About - The Bartel Lab of Whitehead Institute For Biomedical Research


Xiang, K., J. Ly, D.P. Bartel. 2024. Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos. Dev Cell 59:1058–1074.
Ly, J., K. Xiang, K.C. Su, G.B. Sissoko, D.P. Bartel, I.M. Cheeseman. 2024. Nuclear release of eIF1 globally increases stringency of start-codon selection to preserve mitotic arrest physiology. bioRxiv 2024.04.06.588385.


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.


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.


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.


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.


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.


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)


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.


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.


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


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


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.


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


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


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.


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

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.

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)


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


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)


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


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.

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.

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)


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

Lim L.P., M.E. Glasner, S. Yekta, C.B. Burge, and D.P. Bartel. 2003. Vertebrate microRNA genes. Science 299:1540.

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.

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.


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

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.

Curtis, E.A. and D.P. Bartel. 2001. The hammerhead cleavage reaction in monovalent cations. RNA 7:546-552.v


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.