 | Up a level |
ENCODE Project Consortium, (October 2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075
Ahola, H., Stenlund, A., Moreno-Lopez, J., Pettersson, U. (May 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, (March 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. (May 1991) Ac induces homologous recombination at the maize P locus. Genetics, 128 (1). pp. 163-73. ISSN 0016-6731 (Print)0016-6731 (Linking)
Bartlett, M. E., Williams, S. K., Taylor, Z., DeBlasio, S., Goldshmidt, A., Hall, D. H., Schmidt, R. J., Jackson, D. P., Whipple, C. J. (November 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. (September 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)
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 (December 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. (February 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. (February 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. (May 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)
Doseff, A., Martienssen, R., Sundaresan, V. (February 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. (September 2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836
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. (March 2014) A promoter-level mammalian expression atlas. Nature, 507 (7493). pp. 462-470. ISSN 14764687
Hannon, G. J. (November 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. (November 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
Kapranov, P., Sementchenko, V. I., Gingeras, T. R. (April 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. (February 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. (October 2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics, 9. p. 517.
Li, W., Kaneko, K. (December 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. (April 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. (November 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. (February 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
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. (August 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
Oh, S. A., Park, S. K., Jang, I., Howden, R., Moore, J. M., Grossniklaus, U., Twell, D. (July 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. (April 1988) Sv-40 Enhancer Elements Are Composed on Interchangeable Subunits. Journal of Cellular Biochemistry , 38 (S12D). p. 217. ISSN 0733-1959
Perales, R., Erickson, B., Zhang, L., Kim, H., Valiquett, E., Bentley, D. (October 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. (October 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
Rabinowicz, P. D., Grotewold, E. (November 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. (November 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
Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (January 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. (August 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. (January 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. (March 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. (February 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)
Smith, Mervyn G., Burton, K. (1966) Fractionation of deoxyribonucleic acid from phage-infected bacteria. Biochemical Journal, 98 (1). pp. 229-241.
Springer, P. S., Holding, D. R., Groover, A., Yordan, C., Martienssen, R. A. (May 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. (September 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. (July 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
Thomas, E. E., Srebro, N., Sebat, J., Navin, N., Healy, J., Mishra, B., Wigler, M. H. (July 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. (May 2004) High-throughput fluorescent tagging of full-length arabidopsis gene products in planta. Plant Physiology, 135 (1). pp. 25-38. ISSN 0032-0889
Vongs, A., Kakutani, T., Martienssen, R. A., Richards, E. J. (June 1993) Arabidopsis thaliana DNA methylation mutants. Science, 260 (5116). pp. 1926-1928. ISSN 0036-8075
Wang, Z., Jeon, H. Y., Rigo, F., Bennett, C. F., Krainer, A. R. (October 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)
Xie, W. W., Liang, C. Z., Birchler, J. A. (August 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
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. (October 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)
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. (September 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)
