deleidi, C. Boone, E. Fraenkel, B. Berger, S. Lindquist, 2017. Genome-scale networks link neurodegenerative disease genes to α-synuclein through specific molecular pathways. Cell Syst 4:157-170.
|
|||
2016 |
|||
Denzler, R., S.E. McGeary, A.C. Title, V. Agarwal, D.P. Bartel, M. Stoffel, 2016. Impact of microRNA levels, target-site complementarity, and cooperativity on competing endogenous RNA-regulated gene expression. Mol Cell 64:565-579.
|
|||
Guo, J.U. and D.P. Bartel, 2016. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science 353:aaf5371. transcript references
|
|||
Eichhorn, S.W., A.O. Subtelny, I. Kronja, J.C. Kwasnieski, T.L. Orr-Weaver, D.P. Bartel, 2016. mRNA poly(A)-tail changes specified by deadenylation broadly reshape translation in Drosophila oocytes and early embryos. eLife 5:e16955.
|
|||
Weinberg, D.E., P. Shah, S.W. Eichhorn, J.A. Hussmann, J.B. Plotkin, D.P. Bartel, 2016. Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. Cell Rep 14:1787-1799.
|
|||
2015 |
|||
Fang, W., D.P. Bartel, 2015. The menu of features that define primary microRNAs and enable de novo design of microRNA genes. Mol Cell 60:131-145.
|
|||
Wong, S.F.L., V. Agarwal, J.H. Mansfield, N. Denans, M.G. Schwartz, H.M. Prosser, O. Pourquié, D.P. Bartel, C.J. Tabin, and E. McGlinn, 2015. Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs. Proc Natl Acad Sci 112:E4884-E4893.
|
|||
Agarwal, V., G.W. Bell, J-W. Nam, and D.P. Bartel. 2015. Predicting effective microRNA target sites in mammalian mRNAs. eLife 4:e05005. Supplemental Material. eLife Lens view
|
|||
Hezroni, H., D. Koppstein, A.G. Schwartz, A. Avrutin, D.P. Bartel, and I. Ulitsky. 2015. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep 11:1110-1122.
|
|||
Koppstein, D., J. Ashour, and D.P. Bartel. 2015. Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation. Nucleic Acid Res 43:5052-5064. Supplemental Material
|
|||
2014 |
|||
Eichhorn, S.W., H. Guo, S.E. McGeary, R.A. Rodriguez-Mias, C. Shin, D. Baek, S.H. Hsu, K. Ghoshal, J. Villén, and D.P. Bartel. 2014. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 56:104-115. Supplemental Material
|
|||
Guo, J.U., V. Agarwal, H. Guo, and D.P. Bartel. 2014. Expanded identification and characterization of mammalian circular RNAs. Genome Biol 15:409.
|
|||
Kronja, I., B. Yuan, S.W. Eichhorn, K. Dzeyk, J. Krijgsveld, D.P. Bartel, and T.L. Orr-Weaver. 2014. Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition. Cell Rep 7:1495-508.
|
|||
Denzler, R., V. Agarwal, J. Stefano, D.P. Bartel, and M. Stoffel. 2014. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell 54:766-776.
|
|||
Subtelny, A.O., S.W. Eichhorn, G.R. Chen, H. Sive, and D.P. Bartel. 2014. Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508:66-71. Supplemental Material
|
|||
Nam, J-W, O.S. Rissland, D. Koppstein, C. Abreu-Goodger, C.H. Jan, V. Agarwal, M.A. Yildirim, A. Rodriguez, and D.P. Bartel. 2014. Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell 53:1031-1043. Supplemental Material
|
|||
2013 |
|||
Spies, N., C.B. Burge, and D.P. Bartel. 2013. 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res 23:2078-2090.
|
|||
Curtis, E.A. and D.P. Bartel. 2013. Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme. RNA 19:1116-1128.
|
|||
Ulitsky I. and D.P. Bartel. 2013. lincRNAs: genomics, evolution, and mechanisms. Cell 154:26-46.
|
|||
Dumesic, P.A., P. Natarajan, C. Chen, I.A. Drinnenberg, B.J. Schiller, J. Thompson, J.J. Moresco, J.R. Yates III, D.P. Bartel, and H.D. Madhani. 2013. Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 152:957–968.
|
|||
Auyeung, V.C., I. Ulitsky, S.E. McGeary, and D.P. Bartel. 2013. Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152:844-858.
|
|||
2012 |
|||
Nam, J-W. and D.P. Bartel. 2012. Long non-coding RNAs in C. elegans . Genome Res 22:2529-2540. Supplemental Material
|
Ulitsky, I., A. Shkumatava, C.H. Jan, A.O. Subtelny, D. Koppstein, G.W. Bell, H. Sive, and D.P. Bartel. 2012. Extensive alternative polyadenylation during zebrafish development . Genome Res 22:2054-2066.
|
||
Nakanishi K., D.E. Weinberg, D.P. Bartel, and D.J. Patel. Structure of yeast Argonaute with guide RNA. Nature 486:368-374.Supplemental Material
|
|||
Nodine, M.D. and D.P. Bartel. 2012. Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 482:94-97 Supplemental Material
|
|||
2011 |
|||
Bernstein, D.A., V.K. Vyas, D.E. Weinberg, I.A. Drinnenberg, D.P. Bartel, and G.R. Fink. 2011. Candida albicans Dicer (CaDcr1) is required for efficient ribosomal and splicesomal RNA maturation. Proc Natl Acad Sci 109:523-528
|
|||
Ulitsky, I., A. Shkumatava, C.H. Jan, H. Sive, and D.P. Bartel. 2011. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147:1537-1550 Supplemental Material
|
|||
Rissland, O.S., S.J. Hong, and D.P. Bartel. 2011. MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes. Mol Cell 43:993-1004 Supplemental Material
|
|||
Drinnenberg, I.A., G.R. Fink, and D.P. Bartel. 2011. Compatibility with killer explains the rise of RNAi-deficient fungi Science 333:1592 Supplemental Material
|
|||
Garcia, D.M. Baek, D. Shin, C. Bell, G.W., Grimson, A., and Bartel, D.P. 2011. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs Nat Struct Mol Biol 18:1036-1042 Supplemental Material
|
|||
Shechner, D.M. and D.P. Bartel. 2011. The structural basis of RNA-catalyzed RNA polymerization Nat Struct Mol Biol 18 :1036-1042 Supplemental Material
|
|||
Weinberg, D.E., K. Nakanishi, D.J. Patel and D.P. Bartel. 2011. The inside-out mechanism of dicers from budding yeasts. Cell 146:262-276. Supplemental Material
|
|||
Schnall-Levin, M., O.S. Rissland, W.K. Johnston, N. Perrimon, D.P. Bartel and B. Berger. 2011. Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res 21:1395-1403 Supplemental Material
|
|||
Koldobskaya, Y., E.M. Duguid, D.M. Shechner, N.B. Suslov, J. Ye,
S.S. Sidhu, D.P. Bartel, S. Koide, A.A. Kossiakoff and J.A.
Piccirilli. 2011. A portable RNA sequence whose recognition by a synthetic antibody facilitates
structural determination.
Nat Struct Mol Biol 18:100-106. Supplemental Material
|
|||
Jan, C.H., R.C. Friedman, J.G. Ruby and D.P. Bartel.
2011. Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature 469:97-102. Supplemental Material
|
|||
2010 |
|||
Nodine, M. and D.P. Bartel.
2010. MicroRNAs prevent precocious gene expression and enable pattern formation
during plant embryogenesis. GenesDev 24:2678-2692. Supplemental Material
|
|||
Guo, H., N.T. Ingolia, J.S. Weissman and D.P. Bartel.
2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-840. Supplemental Material
|
|||
Shin, C., J-W. Nam, K. K-H. Farh, H. R. Chiang, A. Shkumatava, and D.P. Bartel.
2010. Expanding the microRNA targeting code: functional sites
with centered pairing. Mol Cell 38:789-802. Supplemental Material
|
|||
Chiang, H.R., L.W. Schoenfeld, J.G. Ruby, V.C. Auyeung, N. Spies, D. Baek, W.K.
Johnston, C. Russ, S. Luo, J.E. Barbiarz, R. Blelloch, G.P. Schroth,
C. Nusbaum, and D.P. Bartel. 2010. Mammalian microRNAs: experimental evaluation of novel and previously annotated
genes. GenesDev 24:992-1009.
|
|||
2009 |
|||
Shechner, D.M., R.A. Grant, S.C. Bagby, Y. Koldobskaya, J.A. Piccirilli, and D.P. Bartel. 2009. Crystal structure of the catalytic core of an RNA-polymerase ribozyme. Science 326:1271-1275. Supplemental Material |
|||
Bagby, S.C., N.H. Bergman, D.M. Shechner, C. Yen, and D.P. Bartel. 2009. A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions. RNA 15:2129-2146. Supplemental Material |
|||
Drinnenberg, I.A., D.E. Weinberg, K.T. Xie, J.P. Mower, K.H. Wolfe, G.R. Fink, and D.P. Bartel. 2009. RNAi in budding yeast. Science 326:544-550. Supplemental Material |
|||
McGlinn, E., S. Yekta, J. Mansfield, J. Soutschek, D.P. Bartel and and C.J. Tabin. 2009. In ovo application of antagomiRs indictaes a role for miR-196 in patterning the chick axial skeleton through Hox gene regulation. PNAS 106:18610-18615. Supplemental Material |
|||
Mayr, C. and D.P. Bartel. 2009. Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138: 673-684. Supplemental Material |
|||
Kim, J. and D.P. Bartel. 2009. Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Nature Biotechnology 27:472-477. |
|||
Shkumatava, A., A. Stark, H. Sive, and D.P. Bartel. 2009. Coherent but overlapping expression of microRNAs and their targets during vertebrate
development. Genes Dev 23:466-481. Supplemental Material |
|||
Friedman, R.C., K.K. Farh, C.B. Burge, and D.P. Bartel. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92-105. Supplemental Material |
|||
2008 |
|||
Meyers, B.C., M.J. Axtell, B. Bartel, D.P. Bartel, D. Baulcombe,
J.L. Bowman, X. Cao, J.C. Carrington, X. Chen, P.J. Green, S.
Griffiths-Jones, S.E. Jacobsen, A.C. Mallory, R.A. Martienssen,
R.S. Poethig, Y. Qi, H. Vaucheret, O. Voinnet, Y. Watanabe, D.
Wiegel, and J.K. Zhu. 2008. Criteria for annotation of plant microRNAs. Plant Cell 20:3186-3190.
|
|||
Babiarz, J.E., J.G. Ruby, Y. Wang, D.P. Bartel, and R. Blelloch. 2008. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev 22:2773-2785. Supplemental Material |
|||
Grimson, A., M. Srivasatva, B. Fahey, B.J. Woodcroft, H.R. Chiang, N. King, B.M. Degnan, D.S. Rokhsar, and D.P. Bartel. 2008. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455:1193-1197. Supplemental Material |
|||
Yekta, S., C.J. Tabin, and D.P. Bartel. 2008. MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nat Rev Genet 9:789-796. |
|||
Marson, A., S.S. Levine, M.F. Cole, G.M. Frampton, T. Brambrink, S. Johnstone, M.G. Guenther, W.K. Johnston, M. Wernig, J. Newman, J.M. Calabrese, L.M. Dennis, T.L. Volkert, S. Gupta, J. Love, N. Hannett, P.A. Sharp, D.P. Bartel, R. Jaenisch, and R.A. Young. 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134:521-533. |
|||
Bühler, M., N. Spies, D.P. Bartel, and D. Moazed. 2008. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 15:1015-1023. |
|||
Baek, D., J. Villén, C. Shin, F.D. Camargo, S.P. Gygi, and D.P. Bartel. 2008. The impact of microRNAs on protein output. Nature 455:64-71. Supplemental Material |
|||
Batista, P.J., J.G. Ruby, J.M. Claycomb, R. Chiang, N. Fahlgren, K.D. Kasschau, D.A. Chaves, W. Gu, J.J. Vasale, S. Duan, D. Conte Jr., S. Luo, G.P. Schroth, J.C. Carrington, D.P. Bartel, and C.C. Mello. 2008. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell 31:67-78. |
|||
Stark, A., N. Bushati, C.H. Jan, P. Kheradpour, E. Hodges, J. Brennecke, D.P. Bartel, S.M. Cohen, and M. Kellis. 2008. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. GenesDev 22:8-13. Supplemental Material |
|||
Müller, U.F and D.P. Bartel. 2008. Improved polymerase ribozyme efficiency on hydrophobic assemblies. RNA 14:552-62. |
|||
Okamura, K. W.J. Chung, J.G. Ruby, H. Guo, D.P. Bartel, and E.C. Lai. 2008. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453:803-807. Supplemental Material |
|||
Addo-Quaye, C., T.W. Eshoo, D.P. Bartel, and M.J. Axtell. 2008. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis Degradome. CurrBiol 18:758-762. Supplemental Material (1) (2) |
|||
2007 |
|||
Miska, E.A., E. Alvarez-Saavedra, A.L. Abbott, N.C. Lau, A.B. Hellman, S.M. McGonagle, D.P. Bartel, V.R. Ambros, and H.R. Horvitz. 2007. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3:e215. |
|||
Stark, A., M.F. Lin, P. Kheradpour, J.S. Pederson, L. Parts, J.W. Carlson, M.A. Crosby, M.D. Rasmussen, S. Roy, A.N. Deoras, J.G. Ruby, et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-232. |
|||
Ruby, J.G., A. Stark, W.K. Johnston, M. Kellis, D.P. Bartel, and E.C. Lai. 2007. Evolution, biogenesis, expression, and target predictions of a substantially
expanded set of Drosophila microRNAs. Genome Res. 17:1850-1864. Supplemental Material |
|||
Ruby, J.G., C.H. Jan, and D.P. Bartel. 2007. Initronic microRNA precursors that bypass Drosha processing.Nature 448:83-87. Supplemental Material |
|||
Grimson, A.G., K.K. Farh, W.K. Johnston, P. Garrett-Engele, L.P. Lim and D.P. Bartel. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. MolCell 27:91-105. Supplemental Material |
|||
Axtell, M.A., J. Snyder, and D.P. Bartel. 2007. Common functions for diverse small RNAs of land plants. Plant Cell 19:1750-1769. Supplemental Material |
|||
Mayr, C. M.T. Hemann, and D.P. Bartel. 2007. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation.Science 315: 1576-1579. Supplemental Material |
|||
Zhou, B., S. Wang, C. Mayr, D.P. Bartel, and H.F. Lodish. 2007. miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc Natl Acad Sci USA 104: 7080-7085. Supplemental Material |
|||
2006 |
|||
Ruby, J.G., C. Jan, C. Player, M.J. Axtell, W. Lee, C. Nusbaum, H. Ge, and D.P. Bartel. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193-1207. Supplemental Material |
|||
Rajagopalan, R., H. Vaucheret, J. Trejo, and D.P. Bartel. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. GenesDev 20:3407-3425. |
|||
Axtell, M.A., C. Jan, R. Rajagopalan, and D.P. Bartel. 2006. A two-hit trigger for siRNA biogenesis in plants. Cell 127: 565-577. |
|||
Lau, N.C., A.G. Seto, J. Kim, S. Kuramochi-Miyagawa, T. Nakano, D.P. Bartel, and R.E. Kingston. 2006. Characterization of the piRNA complex from rat tests. Science 313: 363-367. Supplemental Material |
|||
Vaucheret, H., A.C. Mallory, and D.P. Bartel. 2006. AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Mol Cell 22:129-136. |
|||
Jones-Rhoades, M.W., D.P. Bartel, and B. Bartel. 2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant. Biol. 57: 19-53. (Review) |
|||
2005 |
|||
Lewis, B.P., C.B. Burge, and D.P. Bartel. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20. Supplemental Materi |
|||
Lim, L.P., N.C. Lau, P. Garrett-Engele, A. Grimson, J.M. Schelter, J. Castle, D.P. Bartel, P.S. Linsley, and J.M. Johnson. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-773. Supplemental Materia |
|||
Farh, K.K., A.Grimson, C. Jan, B.P. Lewis, W. Johnston, L. P. Lim, C. Burge, and D.P. Bartel. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310:1817-1821. Supplemental Material |
|||
Baskerville, S. and D.P. Bartel. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11:241-247. Supplemental Material |
|||
Giraldez, A.J., R.M. Cinalli, M.E. Glasner, A.J. Enright, M.J. Thomson, S. Baskerville, S.M. Hammond, D.P. Bartel, and A.F. Schier. 2005. MicroRNAs Regulate Brain Morphogenesis in Zebrafish. Science 308: 833-838. Supplemental Material |
|||
Mallory, A.C., D.P. Bartel, and B. Bartel. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17: 1360-1375. Supplemental Material |
|||
Axtell, M.J. and D.P. Bartel. 2005. Antiquity of microRNAs and their targets in plants. Plant Cell 17: 1658-1673. Supplemental Material |
|||
Curtis E.A.and D.P. Bartel. 2005. New catalytic structures from an existing ribozyme. Nat Struct Mol Biol. 12:994-1000. Supplemental Material |
|||
Schultes E.A., A. Spasic, U. Mohanty, and D.P.Bartel. 2005. Compact and ordered collapse of randomly generated RNA sequences. Nat Struct Mol Biol. 12:1130-1136. |
|||
Lawrence, M. and D.P. Bartel. 2005. New ligase-derived RNA polymerase ribozymes. RNA 11:1173-1180. |
|||
Gasciolli, V., A.C. Mallory, D.P. Bartel, and H. Vaucheret. 2005. Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs. CurrBiol 15:1494-1500. |
|||
Matranga C., Y. Tomari, C. Shin, D.P. Bartel, and P.D. Zamore. 2005. Passenger-strand cleavage facilitates assembly of siRNA into ago2-containing RNAi enzyme complexes. Cell 123:607-620. Supplemental Material |
|||
Li M., M.W. Jones-Rhoades, N.C. Lau, D.P. Bartel, and A.E. Rougvie. 2005. Regulatory mutations of mir-48, a C. elegans let-7 family microRNA, cause developmental timing defects. Dev Cell 9:415-422. Supplemental Material |
|||
Abbott A.L., E. Alvarez-Saavedra, E.A. Miska, N.C. Lau, D.P. Bartel, H.R. Horvitz, and V. Ambros. 2005. The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9:403-414. Supplemental Material |
|||
Hornstein, E., J.H. Mansfield, S.Yekta, J.K. Hu, B.D. Harfe, M.T. McManus, S. Baskerville, D.P. Bartel, and C.J. Tabin. 2005. The microRNA miR-196 acts upstream of Hoxb8 and Shh in linb development. Nature 438: 671-674. Supplemental Material |
|||
2004 |
|||
Bartel, D.P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297. (Review) |
|||
Chen, C.Z., L. Li, H.F. Lodish, and D.P. Bartel. 2004. MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83-86. |
|||
Yekta, S., I.H. Shih, and D.P. Bartel. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594-596. |
|||
Jones-Rhoades, M.W. and D.P. Bartel. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787-799. Supplemental Material |
|||
Ohler, U., S. Yekta, L. Lim, D.P. Bartel, and C. Burge. 2004. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10:1309-1322. |
|||
Mallory, A.C., B.J. Reinhart, M.W. Jones-Rhoades, G. Tang, P.D. Zamore, M.K. Barton, and D.P. Bartel. 2004. MicroRNA conrol of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO 23: 3356-3364. |
|||
Mallory, A.C., D.V. Dugas, D.P. Bartel, and B. Bartel. 2004. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 14:1035-1046. |
|||
Bergman N.H., N.C. Lau, V. Lehnert, E. Westhof, and D.P. Bartel. 2004. The three-dimensional architecture of the class I ligase ribozyme. RNA 10:176-184. |
|||
Vaucheret, H.V.F. Vazquez, P. Crete, and D.P. Bartel. 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18: 1187-1197. |
|||
Bartel, D.P. and C.Z. Chen. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet. 5:396-400. (Opinion) |
|||
2003 |
|||
Lim, L.P., N.C. Lau, E.G. Weinstein, A. Abdelhakim, S. Yekta, M.W. Rhoades, C.B. Burge, and D.P. Bartel. 2003. The microRNAs of Caenorhabditis elegans. Genes Dev. 17:991. Supplemental Material |
|||
Lewis B. P., I.H. Shih, M.W. Jones-Rhoades, D.P. Bartel, and C.B. Burge. 2003. Prediction of mammalian microRNA targets. Cell 115:787-798. Supplemental Material TargetScan Web Server |
|||
Bartel, B. and D.P. Bartel. 2003. MicroRNAs: At the Root of Plant Development? Plant Physiology 132:709-717. |
|||
Lawrence, M.S. and D.P. Bartel. 2003. Processivity of ribozyme-catalyzed RNA polymerization. Biochemistry 42:8748-8755. |
|||
Lau, N.C. and D.P. Bartel. 2003. Censors of the Genome. Sci Am 289: 34-41. |
|||
Chapple, K.E., D.P. Bartel, and P.J. Unrau. 2003. Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme. RNA 9:1208-1220. |
|||
Muller, U.F. and D.P. Bartel. 2003. Substrate 2'-hydroxyl groups required for ribozyme-catalyzed polymerization. Chem. Biol. 10: 799-806. |
|||
Unrau, P.J. and D.P. Bartel. 2003. An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects. Proc Natl Acad Sci USA 100:15393-15397. |
|||
Ambros V., B. Bartel, D.P. Bartel, C.B. Burge, J.C. Carrington, X. Chen, G. Dreyfuss, S.R. Eddy, S. Griffiths-Jones, M. Marshall, M. Matzke, G. Ruvkun, and T. Tuschl. 2003. A uniform system for microRNA annotation. RNA 9:277-279. |
|||
2002 |
|||
Reinhart, B.J., E.G. Weinstein, M.W. Rhoades, B. Bartel, and D.P. Bartel. 2002. MicroRNAs in plants. Genes Dev. 16:1616-1626. |
|||
Rhoades, M.W., B.J. Reinhart, L.P. Lim, C.B. Burge, B. Bartel, and D.P. Bartel. 2002. Prediction of plant microRNA targets. Cell 110: 513-520. |
|||
Reinhart, B.J. and D.P. Bartel. 2002. Small RNAs correspond to centromere heterochromatic repeats. Science 297: 1831. |
|||
Glasner, M.E., N.H. Bergman, and D.P. Bartel. 2002. Metal ion requirements for structure and catalysis of an RNA ligase ribozyme. Biochemistry 41:8103-8112. |
|||
Merryman, C., E. Weinstein, S.F. Wnuk, and D.P. Bartel. 2002. A bifunctional tRNA for in vitro selection. Chem. Biol.9:741-746. |
|||
Baskerville, S. and D.P. Bartel. 2002. A ribozyme that ligates RNA to protein.PNAS 99: 9154-9159. |
|||
Mallory, A.C., B.J. Reinhart, D.P. Bartel, V.B. Vance, and L.H. Bowman. 2002. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and microRNAs in tobacco. PNAS 99: 15228-15233. |
|||
2001 |
|||
Johnston, W.K., P.J. Unrau, M.S. Lawrence, M.E. Glasner, and D.P. Bartel. 2001. RNA-catalyzed RNA- polymerization: Accurate and general RNA -templated primer extension. Science 292:1319-1325. Supplemental Material |
|||
Lau, N.C., L.P. Lim, E.G. Weinstein, and D.P. Bartel. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858-862. Supplemental Material |
|||
Szostak, J.W., D.P. Bartel, and L. Luisi. 2001. Synthesizing life. Nature 409:387-439. |
|||
Curtis, E.A. and D.P. Bartel. 2001. The hammerhead cleavage reaction in monovalent cations. RNA 7:546-552.v |
|||
2000 |
|||
Bergman, N.H., W.K. Johnston, and D.P. Bartel. 2000. Kinetic framework for ligation by an efficient RNA ligase ribozyme. Biochemistry 39:3115-3123. |
|||
Zamore, P.D., T. Tuschl, P.A. Sharp, and D.P. Bartel. 2000. RNAi: dsRNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25-33. |
|||
Schultes, E.A and D.P. Bartel. 2000. One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science 289(5478):448-452. |
|||
Glasner M.E., C.C. Yen, E.H. Ekland, and D.P. Bartel. 2000. Recognition of nucleoside triphosphates during RNA-catalyzed primer extension. Biochemistry 39:15556-62. |
|||
1999 |
|||
Bartel, D.P. 1999. Re-creating an RNA replicase. In The RNA World II. Gesteland, R.F., T.R. Cech, and J.F. Atkins, eds. (Cold Spring Harbor Laboratory Press), pp.143-161. |
|||
Zamore, P.D., D.P. Bartel, R. Lehmann, and J.R. Williamson. 1999. The PUMILIO-RNA interaction: A single RNA-binding domain monomer recognizes a bipartite target sequence. Biochemistry 38: 596-604. |
|||
Williams, P.K., K.A. Martindale, and D.P. Bartel. 1999. Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J. 18:5423-5433. |
|||
Bartel, D.P. and P.J. Unrau. 1999. Constructing an RNA world. Trends Biochem. Sci. 24:M9-12; Trends Cell Biol. 9:M9-12; Trends Genet. 15:M9-12 (joint issue). |
|||
Tuschl, T., P.D. Zamore, R. Lehmann, D.P. Bartel, and P.A. Sharp. 1999. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 13:3191-7. |
|||
1998 |
|||
Williams, K.P. and D.P. Bartel. 1998. The tmRNA website. Nucleic Acids Res. 26:163-165. |
|||
Tuschl, T., P.A. Sharp, and D.P. Bartel. 1998. Selection in vitro of novel ribozymes from a partially randomized U2 and U6 snRNA library. EMBO J. 17:2637-2650. |
|||
Unrau, P.J. and D.P. Bartel. 1998. RNA-catalyzed nucleotide synthesis. Nature 395:260-263. |
|||
1997 |
|||
Williams, K.P., X.-H. Liu, T.N.M. Schumacher, H.Y. Lin, D.A. Ausiello, P.S. Kim, and D.P. Bartel. 1997. Bioactive and nuclease-resistant l-DNA ligand of vasopressin. PNAS 94:11285-11290. |
|||
Sabeti, P.C., P.J. Unrau, and D.P. Bartel. 1997. Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol. 4:767-774. |
|||
1996 |
|||
Williams, K.P. and D.P. Bartel. 1996. In vitro selection of catalytic RNA. In Nucleic Acids and Molecular Biology, Vol. 10, F. Eckstein and D.M.J. Lilley, eds. (Springer-Verlag) pp 367-381. |
|||
Williams, K.P. and D.P. Bartel. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2:1306-1310. |
|||
Ekland, E.H. and D.P. Bartel. 1996. RNA-catalyzed RNA polymerization using nucleoside triphosphates. Nature 382:373-6. |
|||
1995 |
|||
Ekland, E.H., J.W. Szostak, and D.P. Bartel. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269:364-370. |
|||
Ekland, E.H. and D.P. Bartel. 1995. Secondary structure and sequence optimization of an RNA ligase ribozyme. Nucleic Acids Res. 23:3231-3238. |
|||
Williams, K.P. and D.P. Bartel. 1995. PCR product with strands of unequal length. Nucleic Acids Res. 23:4220-1. |