Source: http://bartellab.wi.mit.edu/publication.html
Timestamp: 2019-04-24 00:24:14+00:00

Document:
Morgan, J.T., G.R. Fink, D.P. Bartel. 2019. Excised linear introns regulate growth in yeast. Nature 565:606-11.
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 9:4671.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Bartel, D.P. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136:215-233.
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.
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.
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.
Müller, U.F and D.P. Bartel. 2008. Improved polymerase ribozyme efficiency on hydrophobic assemblies. RNA 14:552-62.
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.
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.
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.
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.
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.
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.
Vazquez, F., H. Vaucheret, R. Rajagopalan, C. Lepers, V. Gasciolli, A.C. Mallory, J.-L. Hilbert, D.P. Bartel, and P. Crete. 2004. Endogenous trans-acting siRNAs regaulte the acccumulation of Arabidopsis mRNAs. MolCell 16:69-79.
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.
Lim L.P., M.E. Glasner, S. Yekta, C.B. Burge, and D.P. Bartel. 2003. Vertebrate microRNA genes. Science 299:1540.
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.
Tang, G., B.J. Reinhart, D.P. Bartel, and P.D. Zamore. 2003. A biochemical framework for RNA silencing in plants. Genes Dev. 17:49.
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.
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.
Tuschl, T., P.A. Sharp, and D.P. Bartel. 2001. A ribozyme selected from variants of U6 promotes 2',5'-branch formation. RNA 7:29-43.
Szostak, J.W., D.P. Bartel, and L. Luisi. 2001. Synthesizing life. Nature 409:387-439.
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.
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.
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.
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.
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.
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.

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