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

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Number of items at this level: 66.

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

Barberis, D., Casazza, A., Sordella, R., Corso, S., Artigiani, S., Settleman, J., Comoglio, P. M., Tamagnone, L. (2005) p190 Rho-GTPase activating protein associates with plexins and it is required for semaphorin signalling. Journal of Cell Science, 118 (Pt 20). pp. 4689-700. ISSN 0021-9533

C

Calarco, J. P., Martienssen, R. A. (2011) Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr Opin Genet Dev, 21 (2). pp. 134-9. ISSN 1879-0380 (Electronic) 0959-437X (Linking)

Calarco, Joseph P. (2013) Chromatin Dynamics during Germline Development. PhD thesis, Cold Spring Harbor Laboratory.

Creasey, K. M., Zhai, J., Borges, F., Van Ex, F., Regulski, M., Meyers, B. C., Martienssen, R. A. (2014) miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature, 508 (7496). pp. 411-415. ISSN 0028-0836

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

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

Douglas, R. N., Wiley, D., Sarkar, A., Springer, N., Timmermans, M. C. P., Scanlon, M. J. (2010) Ragged seedling2 Encodes an ARGONAUTE7-Like Protein Required for Mediolateral Expansion, but Not Dorsiventrality, of Maize Leaves. Plant Cell, 22 (5). pp. 1441-1451. ISSN 1040-4651

E

Elkayam, E., Parmar, R., Brown, C. R., Willoughby, J. L., Theile, C. S., Manoharan, M., Joshua-Tor, L. (2017) siRNA carrying an (E)-vinylphosphonate moiety at the 5' end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2. Nucleic Acids Res, 45 (6). pp. 3528-3536. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

F

Faehnle, Christopher R., Joshua-Tor, Leemor (2007) Argonautes confront new small RNAs. Current Opinion in Chemical Biology, 11 (5). pp. 569-577. ISSN 1367-5931 (Print)

Fagegaltier, D., Bougé, A.-L., Berry, B., Poisot, É., Sismeiro, O., Coppée, J.-Y., Théodore, L., Voinnet, O., Antoniewski, C. (2009) The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 106 (50). pp. 21258-21263.

G

Garcia, D., Collier, S. A., Byrne, M. E., Martienssen, R. A. (2006) Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr Biol, 16 (9). pp. 933-8. ISSN 0960-9822 (Print)

Gerbasi, V. R., Preall, J. B., Golden, D. E., Powell, D. W., Cummins, T. D., Sontheimer, E. J. (2011) Blanks, a nuclear siRNA/dsRNA-binding complex component, is required for Drosophila spermiogenesis. Proceedings of the National Academy of Sciences of the United States of America, 108 (8). pp. 3204-3209. ISSN 00278424 (ISSN)

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

H

Hyun, S. W., Anglin, I. E., Liu, A., Yang, S., Sorkin, J. D., Lillehoj, E., Tonks, N. K., Passaniti, A., Goldblum, S. E. (2011) Diverse injurious stimuli reduce protein tyrosine phosphatase-μ expression and enhance epidermal growth factor receptor signaling in human airway epithelia. Experimental Lung Research, 37 (6). pp. 327-343. ISSN 01902148 (ISSN)

I

Irvine, D. V., Zaratiegui, Mi., Tolia, N. H., Goto, D. B., Chitwood, D. H., Vaughn, M. W., Joshua-Tor, L., Martienssen, R. A. (2006) Argonaute slicing is required for heterochromatic silencing and spreading. Science, 313 (5790). pp. 1134-7. ISSN 1095-9203 (Electronic)

J

Janas, J. A., Skowronski, J., Van Aelst, L. (2006) Lentiviral delivery of RNAi in hippocampal neurons. Methods Enzymol, 406. pp. 593-605. ISSN 0076-6879 (Print)

Joshua-Tor, L. (2004) siRNAs at RISC. Structure, 12 (7). pp. 1120-1122. ISSN 0969-2126

Julien, E., Herr, W. (2003) Proteolytic processing is necessary to separate and ensure proper cell growth and cytokinesis functions of HCF-1. Embo Journal, 22 (10). pp. 2360-2369. ISSN 0261-4189

K

Karginov, F. V., Cheloufi, S., Chong, M. M. W., Stark, A., Smith, A. D., Hannon, G. J. (2010) Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases. Molecular Cell, 38 (6). pp. 781-788. ISSN 1097-2765

Karginov, F. V., Hannon, G. J. (2010) The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea. Molecular Cell, 37 (1). pp. 7-19.

Kole, R., Krainer, A. R., Sullenger, B. (2010) RNA & OLIGONUCLEOTIDE THERAPEUTICS. In: 2010 meeting on RNA & OLIGONUCLEOTIDE THERAPEUTICS, April 7–April 10, 2010, Cold Spring Harbor.

Komai, S., Licznerski, P., Cetin, A., Waters, J., Denk, W., Brecht, M., Osten, P. (2006) Postsynaptic excitability is necessary for strengthening of cortical sensory responses during experience-dependent development. Nature Neuroscience, 9 (9). pp. 1125-33. ISSN 1097-6256

Kumar, Rajeev, Conklin, Douglas S., Mittal, Vivek (2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Research, 13 (10). pp. 2333-2340. ISSN 1088-9051

L

Li, F., Martienssen, R. A., Cande, W. Z. (2011) Coordination of DNA replication and histone modification by the Rik1-Dos2 complex. Nature, 475 (7355). 244-U2562. ISSN 0028-0836

Lippman, Z., May, B., Yordan, C., Singer, T., Martienssen, R. (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS biology, 1 (3). pp. 420-428. ISSN 1545-7885 (Electronic)1544-9173 (Linking)

Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson, J. M., Song, J. J., Hammond, S. M., Joshua-Tor, L., Hannon, G. J. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science, 305 (5689). pp. 1437-41. ISSN 1095-9203 (Electronic)

M

MacDiarmid, J. A., Amaro-Mugridge, N. B., Madrid-Weiss, J., Sedliarou, I., Wetzel, S., Kochar, K., Brahmbhatt, V. N., Phillips, L., Pattison, S. T., Petti, C., Stillman, B., Graham, R. M., Brahmbhatt, H. (2009) Sequential treatment of drug-resistant tumors with targeted minicells containing siRNA or a cytotoxic drug. Nature Biotechnology, 27 (7). pp. 643-651. ISSN 1087-0156

Mahajan, Ujwal Mukund, Teller, Steffen, Sendler, Matthias, Schwaiger, Theresa, Glöckl, Gunner, Aurich, Konstanze, Partecke, Lars Ivo, Hadlich, Steffen, Weiss, Frank Ulrich, Kühn, Jens P., Tuveson, David, Lerch, Markus M., Mayerle, Julia (2013) In vivo imaging and targeted siRNA delivery using superparamagnetic nanoparticles in pancreatic ductal adenocarcinoma. Pancreatology, 13 (3, Sup). S19. ISSN 1424-3903

Maroney, P. A., Hannon, G. J., Denker, J. A., Nilsen, T. W. (1990) The nematode spliced leader RNA participates in trans-splicing as an Sm snRNP. Embo Journal, 9 (11). pp. 3667-3673. ISSN 0261-4189

Martienssen, R. A. (2008) Great leap forward? Transposable elements, small interfering RNA and adaptive Lamarckian evolution. New Phytologist, 179 (3). pp. 570-572. ISSN 0028-646X

Martienssen, R. A. (2010) Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytologist, 186 (1). pp. 46-53. ISSN 0028-646X

Martienssen, Robert A., Doerge, R. W., Colot, Vincent (2005) Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res, 13 (3). pp. 299-308. ISSN 0967-3849 (Print)

McCaffrey, A. P., Meuse, L., Pham, T. T. T., Conklin, D. S., Hannon, G. J., Kay, M. A. (2002) Gene expression - RNA interference in adult mice. Nature, 418 (6893). pp. 38-39. ISSN 0028-0836

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., Chitwood, D. H., Madi, S., Ohtsu, K., Schnable, P. S., Scanlon, M. J., Timmermans, M. C. P. (2009) Regulation of Small RNA Accumulation in the Maize Shoot Apex. Plos Genetics, 5 (1). e1000320. ISSN 1553-7390

O

Olson, A., Sheth, N., Lee, J. S., Hannon, G. J., Sachidanandam, R. (2006) RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. Nucleic Acids Res, 34 (Databa). D153-7. ISSN 1362-4962 (Electronic)

Olson, A. J., Tully, T., Sachidanandam, R. (2005) GeneSeer: a sage for gene names and genomic resources. BMC Genomics, 6 (1). p. 134. ISSN 1471-2164 (Electronic)

P

Paddison, P. J., Caudy, A. A., Sachidanandam, R., Hannon, G. J. (2004) Short hairpin activated gene silencing in mammalian cells. In: RNA Interference, Editing and Modification: methods and protocols. Methods Mol Biol, 265 . Springer, pp. 85-100.

Paddison, P. J., Hannon, G. J. (2003) siRNAs and shRNAs: Skeleton keys to the human genome. Current Opinion in Molecular Therapeutics, 5 (3). pp. 217-224. ISSN 14648431 (ISSN)

Paddison, P. J., Silva, J. M., Conklin, D. S., Schlabach, M., Li, M., Aruleba, S., Balija, V., O'Shaughnessy, A., Gnoj, L., Scobie, K., Chang, K., Westbrook, T., Cleary, M., Sachidanandam, R., McCombie, W. R., Elledge, S. J., Hannon, G. J. (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature, 428 (6981). pp. 427-31. ISSN 1476-4687 (Electronic)

Petsch, K., Manzotti, P. S., Tam, O. H., Meeley, R., Hammell, M., Consonni, G., Timmermans, M. C. (2015) Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development. Plant Cell, 27 (8). pp. 2163-2177. ISSN 1532-298X (Electronic)1040-4651 (Linking)

Plavskin, Yevgeniy, Nagashima, Akitomo, Perroud, Pierre-François, Hasebe, Mitsuyasu, Quatrano, Ralph S, Atwal, Gurinder S, Timmermans, Marja C P. (2016) Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response. Developmental Cell, 36 (3). pp. 276-289. ISSN 1534-5807

Prasanth, S. G., Shen, Z., Prasanth, K. V. , Stillman, B. (2010) Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization. Proceedings of the National Academy of Sciences of the United States of America, 107 (34). pp. 15093-8. ISSN 0027-8424

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, Denli, Ahmet M., Hannon, Gregory J. (2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell, 19 (3). pp. 421-8. ISSN 1097-2765 (Print)

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

Rozhkov, N. V., Aravin, A. A., Zelentsova, E. S., Schostak, N. G., Sachidanandam, R., McCombie, W. R., Hannon, G. J., Evgen'ev, M. B. (2010) Small RNA-based silencing strategies for transposons in the process of invading Drosophila species. RNA, 16 (8). pp. 1634-1645. ISSN 1355-8382

S

Schalch, T., Job, G., Noffsinger, V. J., Shanker, S., Kuscu, C., Joshua-Tor, L., Partridge, J. F. (2009) High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin. Mol Cell, 34 (1). pp. 36-46. ISSN 1097-4164 (Electronic)

Schramke, V., Sheedy, D. M., Denli, A. M., Bonila, C., Ekwall, K., Hannon, G. J., Allshire, R. C. (2005) RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature, 435 (7046). pp. 1275-1279. ISSN 0028-0836

Silva, J., Chang, K., Hannon, G. J., Rivas, F. V. (2004) RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age. Oncogene, 23 (51). pp. 8401-9. ISSN 0950-9232 (Print)

Silva, J. M., Li, M. Z., Chang, K., Ge, W., Golding, M. C., Rickles, R. J., Siolas, D., Hu, G., Paddison, P. J., Schlabach, M. R., Sheth, N., Bradshaw, J., Burchard, J., Kulkarni, A., Cavet, G., Sachidanandam, R., McCombie, W. R., Cleary, M. A., Elledge, S. J., Hannon, G. J. (2005) Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet, 37 (11). pp. 1281-8.

Song, J. J. (2005) STRUCTURAL AND BIOCHEMICAL STUDIES OF ARGONAUTE REVEAL THE SLICING MECHANISM OF RISC – RNAI EFFECTOR COMPLEX. PhD thesis, Cold Spring Harbor Laboratory.

Song, J. J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., Joshua-Tor, L. (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol, 10 (12). pp. 1026-32. ISSN 1072-8368 (Print)

Song, J. J., Smith, S. K., Hannon, G. J., Joshua-Tor, L. (2004) Crystal structure of argonaute and its implications for RISC slicer activity. Science, 305 (5689). pp. 1434-1437. ISSN 0036-8075

Stein, P., Rozhkov, N. V., Li, F., Cardenas, F. L., Davydenk, O., Vandivier, L. E., Gregory, B. D., Hannon, G. J., Schultz, R. M. (2015) Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes. PLoS Genetics, 11 (2). e1005013. ISSN 1553-7390

T

Tam, O. H., Aravin, A. A., Stein, P., Girard, A., Murchison, E. P., Cheloufi, S., Hodges, E., Anger, M., Sachidanandam, R., Schultz, R. M., Hannon, G. J. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature, 453 (7194). pp. 534-538. ISSN 00280836 (ISSN)

Thiebaut, F., Rojas, C. A., Grativol, C., Motta, M. R., Vieira, T., Regulski, M., Martienssen, R. A., Farinelli, L., Hemerly, A. S., Ferreira, P. C. G. (2014) Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics, 15. p. 766. ISSN 1471-2164

Trimborn, M., Schindler, D., Neitzel, H., Hirano, T. (2006) Misregulated chromosome condensation in MCPH1 primary microcephaly is mediated by condensin II. Cell Cycle, 5 (3). pp. 322-326. ISSN 15384101

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

Vaughn, M. W., Martienssen, R. (2005) It's a small RNA world, after all. Science, 309 (5740). pp. 1525-6. ISSN 1095-9203 (Electronic)

Vaughn, M. W., Martienssen, R. A. (2005) Finding the right template: RNA Pol IV, a plant-specific RNA polymerase. Mol Cell, 17 (6). pp. 754-6. ISSN 1097-2765 (Print)

W

Wen, J., Mohammed, J., Bortolamiol-Becet, D., Tsai, H., Robine, N., Westholm, J. O., Ladewig, E., Dai, Q., Okamura, K., Flynt, A. S., Zhang, D., Andrews, J., Cherbas, L., Kaufman, T. C., Cherbas, P., Siepel, A., Lai, E. C. (2014) Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research, 24 (7). pp. 1236-50. ISSN 1088-9051

Y

Yuan, T. L., Fellmann, C., Lee, C. S., Ritchie, C. D., Thapar, V., Lee, L. C., Hsu, D. J., Grace, D., Carver, J. O., Zuber, J., Luo, J., McCormick, F., Lowe, S. W. (2014) Development of siRNA payloads to target KRAS-mutant cancer. Cancer Discovery, 4 (10). p. 1182. ISSN 21598274

Z

Zhang, X., Douglas, R. N., Strable, J., Lee, M., Buckner, B., Janick-Buckner, D., Schnable, P. S., Timmermans, M. C. P., Scanlon, M. J. (2012) Punctate vascular expression1 is a novel maize gene required for leaf pattern formation that functions downstream of the trans-acting small interfering RNA pathway. Plant Physiology, 159 (4). pp. 1453-1462. ISSN 0032-0889

Zhou, R., Czech, B., Brennecke, J., Sachidanandam, R., Wohlschlegel, J. A., Perrimon, N., Hannon, G. J. (2009) Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA, 15 (10). pp. 1886-1895. ISSN 13558382 (ISSN)

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