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

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Number of items at this level: 63.

ENCODE Project Consortium, (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075

A

Ahola, H., Stenlund, A., Moreno-Lopez, J., Pettersson, U. (1983) Sequences of bovine papillomavirus type 1 DNA--functional and evolutionary implications. Nucleic Acids Res, 11 (9). pp. 2639-50. ISSN 0305-1048 (Print)0305-1048 (Linking)

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jorgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Muller, F., Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., FANTOM Consortium, (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 (7493). pp. 455-61. ISSN 0028-0836

Athma, P., Peterson, T. (1991) Ac induces homologous recombination at the maize P locus. Genetics, 128 (1). pp. 163-73. ISSN 0016-6731 (Print)0016-6731 (Linking)

B

Bartlett, M. E., Williams, S. K., Taylor, Z., DeBlasio, S., Goldshmidt, A., Hall, D. H., Schmidt, R. J., Jackson, D. P., Whipple, C. J. (2015) The Maize PI/GLO Ortholog Zmm16/sterile tassel silky ear1 Interacts with the Zygomorphy and Sex Determination Pathways in Flower Development. Plant Cell, 27 (11). pp. 3081-3098. ISSN 1532-298X (Electronic)1040-4651 (Linking)

Batut, P., Gingeras, T. R. (2013) RAMPAGE: Promoter activity profiling by paired-end sequencing of 5'-complete cDNAs. Current Protocols in Molecular Biology (SUPPL). Unit25B. ISSN 19343639 (ISSN)

Batut, P. J., Dobin, A., Plessy, C., Carninci, P., Gingeras, T. R. (2013) High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res, 23 (1). pp. 169-180. ISSN 1549-5469 (Electronic)1088-9051 (Linking)

Bell, S., Li, J., Walter, J. (2011) EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE. In: 2011 meeting on EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE, September 6–September 10, 2011.

Brown, P., Cervenáková, L., Goldfarb, L. G., McCombie, W. R., Rubenstein, R., Will, R. G., Pocchiari, M., Martinez-Lage, J. F., Scalici, C., Masullo, C., Graupera, G., Ligan, J., Gajdusek, D. C. (1994) Iatrogenic Creutzfeldt-Jakob disease: An example of the interplay between ancient genes and modern medicine. Neurology, 44 (2). pp. 291-293. ISSN 00283878 (ISSN)

C

Cai, Na, Li, Yihan, Chang, Simon, Liang, Jieqin, Lin, Chongyun, Zhang, Xiufei, Liang, Lu, Hu, Jingchu, Chan, Wharton, Kendler, Kenneth S, Malinauskas, Tomas, Huang, Guo-Jen, Li, Qibin, Mott, Richard, Flint, Jonathan (2015) Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder. Current Biology, 25 (24). pp. 3170-3177. ISSN 0960-9822

Chabes, A., Georgieva, B., Domkin, V., Zhao, X. L., Rothstein, R., Thelander, L. (2003) Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase. Cell, 112 (3). pp. 391-401. ISSN 0092-8674

Chen, J. F., Murchison, E. P., Tang, R., Callis, T. E., Tatsuguchi, M., Deng, Z., Rojas, M., Hammond, S. M., Schneider, M. D., Selzman, C. H., Meissner, G., Patterson, C., Hannon, G. J., Wang, D. Z. (2008) Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure. Proc Natl Acad Sci U S A, 105 (6). pp. 2111-2116. ISSN 0027-8424

Chen, N. (2004) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics, Chapte. Unit 4.10.

Creasey, K. M., Martienssen, R. A. (2011) Germline Reprogramming of Heterochromatin in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 75. pp. 269-274. ISSN 00917451 (ISSN)

D

Doseff, A., Martienssen, R., Sundaresan, V. (1991) Somatic excision of the Mu1 transposable element of maize. Nucleic Acids Research, 19 (3). pp. 579-584. ISSN 0305-1048

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

F

Fan, S., Zhang, M. Q., Zhang, X. (2008) Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochemical and Biophysical Research Communications, 374 (3). pp. 559-564. ISSN 0006291X

Feigin, M. E., Malbon, C. C. (2008) OSTM1 regulates beta-catenin/Lef1 interaction and is required for Wnt/beta-catenin signaling. Cell Signal, 20 (5). 949-957 .

Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Altschuler, I. A., Albanese, D., Altschule, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J. I., Geijtenbeek, T. B., Gibson, A. P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Sui, S. J. H., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L. (2014) A promoter-level mammalian expression atlas. Nature, 507 (7493). pp. 462-470. ISSN 14764687

H

Hannon, G. J. (2012) Talk from Greg Hannon at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Hicks, J., Strathern, J. N., Klar, A. J. S. (1979) Transposable mating type genes in Saccharomyces cerevisiae. Nature, 282 (5738). pp. 478-483. ISSN 00280836 (ISSN)

Hirano, M., Hirano, T. (2002) Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA. Embo Journal, 21 (21). pp. 5733-5744. ISSN 0261-4189

K

Kapranov, P., Sementchenko, V. I., Gingeras, T. R. (2003) Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Briefings in Functional Genomics & Proteomics, 2 (1). pp. 47-56. ISSN 1473-9550 (Print)1473-9550

Kelly, T. J., Stillman, B. (2006) Duplication of DNA in eukaryotic cells. In: DNA replication and human disease. Cold Spring Harbor Monograph Series, 46 . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 1-30. ISBN 0879697660

Kole, R., Krainer, A. R., Altman, S. (2012) RNA therapeutics: Beyond RNA interference and antisense oligonucleotides. Nature Reviews Drug Discovery, 11 (2). pp. 125-140. ISSN 14741776 (ISSN)

Kurtz, S., Narechania, A., Stein, J. C., Ware, D. H. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics, 9. p. 517.

L

Li, W., Kaneko, K. (1992) DNA correlations. Nature, 360 (6405). pp. 635-6. ISSN 0028-0836 (Print)0028-0836 (Linking)

Li, W., Prazak, L., Chatterjee, N., Gruninger, S., Krug, L., Theodorou, D., Dubnau, J. (2013) Activation of transposable elements during aging and neuronal decline in Drosophila. Nature Neuroscience, 16. pp. 529-531. ISSN 1546-1726 (Electronic)1097-6256 (Linking)

Lister, C., Jackson, D., Martin, C. (1993) Transposon-induced inversion in Antirrhinum modifies nivea gene expression to give a novel flower color pattern under the control of cycloidearadialis. Plant Cell, 5 (11). pp. 1541-53. ISSN 1040-4651 (Print)1040-4651

Lorenz, P., Baker, B. F., Bennett, C. F., Spector, D. L. (1998) Phosphorothioate antisense oligonucleotides induce the formation of nuclear bodies. Molecular Biology of the Cell, 9 (5). pp. 1007-1023. ISSN 1059-1524

Lucito, R., Byrnes, J. (2009) Comparative genomic hybridization by representational oligonucleotide microarray analysis. Methods Mol Biol, 556. pp. 33-46.

Lucito, R., Wigler, M. H. (2003) Preparation of target DNA. In: DNA microarrays : a molecular cloning manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 386-393. ISBN 0879696257

M

Martienssen, R., Barkan, A., Taylor, W. C., Freeling, M. (1990) Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize. Genes and Development, 4 (3). pp. 331-343. ISSN 08909369 (ISSN)

Martienssen, R. A. (1996) Epigenetic Silencing of Mu Transposable Elements in Maize. In: Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., p. 593. ISBN 0270-1847

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

Meyers, D. A., Antonarakis, S. E., Fearon, E. R., Mallonee, R. L., Waber, P. G., Phillips, J. A., Kazazian, H. H., Levine, M., Kronenberg, H. M., Wigler, M. H., Ullrich, A. (1984) Use of DNA Polymorphisms to Establish the Linkage Map of the Pth, Beta-Globin, C-Ha-Ras-1, and Insulin Loci on 11p. Cytogenetics and Cell Genetics, 37 (1-4). pp. 540-541. ISSN 0301-0171

O

Oh, S. A., Park, S. K., Jang, I., Howden, R., Moore, J. M., Grossniklaus, U., Twell, D. (2003) halfman, an Arabidopsis male gametophytic mutant associated with a 150 kb chromosomal deletion adjacent to an introduced Ds transposable element. Sexual Plant Reproduction, 16 (2). pp. 99-102. ISSN 0934-0882

Ondek, B., Gloss, L., Herr, W. (1988) Sv-40 Enhancer Elements Are Composed on Interchangeable Subunits. Journal of Cellular Biochemistry , 38 (S12D). p. 217. ISSN 0733-1959

P

Perales, R., Erickson, B., Zhang, L., Kim, H., Valiquett, E., Bentley, D. (2013) Gene promoters dictate histone occupancy within genes. Embo Journal, 32 (19). pp. 2645-2656. ISSN 02614189 (ISSN)

Perucho, M., Wigler, M. H. (1981) Linkage and expression of foreign DNA in cultured animal cells. Cold Spring Harb Symp Quant Biol, 45 (2). pp. 829-838. ISSN 0091-7451 (Print)0091-7451 (Linking)

Peterson, T. (1990) Intragenic transposition of Ac generates a new allele of the maize P gene. Genetics, 126 (2). pp. 469-76. ISSN 0016-6731 (Print)0016-6731 (Linking)

Pfeifer, F., Betlach, M., Martienssen, R., Friedman, J., Boyer, H. W. (1983) Transposable elements of halobacterium-halobium. Molecular & General Genetics, 191 (2). pp. 182-188. ISSN 0026-8925

R

Rabinowicz, P. D., Grotewold, E. (2000) A novel reverse-genetic approach (SIMF) identifies Mutator insertions in new Myb genes. Planta, 211 (6). pp. 887-893. ISSN 0032-0935

Reilly, M. T., Faulkner, G. J., Dubnau, J., Ponomarev, I., Gage, F. H. (2013) The role of transposable elements in health and diseases of the central nervous system. Journal of Neuroscience, 33 (45). pp. 17577-86. ISSN 0270-6474

S

Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant Journal, 66 (2). pp. 241-246. ISSN 0960-7412

Sedman, J., Stenlund, A. (1998) The papillomavirus E1 protein forms a DNA-dependent hexameric complex with ATPase and DNA helicase activities. J Virol, 72 (8). pp. 6893-7. ISSN 0022-538X (Print)

Settles, A. M., Baron, A., Barkan, A., Martienssen, R. A. (2001) Duplication and suppression of chloroplast protein translocation genes in maize. Genetics, 157 (1). pp. 349-360. ISSN 0016-6731

Singer, T., Yordan, C., Martienssen, R. A. (2001) Robertson's Mutator transposons in A-thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1). Genes & Development, 15 (5). pp. 591-602. ISSN 0890-9369

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)

Springer, P. S., Holding, D. R., Groover, A., Yordan, C., Martienssen, R. A. (2000) The essential Mcm7 protein PROLIFERA is localized to the nucleus of dividing cells during the G(1) phase and is required maternally for early Arabidopsis development. Development, 127 (9). pp. 1815-1822. ISSN 0950-1991

Stebbins, M. J., Urlinger, S., Byrne, G., Bello, B., Hillen, W., Yin, J. C. P. (2001) Tetracycline-inducible systems for Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 98 (19). pp. 10775-10780. ISSN 0027-8424

Strathern, J. N., Spatola, E., McGill, C., Hicks, J. B. (1980) Structure and organization of transposable mating type cassettes in Saccharomyces yeasts. Proceedings of the National Academy of Sciences of the United States of America, 77 (5 I). pp. 2839-2843. ISSN 00278424 (ISSN)

Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J. D. G., Dean, C., Ma, H., Martienssen, R. (1995) Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes & Development, 9 (14). pp. 1797-1810. ISSN 0890-9369

T

Thomas, E. E., Srebro, N., Sebat, J., Navin, N., Healy, J., Mishra, B., Wigler, M. H. (2004) Distribution of short paired duplications in mammalian genomes. Proc Natl Acad Sci U S A, 101 (28). pp. 10349-54. ISSN 0027-8424 (Print)

Tian, G. W., Mohanty, A., Chary, S. N., Li, S. J., Paap, B., Drakakaki, G., Kopec, C. D., Li, J. X., Ehrhardt, D., Jackson, D., Rhee, S. Y., Raikhel, N. V., Citovsky, V. (2004) High-throughput fluorescent tagging of full-length arabidopsis gene products in planta. Plant Physiology, 135 (1). pp. 25-38. ISSN 0032-0889

V

Vongs, A., Kakutani, T., Martienssen, R. A., Richards, E. J. (1993) Arabidopsis thaliana DNA methylation mutants. Science, 260 (5116). pp. 1926-1928. ISSN 0036-8075

W

Wang, Z., Jeon, H. Y., Rigo, F., Bennett, C. F., Krainer, A. R. (2012) Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides. Open Biol, 2 (10). p. 120133. ISSN 2046-2441 (Electronic)2046-2441 (Linking)

X

Xie, W. W., Liang, C. Z., Birchler, J. A. (2011) Inhibition of RNA Interference and Modulation of Transposable Element Expression by Cell Death in Drosophila. Genetics, 188 (4). pp. 823-834. ISSN 0016-6731

Y

Yang, A., Zhu, Z., Kapranov, P., McKeon, F., Church, G. M., Gingeras, T. R., Struhl, K. (2006) Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Molecular Cell, 24 (4). pp. 593-602. ISSN 10972765 (ISSN)

Yu, M., Lin, G., Arshadi, N., Kalatskaya, I., Xue, B., Haider, S., Nguyen, F., Boutros, P. C., Elson, A., Muthuswamy, L. B., Tonks, N. K., Muthuswamy, S. K. (2012) Expression profiling during mammary epithelial cell 3D morphogenesis identifies PTPRO as a novel regulator of morphogenesis and ErbB2 mediated transformation. Mol Cell Biol, 32 (19). pp. 3913-3924. ISSN 1098-5549 (Electronic)0270-7306 (Linking)

Z

Zhang, M. Q. (2003) Prediction, annotation, and analysis of human promoters. Cold Spring Harbor Symposia on Quantitative Biology, 68. pp. 217-25. ISSN 0091-7451 (Print)

Zhao, Z. Y., Sundaresan, V. (1991) Binding sites for maize nuclear proteins in the terminal inverted repeats of the Mu1 transposable element. Mol Gen Genet, 229 (1). pp. 17-26. ISSN 0026-8925 (Print)0026-8925 (Linking)

Zheng, D., Frankish, A., Baertsch, R., Kapranov, P., Reymond, A., Siew, W. C., Lu, Y., Denoeud, F., Antonarakis, S. E., Snyder, M., Ruan, Y., Wei, C. L., Gingeras, T. R., Guigó, R., Harrow, J., Gerstein, M. B. (2007) Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Research, 17 (6). pp. 839-851. ISSN 10889051 (ISSN)

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