Items where Subject is "bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA"

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Number of items at this level: 77.

A

Abdelhamid, R. F., Plessy, C., Yamauchi, Y., Taoka, M., de Hoon, M., Gingeras, T. R., Isobe, T., Carninci, P. (2014) Multiplicity of 5' Cap Structures Present on Short RNAs. PLoS One, 9 (7). e102895. ISSN 1932-6203

Aravin, A. A., Bourc'his, D. (2008) Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev, 22 (8). pp. 970-5.

Aravin, A. A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J., Kuramochi-Miyagawa, S., Nakano, T., Chien, M. C., Russo, J. J., Ju, J. Y., Sheridan, R., Sander, C., Zavolan, M. , Tuschl, T. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442 (7099). pp. 203-7. ISSN 1476-4687 (Electronic)

Aravin, A. A., Hannon, G. J., Brennecke, J. (2007) The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race. Science, 318 (5851). pp. 761-764. ISSN 1095-9203 (Electronic)

Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K., Hannon, G. J. (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science, 316 (5825). pp. 744-7. ISSN 1095-9203 (Electronic)

B

Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., Depamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Correa, L. G. G., Dacre, M., Debarry, J., Dreyer, I., Elias, M., Engstrom, E. M., Estelle, M., Feng, L., Finet, C., Floyd, S. K., Frommer, W. B., Fujita, T., Gramzow, L., Gutensohn, M., Harholt, J., Hattori, M., Heyl, A., Hirai, T., Hiwatashi, Y., Ishikawa, M., Iwata, M., Karol, K. G., Koehler, B., Kolukisaoglu, U., Kubo, M., Kurata, T., Lalonde, S., Li, K., Li, Y., Litt, A., Lyons, E., Manning, G., Maruyama, T., Michael, T. P., Mikami, K., Miyazaki, S., Morinaga, S., Murata, T., Mueller-roeber, B., Nelson, D. R., Obara, M., Oguri, Y., Olmstead, R. G., Onodera, N., Petersen, B. L., Pils, B., Prigge, M., Rensing, S. A., Riaño-Pachón, D. M., Roberts, A. W., Sato, Y., Scheller, H. V., Schulz, B., Schulz, C., Shakirov, E. V., Shibagaki, N., Shinohara, N., Shippen, D. E., Sørensen, I., Sotooka, R., Sugimoto, N., Sugita, M., Sumikawa, N., Tanurdzic, M., Theiben, G., Ulvskov, P., Wakazuki, S., Weng, J., Willats, W. W. G. T., Wipf, D., Wolf, P. G., Yang, L., Zimmer, A. D., Zhu, Q., Mitros, T., Hellsten, U., Loqué, D., Otillar, R., Salamov, A., Schmutz, J., Shapiro, H., Lindquist, E. (2011) The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science, 332 (6032). pp. 963-966. ISSN 00368075

Benkovics, A. H., Timmermans, M. C. (2014) Developmental patterning by gradients of mobile small RNAs. Current Opinion in Genetics & Development, 27C. pp. 83-91. ISSN 0959-437X

Berezikov, E., Robine, N., Samsonova, A., Westholm, J. O., Naqvi, A., Hung, J. H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y. J., Zamore, P. D., Hannon, G. J., Marra, M. A., Weng, Z. P., Perrimon, N., Lai, E. C. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21 (2). pp. 203-215. ISSN 1088-9051

Boccara, M., Sarazin, A., Billoud, B., Jolly, V., Martienssen, R., Baulcombe, D., Colot, V. (2007) New approaches for the analysis of Arabidopsis thaliana small RNAs. Biochimie, 89 (10). pp. 1252-6. ISSN 0300-9084 (Print)

Borges, F., Martienssen, R. A. (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol, 16. pp. 727-741. ISSN 1471-0080 (Electronic)1471-0072 (Linking)

Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., Hannon, G. J. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128 (6). pp. 1089-103. ISSN 0092-8674 (Print)

C

Calarco, J. P., Borges, F., Donoghue, M, Van Ex, F., Jullien, P. E., Lopes, T., Gardner, R., Berger, F., Feijó, J. A, Becker, J. D., Martienssen, R. A. (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell, 151 (1). pp. 194-205. ISSN 0092-8674

Chitwood, D. H. (2009) Patterning in Leaves via a Cascade of Small RNAs. PhD thesis, Cold Spring Harbor Laboratory.

Chitwood, D. H., Guo, M., Nogueira, F. T. S., Timmermans, M. C. P. (2007) Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex. Development, 134 (5). pp. 813-23. ISSN 0950-1991 (Print)

Chitwood, D. H., Nogueira, F. T. S., Howell, M. D., Montgomery, T. A., Carrington, J. C., Timmermans, M. C. P. (2009) Pattern formation via small RNA mobility. Genes Dev, 23 (5). pp. 549-554. ISSN 0890-9369

Czech, B., Hannon, G. J. (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet, 12 (1). pp. 19-31. ISSN 1471-0064 (Electronic) 1471-0056 (Linking)

D

Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F., Hannon, G. J. (2004) Processing of primary microRNAs by the Microprocessor complex. Nature, 432 (7014). pp. 231-5. ISSN 1476-4687 (Electronic)

Dotto, M. C., Petsch, K. A., Aukerman, M. J., Beatty, M., Hammell, M., Timmermans, M. C. (2014) Genome-Wide Analysis of leafbladeless1-Regulated and Phased Small RNAs Underscores the Importance of the TAS3 ta-siRNA Pathway to Maize Development. PLoS Genetics, 10 (12). e1004826. ISSN 1553-7390

E

Eppig, J., Fuller, M., Newmark, P. (2010) GERM CELLS. In: 2010 Meeting of Germ Cells, October 5–October 9, 2010.

F

Fejes-Toth, K., Sotirova, V., Sachidanandam, R., Assaf, G., Hannon, G. J., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., Dumais, E., Gingeras, T. R. (2009) Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature, 457 (7232). pp. 1028-1032. ISSN 0028-0836

Foster, Toshi M, Timmermans, Marja C. P. (2009) Axial Patterning of the Maize Leaf. In: Handbook of Maize: Its Biology. Springer New York, pp. 161-178. ISBN 978-0-387-79417-4

G

Girard, A., Hannon, G. J. (2007) [The role of piRNAs in mouse spermatogenesis.]. J Soc Biol, 201 (4). pp. 411-8.

Girard, A., Sachidanandam, R., Hannon, G. J., Carmell, M. A. (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature, 442 (7099). pp. 199-202. ISSN 00280836

H

Hammell, M. (2011) Talk from Molly Hammell at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Hannon, Gregory J., Zamore, Phillip D. (2003) Small RNAs, big biology: biochemical studies of RNA interference. In: RNAi: a guide to gene silencing. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., pp. 87-108. ISBN 978-087969641-2

Houwing, S., Kamminga, L. M., Berezikov, E., Cronembold, D., Girard, A., van den Elst, H., Filippov, D. V., Blaser, H., Raz, E., Moens, C. B., Plasterk, R. H. A., Hannon, G. J., Draper, B. W., Ketting, R. F. (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell, 129 (1). pp. 69-82. ISSN 0092-8674

J

Javelle, M., Timmermans, M. C. (2012) In situ localization of small RNAs in plants by using LNA probes. Nat Protoc, 7 (3). pp. 533-41. ISSN 1750-2799 (Electronic)1750-2799 (Linking)

Jiang, L. C., Schlesinger, F. J., Davis, C. A., Zhang, Y., Li, R. H., Salit, M., Gingeras, T. R., Oliver, B. (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Research, 21 (9). pp. 1543-1551. ISSN 1088-9051

K

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Hertel, J., Hackermüller, J., Hofacker, I. L., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Patel, S., Helt, G., Ganesh, M., Ghosh, S., Piccolboni, A., Sementchenko, V., Tammana, H., Gingeras, T. R. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316 (5830). pp. 1484-1488. ISSN 00368075 (ISSN)

Kidner, C. A., Martienssen, R. A. (2005) The developmental role of microRNA in plants. Current Opinion in Plant Biology, 8 (1). pp. 38-44. ISSN 1369-5266

Kuhn, C. D., Wilusz, J. E., Zheng, Y., Beal, P. A., Joshua-Tor, L. (2015) On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme. Cell, 160 (4). pp. 644-658. ISSN 0092-8674

Kuhn, C. D., Wilusz, J. E., Zheng, Y., Beal, P. A., Joshua-Tor, L. (2015) On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Febs Journal, 282 (Supple). p. 37. ISSN 1742-464X

L

Lindsay, J., Carone, D. M., Brown, J., Hall, L., Qureshi, S., Mitchell, S. E., Jannetty, N., Hannon, G., Renfree, M., Pask, A., O'Neill, M., O'Neill, R. (2012) Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics, 13. p. 559. ISSN 1471-2164 (Electronic)1471-2164 (Linking)

Liu, J., Valencia-Sanchez, M. A., Hannon, G. J., Parker, R. (2005) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nature Cell Biology, 7 (7). pp. 719-23. ISSN 1465-7392

M

Malone, C. D., Hannon, G. J. (2009) Small RNAs as Guardians of the Genome. Cell, 136 (4). pp. 656-668. ISSN 0092-8674

Martienssen, R. (2010) Small RNA Makes Its Move. Science, 328 (5980). pp. 834-835. ISSN 0036-8075

McGinn, J., Czech, B. (2014) Small RNA library construction for high-throughput sequencing. Methods in Molecular Biology, 1093. pp. 195-208. ISSN 10643745 (ISSN); 9781627036931 (ISBN)

Mi, S. J., Cai, T., Hu, Y. G., Chen, Y., Hodges, E., Ni, F. R., Wu, L., Li, S., Zhou, H., Long, C. Z., Chen, S., Hannon, G. J., Qi, Y. J. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell, 133 (1). pp. 116-127. ISSN 0092-8674

Muerdter, F., Olovnikov, I., Molaro, A., Rozhkov, N. V., Czech, B., Gordon, A., Hannon, G. J., Aravin, A. A. (2012) Production of artificial piRNAs in flies and mice. RNA, 18 (1). pp. 42-52. ISSN 1355-8382

Murchison, E. P., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Grutzner, F., Stark, A., Hannon, G. J. (2008) Conservation of small RNA pathways in platypus. Genome Research, 18 (6). pp. 995-1004. ISSN 1088-9051

N

Nogueira, F. T., Madi, S., Chitwood, D. H., Juarez, M. T., Timmermans, M. C. P. (2007) Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev, 21 (7). pp. 750-5. ISSN 0890-9369 (Print)

Nogueira, F. T. S., Timmermans, M. C. (2007) An Interplay Between Small Regulatory RNAs Patterns Leaves. Plant Signaling & Behavior, 2 (6). pp. 519-21. ISSN 1559-2316 (Print)

Nogueira, F. T., Sarkar, A. K., Chitwood, D. H., Timmermans, M. C. (2006) Organ Polarity in Plants Is Specified through the Opposing Activity of Two Distinct Small Regulatory RNAs. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 157-64. ISSN 00917451 (ISSN)

O

Olmedo-Monfil, V., Durán-Figueroa, N., Arteaga-Vázquez, M., Demesa-Arévalo, E., Autran, D., Grimanelli, D., Slotkin, R. K., Martienssen, R. A., Vielle-Calzada, J. P. (2010) Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature, 464 (7288). pp. 628-632.

P

Plavskin, Y., Timmermans, M. C. (2013) Small RNA-Regulated Networks and the Evolution of Novel Structures in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 77. ISSN 00917451 (ISSN)

Plavskin, Yevgeniy (2013) Regulation of the auxin response by an ancient small RNA pathway. PhD thesis, Cold Spring Harbor Laboratoy.

Q

Qi, Y., He, X., Wang, X. J., Kohany, O., Jurka, J., Hannon, G. J. (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature, 443 (7114). pp. 1008-12. ISSN 1476-4687 (Electronic)

Qi, Yijun, Hannon, Gregory J. (2005) Uncovering RNAi mechanisms in plants: biochemistry enters the foray. FEBS Lett, 579 (26). pp. 5899-903. ISSN 0014-5793 (Print)

R

Rangan, P., Malone, Colin D. , Navarro, C., Newbold, S. P, Hayes, P. S, Sachidanandam, R., Hannon, G. J., Lehmann, R. (2011) piRNA Production Requires Heterochromatin Formation in Drosophila. Current Biology, 21 (16). pp. 1373-1379. ISSN 0960-9822

Rechavi, O., Erlich, Y., Amram, H., Flomenblit, L., Karginov, F. V., Goldstein, I., Hannon, G. J., Kloog, Y. (2009) Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs. Genes and Development, 23 (16). pp. 1971-1979. ISSN 08909369 (ISSN)

Rechavi, Oded, Houri-Ze’evi, Leah, Anava, Sarit, Goh, Wee Siong Sho, Kerk, Sze Yen, Hannon, Gregory J, Hobert, Oliver (2014) Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans. Cell, 158 (2). pp. 277-287. ISSN 0092-8674

Reddy, R., Henning, D., Liu, M. H., Spector, D., Busch, H. (1985) Identification and characterization of a polyadenylated small RNA (s-poly A+ RNA) in dinoflagellates. Biochemical and Biophysical Research Communications, 127 (2). pp. 552-7. ISSN 0006-291X (Print)0006-291x

Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R. (2013) The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research, 23 (10). pp. 1651-1662. ISSN 10889051 (ISSN)

Roca, Xavier, Sachidanandam, Ravi, Krainer, Adrian R. (2005) Determinants of the inherent strength of human 5' splice sites. Rna, 11 (5). pp. 683-98. ISSN 1355-8382 (Print)

Rozhkov, N. V., Schostak, N. G., Zelentsova, E. S., Yushenova, I. A., Zatsepina, O. G., Evgen'ev, M. B. (2013) Evolution and Dynamics of Small RNA Response to a Retroelement Invasion in Drosophila. Molecular Biology and Evolution, 30 (2). pp. 397-408. ISSN 0737-4038

S

Sabin, L. R., Cherry, S. (2013) Small creatures use small RNAs to direct antiviral defenses. European Journal of Immunology, 43 (1). pp. 27-33. ISSN 1521-4141 (Electronic)0014-2980 (Linking)

Schwab, R., Maizel, A., Ruiz-Ferrer, V., Garcia, D., Bayer, M., Crespi, M., Voinnet, O., Martienssen, R. A. (2009) Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana. PloS one, 4 (6). e5980. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Sheldon, M., Ratnasabapathy, R., Hernandez, N. (1993) Characterization of the inducer of short transcripts, a human immunodeficiency virus type 1 transcriptional element that activates the synthesis of short RNAs. Mol Cell Biol, 13 (2). pp. 1251-63. ISSN 0270-7306 (Print)

Skopelitis, D. S., Husbands, A. Y., Timmermans, M. C. (2012) Plant small RNAs as morphogens. Current Opinion in Cell Biology, 24 (2). pp. 217-224.

Slotkin, R. K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J. D., Feijo, J. A., Martienssen, R. A. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell, 136 (3). pp. 461-72. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Stillman, B., Stewart, D. (2006) Regulatory RNAs. Cold Spring Harb Symp Quant Biol, 71. ISSN 1943-4456 (Electronic) 0091-7451 (Linking)

T

Tam, O. H. (2010) Characterization of small RNA populations and DNA methylation in mammalian development. PhD thesis, Cold Spring Harbor Laboratory.

Thiebaut, F., Grativol, C., Tanurdzic, M., Carnavale-Bottino, M., Vieira, T., Motta, M. R., Rojas, C., Vincentini, R., Chabregas, S. M., Hemerly, A. S., Martienssen, R. A., Ferreira, P. C. (2014) Differential sRNA Regulation in Leaves and Roots of Sugarcane under Water Depletion. PLoS One, 9 (4). e93822. ISSN 1932-6203

Timmermans, M. C., Chitwood, D., Nogueira, F., Madi, S. (2008) Small RNAs as Mobile Signals in Development. Faseb Journal, 22. p. 1. ISSN 0892-6638

Timmermans, M. C. P., Chitwood, D., Nogueira, F., Madi, S. (2008) Pattern formation by small RNA signals. Developmental Biology, 319 (2). pp. 463-464. ISSN 0012-1606

Tolia, N. H., Joshua-Tor, L. (2007) Slicer and the Argonautes. Nature Chemical Biology, 3 (1). pp. 36-43. ISSN 1552-4450

Tschudi, C., Krainer, A. R., Ullu, E. (1988) The U6 small nuclear RNA from Trypanosoma brucei. Nucleic Acids Research, 16 (23). p. 11375. ISSN 0305-1048

V

Valencia-Sanchez, M. A., Liu, J., Hannon, G. J., Parker, R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes and Development, 20 (5). pp. 515-524. ISSN 08909369

Van Ex, F., Jacob, Y., Martienssen, R. A. (2011) Multiple roles for small RNAs during plant reproduction. Current opinion in plant biology, 14 (5). pp. 588-93. ISSN 1879-0356 (Electronic)1369-5266 (Linking)

W

Wang, J., Czech, B., Crunk, A., Wallace, A., Mitreva, M., Hannon, G. J., Davis, R. E. (2011) Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Research, 21 (9). pp. 1462-1477. ISSN 10889051 (ISSN)

Wilusz, J. E. (2009) 3’ end processing of long nuclear-retained non-coding RNAs yields tRNA-like small RNAs. PhD thesis, Cold Spring Harbor Laboratory.

Wilusz, J. E., Freier, S. M., Spector, D. L. (2008) 3' End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA. Cell, 135 (5). pp. 919-932. ISSN 0092-8674

X

Xu, X. M., Jackson, D. P. (2010) Lights at the end of the tunnel: new views of plasmodesmal structure and function. Curr Opin Plant Biol, 13 (6). pp. 684-692. ISSN 1879-0356 (Electronic) 1369-5266 (Linking)

Y

Yigit, E., Batista, P. J., Bei, Y., Pang, K. M., Chen, C. C. G., Tolia, N. H., Joshua-Tor, L., Mitani, S., Simard, M. J., Mello, C. C. (2006) Analysis of the C. elegans Argonaute Family Reveals that Distinct Argonautes Act Sequentially during RNAi. Cell, 127 (4). pp. 747-757. ISSN 00928674

Z

Zaratiegui, M., Martienssen, R. A. (2012) SnapShot: Small RNA-Mediated Epigenetic Modifications. Cell, 151 (2). 456-456 e1. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Zhai, J. X., Zhao, Y. Y., Simon, S. A., Huang, S., Petsch, K., Arikit, S., Pillay, M., Ji, L. J., Xie, M., Cao, X. F., Yu, B., Timmermans, M., Yang, B., Chen, X. M., Meyers, B. C. (2013) Plant MicroRNAs Display Differential 3 ' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species. Plant Cell, 25 (7). pp. 2417-2428. ISSN 1040-4651

Zhou, R., Hotta, I., Denli, A. M., Hong, P., Perrimon, N., Hannon, G. J. (2008) Comparative Analysis of Argonaute-Dependent Small RNA Pathways in Drosophila. Molecular Cell, 32 (4). pp. 592-599. ISSN 10972765 (ISSN)

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