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

Up a level
Export as [feed] Atom [feed] RSS 1.0 [feed] RSS 2.0
Group by: Authors | Item Type
Jump to: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | V | W | X | Y | Z
Number of items at this level: 406.

A

Al-Balool, H. H., Weber, D., Liu, Y., Wade, M., Guleria, K., Nam, P. L. P., Clayton, J., Rowe, W., Coxhead, J., Irving, J., Elliott, D. J., Hall, A. G., Santibanez-Koref, M., Jackson, M. S. (2011) Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Research, 21 (11). pp. 1788-1799. ISSN 10889051 (ISSN)

Alexandre, C., Gilman, M. (1993) Interaction of Mcm1 with Members of the Kappa-B/Rel Family. Journal of Cellular Biochemistry, 53 (Supple). p. 142. ISSN 0730-2312

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Arndt, K. T., Styles, C. A., Fink, G. R. (1989) A Suppressor of a His4 Transcriptional Defect Encodes a Protein with Homology to the Catalytic Subunit of Protein Phosphatases. Cell, 56 (4). pp. 527-538. ISSN 1097-4172

Assamunt, N., Mortishiresmith, R. J., Aurora, R., Herr, W., Wright, P. E. (1993) The Solution Structure of the Oct-1 Pou-Specific Domain Reveals a Striking Similarity to the Bacteriophage-Lambda Repressor DNA-Binding Domain. Cell, 73 (1). pp. 193-205. ISSN 0092-8674

Atkins, J. F., McGill, C., Chow, L., Broach, J. R. (1979) Regulation of Transcription of the Yeast Plasmid 2 Mu Circle. Journal of Supramolecular Structure, 8 (SUPPL.). p. 56.

Attar, R. M., Gilman, M. Z. (1992) Expression cloning of a novel zinc finger protein that binds to the c-fos serum response element. Mol Cell Biol, 12 (5). pp. 2432-43. ISSN 0270-7306 (Print)0270-7306 (Linking)

Aurora, R., Herr, W. (1992) Segments of the POU domain influence one another's DNA-binding specificity. Mol Cell Biol, 12 (2). pp. 455-67. ISSN 0270-7306 (Print)0270-7306 (Linking)

B

Baker, S. J., Kerppola, T. K., Luk, D., Vandenberg, M. T., Marshak, D. R., Curran, T., Abate, C. (1992) Jun Is Phosphorylated by Several Protein-Kinases at the Same Sites That Are Modified in Serum-Stimulated Fibroblasts. Molecular and Cellular Biology, 12 (10). pp. 4694-4705. ISSN 0270-7306

Ballard, D. W., Lowenthal, J. W., Bohnlein, E., Franza, B. R., Greene, W. C. (1989) Transcriptional Activation of the Interleukin-2 Receptor-Alpha Gene Is Coordinately Regulated by Multiple Inducible and Constitutive DNA-Binding Proteins. Clinical Research, 37 (2). A555-A555. ISSN 0009-9279

Ballesteros, M. L., Bolle, C., Lois, L. M., Moore, J. M., Vielle-Calzada, J. P., Grossniklaus, U., Chua, N. H. (2001) LAF1, a MYB transcription activator for phytochrome A signaling. Genes & Development, 15 (19). pp. 2613-2625. ISSN 0890-9369

Banerjee, N., Zhang, M. Q. (2002) Functional genomics as applied to mapping transcription regulatory networks. Current Opinion in Microbiology, 5 (3). pp. 313-317. ISSN 1369-5274

Barnes, S., Jones, D., Belliveau, N., Sundaresh, S., Kinney, J., Phillips, R. (2014) Identification and Analysis of the Transcriptional Regulatory Networks Governing Mechanosensitive Channels in E. coli. Biophysical Journal, 106 (2; Sup). 487A-487A. ISSN 0006-34951542-0086

Bassuner, B. M., Lam, R., Lukowitz, W., Yeung, E. C. (2007) Auxin and root initiation in somatic embryos of Arabidopsis. Plant Cell Reports, 26 (1). pp. 1-11. ISSN 0721-7714

Basu, A., Dong, B., Krainer, A. R., Howe, C. C. (1997) The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA- and DNA-binding protein p54nrb/NonO. Molecular and Cellular Biology, 17 (2). pp. 677-86. ISSN 0270-7306 (Print)0270-7306

Batut, Philippe (2014) Promoter Evolution in Drosophila: Non-Coding Transcription & Transposon-Driven Innovation. PhD thesis, Cold Spring Harbor Laboratory.

Becker, J. D., Takeda, S., Borges, F., Dolan, L., Feijo´, J. A. (2014) Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC Plant Biology, 14 (1). ISSN 14712229

Belcher, C., Drenkow, J., Gingeras, T. R., McNamara, N., Basbaum, C., Relman, D. (2000) A role for mucin in Bordetella pertussis pathogenesis is revealed in the transcriptional profile of infected human bronchial epithelial cells. Pediatric Research, 47 (4). 257A-257A. ISSN 0031-3998

Belcher, C. E., Drenkow, J., Kehoe, B., Gingeras, T. R., McNamara, N., Lemjabbar, H., Basbaum, C., Relman, D. A. (2000) The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies. Proceedings of the National Academy of Sciences of the United States of America, 97 (25). pp. 13847-13852. ISSN 0027-8424

Bell, S. P., Kobayashi, R., Stillman, B. (1994) Transcriptional Silencing, DNA-Replication, and the Yeast Origin Recognition Complex. Journal of Cellular Biochemistry, 56 (S18C). p. 82. ISSN 0730-2312

Bell, S. P., Kobayashi, R., Stillman, B. (1993) Yeast origin recognition complex functions in transcription silencing and DNA replication. Science, 262 (5141). pp. 1844-9. ISSN 0036-8075 (Print)

Benitah, S. A., Valeron, P. F., Van Aelst, L., Marshall, C. J., Lacal, J. C. (2004) Rho GTPases in human cancer: an unresolved link to upstream and downstream transcriptional regulation. Biochimica Et Biophysica Acta-Reviews on Cancer, 1705 (2). pp. 121-132. ISSN 0304-419X

Berezikov, E., Liu, N., Flynt, A. S., Hodges, E., Rooks, M., Hannon, G. J., Lai, E. C. (2010) Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nature Genetics, 42 (1). pp. 6-9. ISSN 1061-4036

Bergmann, J. H., Rodriguez, M. G., Martins, N. M. C., Kimura, H., Kelly, D. A., Masumoto, H., Larionov, V., Jansen, L. E. T., Earnshaw, W. C. (2011) Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore. EMBO Journal, 30 (2). pp. 328-340.

Berkowitz, L. A., Gilman, M. Z. (1990) The Role of Creb in Transcriptional Activation of the C-Fos Gene by Cyclic Amp. Journal of Cellular Biochemistry, 44 (S14E). p. 171.

Bernstein, B., Bulyk, M., Bussemaker, H., Walhout, M. (2010) SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION. In: 2010 meeting on SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION, March 23–March 27, 2010.

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Siepel, A. C. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 00280836 (ISSN)

Blobel, G. A., Kadauke, S., Wang, E., Lau, A. W., Zuber, J., Chou, M. M., Vakoc, C. R. (2009) A Reconfigured Pattern of MLL Occupancy within Mitotic Chromatin Promotes Rapid Transcriptional Reactivation Following Mitotic Exit. Molecular Cell, 36 (6). pp. 970-983.

Broach, J. R., Atkins, J. F., McGill, C., Chow, L. (1979) Identification and mapping of the transcriptional and translational products of the yeast plasmid, 2mu circle. Cell, 16 (4). pp. 827-39. ISSN 0092-8674 (Print)0092-8674 (Linking)

Broker, T. R., Chow, L. T. (1979) Alternative Rna Splicing Patterns and the Clustered Transcription and Splicing Signals of Human Adenovirus 2. In: Eucaryotic gene regulation. ICN-UCLA symposia on molecular and cellular biology, 14 (ED.). Academic Press, New York, pp. 611-636.

Buchkovich, K., Dyson, N., Whyte, P., Harlow, E. (1990) Cellular proteins that are targets for transformation by DNA tumour viruses. Ciba Found Symp, 150. 262-71; discussion 271. ISSN 0300-5208 (Print)0300-5208 (Linking)

C

Caceres, J. F., Krainer, A. R., Kornblihtt, A. R. (2007) The pathology of pre-mRNA splicing: a meeting in the Italian Alps - Workshop on pre-mRNA processing and disease. Embo Reports, 8 (8). pp. 730-734. ISSN 1469-221X

Caligiuri, M., Beach, D. (1993) Sct1 functions in partnership with Cdc10 in a transcription complex that activates cell cycle START and inhibits differentiation. Cell, 72 (4). pp. 607-19. ISSN 0092-8674 (Print)

Caligiuri, M., Connolly, T., Beach, D. (1997) Ran1 functions to control the Cdc10/Sct1 complex through Puc1. Molecular Biology of the Cell, 8 (6). pp. 1117-28. ISSN 1059-1524 (Print)

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A. F., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S. (2005) The transcriptional landscape of the mammalian genome. Science, 309 (5740). pp. 1559-1563. ISSN 10959203 (ISSN)

Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S., Brown, M. (2006) Genome-wide analysis of estrogen receptor binding sites. Nature Genetics, 38 (11). pp. 1289-1297. ISSN 1061-4036

Castel, S. E., Martienssen, R. A. (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet, 14 (2). pp. 100-12. ISSN 1471-0064 (Electronic)1471-0056 (Linking)

Castel, S. E. (2014) Transcriptional regulation in the context of DNA replication by RNA interference in fission yeast. PhD thesis, Cold Spring Harbor Laboratory.

Castel, Stephane E, Ren, Jie, Bhattacharjee, Sonali, Chang, An-Yun, Sánchez, Mar, Valbuena, Alberto, Antequera, Francisco, Martienssen, Robert A (2014) Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability. Cell, 159 (3). pp. 572-583. ISSN 0092-8674

Castellano, L., Giamas, G., Jacob, J., Coombes, R. C., Lucchesi, W., Thiruchelvam, P., Barton, G., Jiao, L. R., Wait, R., Waxman, J., Hannon, G. J., Stebbing, J. (2009) The estrogen receptor-α-induced microRNA signature regulates itself and its transcriptional response. Proceedings of the National Academy of Sciences of the United States of America, 106 (37). pp. 15732-15737. ISSN 00278424 (ISSN)

Chang, K., Elledge, S. J., Hannon, G. J. (2006) Lessons from Nature: microRNA-based shRNA libraries. Nat Methods, 3 (9). pp. 707-14. ISSN 1548-7091 (Print)

Chen, H., Jackson, D., Kim, J. Y. (2014) Identification of evolutionarily conserved amino acid residues in homeodomain of KNOX proteins for intercellular trafficking. Plant Signaling and Behavior, 9 (2). ISSN 1559-2316

Chen, N., Mah, A., Blacque, O. E., Chu, J., Phgora, K., Bakhoum, M. W., Newbury, C. R. Hunt, Khattra, J., Chan, S. W., Go, A., Efimenko, E., Johnsen, R. C., Phirke, P., Swoboda, P., Marra, M., Moerman, D. G., Leroux, M. R., Baillie, D. L., Stein, L. D. (2006) Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biology, 7 (12). R126. ISSN 1474-760X

Chen, N., Stein, L. D. (2006) Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res, 16 (5). pp. 606-17. ISSN 1088-9051 (Print)

Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., Sementchenko, V., Piccolboni, A., Bekiranov, S., Bailey, D. K., Ganesh, M., Ghosh, S., Bell, I., Gerhard, D. S., Gingeras, T. R. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308 (5725). pp. 1149-1154. ISSN 00368075 (ISSN)

Cheng, Y., Ma, Z., Kim, B. H., Wu, W., Cayting, P., Boyle, A. P., Sundaram, V., Xing, X., Dogan, N., Li, J., Euskirchen, G., Lin, S., Lin, Y., Visel, A., Kawli, T., Yang, X., Patacsil, D., Keller, C. A., Giardine, B., Kundaje, A., Wang, T., Pennacchio, L. A., Weng, Z., Hardison, R. C., Snyder, M. P., Consortium, Mouse ENCODE (2014) Principles of regulatory information conservation between mouse and human. Nature, 515 (7527). pp. 371-5. ISSN 0028-0836

Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., Carlson, J. W., Landolin, J. M., Kapranov, P., Dumais, J., Samsonova, A., Choi, J. H., Roberts, J., Davis, C. A., Tang, H., Van Baren, M. J., Ghosh, S., Dobin, A., Bell, K. G., Lin, W., Langton, L., Duff, M. O., Tenney, A. E., Zaleski, C., Brent, M. R., Hoskins, R. A., Kaufman, T. C., Andrews, J., Graveley, B. R., Perrimon, N., Celniker, S. E., Gingeras, T. R., Cherbas, P. (2011) The transcriptional diversity of 25 Drosophila cell lines. Genome Research, 21 (2). pp. 301-314. ISSN 10889051 (ISSN)

Chiodi, I., Corioni, M., Giordano, M., Valgardsdottir, R., Ghigna, C., Cobianchi, F., Xu, R. M., Riva, S., Biamonti, G. (2004) RNA recognition motif 2 directs the recruitment of SF2/ASF to nuclear stress bodies. Nucleic Acids Research, 32 (14). pp. 4127-4136. ISSN 0305-1048

Chong, M. M. W., Zhang, G. A., Cheloufi, S., Neubert, T. A., Hannon, G. J., Littman, D. R. (2010) Canonical and alternate functions of the microRNA biogenesis machinery. Genes & Development, 24 (17). pp. 1951-1960. ISSN 0890-9369

Chou, S. T., Bailey, C. L., Hardison, R. C., Blobel, G. A., Vakoc, C. R., Weiss, M. J. (2007) GATA-1 represses PU.1/Sfpi-1 gene transcription in erythroMegakaryocytic progenitors. Blood, 110 (11). 371A-371A. ISSN 0006-4971

Chow, L. T., Broker, T. R. (1978) The spliced structures of adenovirus 2 fiber message and the other late mRNAs. Cell, 15 (2). pp. 497-510. ISSN 0092-8674 (Print)0092-8674 (Linking)

Chow, L. T., Broker, T. R., Lewis, J. B. (1979) Complex splicing patterns of RNAs from the early regions of adenovirus-2. J Mol Biol, 134 (2). pp. 265-303. ISSN 0022-2836 (Print)0022-2836 (Linking)

Chow, L. T., Kilpatrick, B. A., Lewis, J. B., Grodzicker, T., Sambrook, J., Gelinas, R. E., Broker, T. R. (1979) Splicing Patterns and Pathways of Adenoviral Rna Transcripts. Journal of Supramolecular Structure, 8 (SUPPL.). p. 45.

Chow, L. T., Lewis, J. B., Broker, T. R. (1980) RNA transcription and splicing at early and intermediate times after adenovirus-2 infection. Cold Spring Harb Symp Quant Biol, 44 (1). pp. 401-414.

Chuang, P. Y., Xu, J., Dai, Y., Jia, F., Mallipattu, S. K., Yacoub, R., Gu, L., Premsrirut, P. K., He, J. C. (2014) In Vivo RNA interference models of inducible and reversible sirt1 knockdown in kidney cells. The American Journal of Pathology, 184 (7). pp. 1940-56. ISSN 0002-9440

Clark, M. B., Amaral, P. P., Schlesinger, F. J., Dinger, M. E., Taft, R. J., Rinn, J. L., Ponting, C. P., Stadler, P. F., Morris, K. V., Morillon, A., Rozowsky, J. S., Gerstein, M. B., Wahlestedt, C., Hayashizaki, Y., Carninci, P., Gingeras, T. R., Mattick, J. S. (2011) The reality of pervasive transcription. Plos Biology, 9 (7). ISSN 15449173

Cleary, M. A., Pendergrast, P. S., Herr, W. (1997) Structural flexibility in transcription complex formation revealed by protein-DNA photocrosslinking. Proceedings of the National Academy of Sciences, 94 (16). pp. 8450-5. ISSN 0027-8424 (Print)

Cleary, M. A., Stern, S., Tanaka, M., Herr, W. (1993) Differential positive control by Oct-1 and Oct-2: activation of a transcriptionally silent motif through Oct-1 and VP16 corecruitment. Genes Dev, 7 (1). pp. 72-83. ISSN 0890-9369 (Print)

Collins, G. A. (2010) Activator Turnover and Proteolysis In Transcriptional Activation. PhD thesis, Cold Spring Harbor Laboratory.

Collins, G. A., Lipford, J. R., Deshaies, R. J., Tansey, W. P. (2009) Gal4 turnover and transcription activation. Nature, 461 (7265). E7-E7.

Collins, G. A., Tansey, W. P. (2006) The proteasome: a utility tool for transcription? Curr Opin Genet Dev, 16 (2). pp. 197-202. ISSN 0959-437X (Print)

Connolly, T., Caligiuri, M., Beach, D. (1997) The Cdc2 protein kinase controls Cdc10/Sct1 complex formation. Molecular Biology of the Cell, 8 (6). pp. 1105-15. ISSN 1059-1524 (Print)

Croston, G. E., Kerrigan, L. A., Lira, L. M., Marshak, D. R., Kadonaga, J. T. (1991) Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science, 251 (4994). pp. 643-9. ISSN 0036-8075 (Print)0036-8075 (Linking)

Curtin, K. D., Huang, Z. J., Rosbash, M. (1995) Temporally regulated nuclear entry of the Drosophila period protein contributes to the circadian clock. Neuron, 14 (2). pp. 365-372. ISSN 08966273 (ISSN)

D

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., Kraus, W. L. (2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell, 50 (2). pp. 212-22. ISSN 1097-2765

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T., Siepel, A. (2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods, 12 (5). pp. 433-8. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Das, D , Nahlé, Z , Zhang, M. Q. (2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol, 2. pp. 2006-2029. ISSN 1744-4292 (Electronic)

Das, G., Herr, W. (1993) Enhanced activation of the human histone H2B promoter by an Oct-1 variant generated by alternative splicing. J Biol Chem, 268 (33). pp. 25026-32. ISSN 0021-9258 (Print)

Das, R., Yu, J., Zhang, Z., Gygi, M. P., Krainer, A. R., Gygi, S. P., Reed, R. (2007) SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Molecular Cell, 26 (6). pp. 867-881. ISSN 1097-2765

Das, S., Anczuków, O., Akerman, M., Krainer, A. R (2012) Oncogenic Splicing Factor SRSF1 Is a Critical Transcriptional Target of MYC. Cell Reports, 1 (2). pp. 110-117. ISSN 2211-1247

Dasen, J. S., Martinez Barbera, J. P., Herman, T. S., Connell, S. O., Olson, L., Ju, B., Tollkuhn, J., Baek, S. H., Rose, D. W., Rosenfeld, M. G. (2001) Temporal regulation of a paired-like homeodomain repressor/TLE corepressor complex and a related activator is required for pituitary organogenesis. Genes Dev, 15 (23). pp. 3193-207. ISSN 0890-9369 (Print)0890-9369 (Linking)

Daulny, A., Geng, F., Muratani, M., Geisinger, J. M., Salghetti, S. E., Tansey, W. P. (2008) Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc Natl Acad Sci U S A, 105 (50). 19649-19654 .

Daulny, A., Tansey, W. P. (2009) Damage control: DNA repair, transcription, and the ubiquitin-proteasome system. DNA Repair, 8 (4). pp. 444-448.

Davis, G. R., Blumeyer, K., DiMichele, L. J., Whitfield, K. M., Chappelle, H., Riggs, N., Ghosh, S. S., Kao, P. M., Fahy, E., Kwoh, D. Y., Guatelli, J. C., Spector, S. A., Richman, D. D., Gingeras, T. R. (1990) Detection of human immunodeficiency virus type 1 in AIDS patients using amplification-mediated hybridization analyses: Reproducibility and quantitative limitations. Journal of Infectious Diseases, 162 (1). pp. 13-20. ISSN 00221899 (ISSN)

DeNicola, G. M., Karreth, F. A., Humpton, T. J., Gopinathan, A., Wei, C., Frese, K., Mangal, D., Yu, K. H., Yeo, C. J., Calhoun, E. S., Scrimieri, F., Winter, J. M., Hruban, R. H., Iacobuzio-Donahue, C., Kern, S. E., Blair, I. A., Tuveson, D. A. (2011) Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature, 475 (7354). pp. 106-9. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Delmore, J. E., Issa, G. C., Lemieux, M. E., Rahl, P. B., Shi, J. W., Jacobs, H. M., Kastritis, E., Gilpatrick, T., Paranal, R. M., Qi, J., Chesi, M., Schinzel, A. C., McKeown, M. R., Heffernan, T. P., Vakoc, C. R., Bergsagel, P.  , Ghobrial, I. M., Richardson, P. G., Young, R. A., Hahn, W. C., Anderson, K. C., Kung, A. L., Bradner, J. E., Mitsiades, C. S. (2011) BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc. Cell, 146 (6). pp. 904-917. ISSN 00928674 (ISSN)

Denoeud, F., Kapranov, P., Ucla, C., Frankish, A., Castelo, R., Drenkow, J., Lagarde, J., Alioto, T., Manzano, C., Chrast, J., Dike, S., Wyss, C., Henrichsen, C. N., Holroyd, N., Dickson, M. C., Taylor, R., Hance, Z., Foissac, S., Myers, R. M., Rogers, J., Hubbard, T., Harrow, J., Guigó, R., Gingeras, T. R., Antonarakis, S. E., Reymond, A. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research, 17 (6). pp. 746-759. ISSN 10889051 (ISSN)

Devlin, C., Tice-Baldwin, K., Shore, D., Arndt, K. T. (1991) RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol Cell Biol, 11 (7). pp. 3642-51. ISSN 0270-7306 (Print)0270-7306 (Linking)

Di Como, C. J., Chang, H., Arndt, K. T. (1995) Activation of CLN1 and CLN2 G1 cyclin gene expression by BCK2. Mol Cell Biol, 15 (4). pp. 1835-46. ISSN 0270-7306 (Print)

Diffley, J. F. X., Stillman, B. (1989) Transcriptional Silencing and Lamins. Nature, 342 (6245). p. 24. ISSN 0028-0836

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P., Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P., Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L. H., Shahab, A., Skancke, J., Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters, N., Wang, H., Wrobel, J., Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J., Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guig, R., Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature, 489 (7414). pp. 101-108. ISSN 0028-0836

Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J. M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R. R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M. L., Gelpí, J. L., Orozco, M., Valencia, A., van Berkum, N. L., Lajoie, B. R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S. E., Guigó, R., Gingeras, T. R. (2012) Evidence for transcript networks composed of chimeric RNA's in human cells. PLoS ONE, 7 (1). ISSN 19326203 (ISSN)

Docquier, A., Harmand, P. O., Fritsch, S., Chanrion, M., Darbon, J. M., CavaillEs, V. (2010) The transcriptional coregulator RIP140 represses E2F1 activity and discriminates breast cancer subtypes. Clinical Cancer Research, 16 (11). pp. 2959-2970.

Dore, L. C., Vakoc, C. R., Blobel, G. A., Hardison, R. C., Bodine, D. M., Gallagher, P. G., Weiss, M. J. (2005) Genomic organization, chromatin structure, and transcriptional regulation of the murine Alpha Hemoglobin Stabilizing Protein (AHSP) gene. Blood, 106 (11). 1012A-1012A. ISSN 0006-4971

Doria, M., Klein, N., Lucito, R., Schneider, R. J. (1995) The hepatitis B virus HBx protein is a dual specificity cytoplasmic activator of Ras and nuclear activator of transcription factors. Embo J, 14 (19). pp. 4747-57.

Dowen, Jill M., Bilodeau, Steve, Orlando, David A., Hübner, Michael R., Abraham, Brian J., Spector, David L., Young, Richard A. (2013) Multiple Structural Maintenance of Chromosome Complexes at Transcriptional Regulatory Elements. Stem Cell Reports, 1 (5). pp. 371-378. ISSN 2213-6711

Druker, B. J., Neumann, M., Okuda, K., Franza, B. R., Griffin, J. D. (1994) Rel Is Rapidly Tyrosine-Phosphorylated Following Granulocyte-Colony-Stimulating Factor Treatment of Human Neutrophils. Journal of Biological Chemistry, 269 (7). pp. 5387-5390. ISSN 0021-9258

Dubois, M., Van den Broeck, L., Claeys, H., Van Vlierberghe, K., Matsui, M., Inze, D. (2015) The ETHYLENE RESPONSE FACTORs ERF6 and ERF11 Antagonistically Regulate Mannitol-Induced Growth Inhibition in Arabidopsis. Plant Physiol, 169 (1). pp. 166-79. ISSN 1532-2548 (Electronic)0032-0889 (Linking)

Dynan, W. S., Gilman, M. Z. (1993) Transcriptional Control and Signal Transduction - of Soap-Opera and Reductionism. Trends Genet, 9 (5). pp. 154-156. ISSN 0168-9525

Dyson, N., Buchkovich, K., Hu, Q., Harlow, E. (1990) Cellular Targets for Transformation by DNA Tumor Viruses. Journal of Cellular Biochemistry, 44 (S14C). p. 257.

E

Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett-Jones, D. P., Le Grice, S., McKay, R. D. G., Buetow, K. H., Gingeras, T. R., Misteli, T., Meshorer, E. (2008) Global Transcription in Pluripotent Embryonic Stem Cells. Cell Stem Cell, 2 (5). pp. 437-447. ISSN 19345909 (ISSN)

Ejkova, Elena, Tansey, William P. (2002) Old dogs and new tricks: meeting on mechanisms of eukaryotic transcription. Embo Reports, 3 (3). pp. 219-23. ISSN 1469-221X

Ellisen, L. W., Palmer, R. E., Maki, R. G., Truong, V. B., Tamayo, P., Oliner, J. D., Haber, D. A. (2001) Cascades of transcriptional induction during human lymphocyte activation. Eur J Cell Biol, 80 (5). pp. 321-8. ISSN 0171-9335 (Print)0171-9335 (Linking)

Enikolopov, G., Peunova, N. (1993) Nitric-oxide potentiates the effect of calcium on transcription in neuronal cells. Journal of Cellular Biochemistry, 53 (Suppl ). p. 254. ISSN 0730-2312

Ezhkova, E. (2005) Role of the Proteasome in Gene Control. PhD thesis, Cold Spring Harbor Laboratory.

F

Fahy, E., Kwoh, D. Y., Gingeras, T. R. (1991) Self-sustained sequence replication (3SR): An isothermal transcription-based amplification system alternative to PCR. Genome Research, 1 (1). pp. 25-33. ISSN 10889051 (ISSN)

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 .

Fernald, G. H., Knott, S., Pachner, A., Caillier, S. J., Narayan, K., Oksenberg, J. R., Mousavi, P., Baranzini, S. E. (2007) Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans. J Immunol, 178 (8). pp. 5076-85. ISSN 0022-1767 (Print)0022-1767

Floer, M., Wang, X., Prabhu, V., Berrozpe, G., Narayan, S., Spagna, D., Alvarez, D., Kendall, J. T., Krasnitz, A., Stepansky,  A., Hicks, J. B., Bryant, G. O., Ptashne, M. (2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell, 141 (3). pp. 407-418.

Franza, B. R. Jr (1990) Strategies for the Study of the Regulation of Proteins That Control Mammalian Transcription. Proceedings American Association for Cancer Research Annual Meeting. p. 512.

Franza, B. R. Jr, Rauscher, F. J., Cohen, D., Voulalas, P. J., Ferreira, P. C. P., Gentz, R., Curran, T. (1989) Cooperative Interactions of Transcription Factors at the DNA Structure Designated an Ap-1 Site. Proceedings American Association for Cancer Research Annual Meeting, 80. p. 429. ISSN 1948-3279

Futcher, B. (2000) Microarrays and cell cycle transcription in yeast. Current Opinion in Cell Biology, 12 (6). pp. 710-715. ISSN 0955-0674

Futcher, B. (1988) Supercoiling and Transcription or Vice Versa. Trends in Genetics, 4 (10). pp. 271-272. ISSN 0168-9525

G

Galaktionov, K., Chen, X., Beach, D. (1996) Cdc25 cell-cycle phosphatase as a target of c-myc. Nature, 382 (6591). pp. 511-7. ISSN 0028-0836 (Print)

Gallavotti, A., Long, J. A., Stanfield, S., Yang, X. A., Jackson, D. P., Vollbrecht, E., Schmidt, R. J. (2010) The control of axillary meristem fate in the maize ramosa pathway. Development, 137 (17). pp. 2849-2856. ISSN 0950-1991

Gann, A., Himelfarb, H.J., Ptashne, M. (1992) Gal11, Gal11P and the action of Gal4. Transcriptional regulation, 2 . Cold Spring Harbor Laboratory Press. ISBN 9780879694104

Gann, A. A., Gates, P. B., Stark, D., Brockes, J. P. (1996) Receptor isoform specificity in a cellular response to retinoic acid. Proceedings of the Royal Society B: Biological Sciences, 263 (1371). pp. 729-34. ISSN 0962-8452 (Print)0962-8452

Gilman, M. (1993) Viral Transactivation - Pleiotropy and Henchman-X. Nature, 361 (6414). pp. 687-688. ISSN 0028-0836

Gingeras, T. R. (2009) Implications of chimaeric non-co-linear transcripts. Nature, 461 (7261). pp. 206-11. ISSN 1476-4687 (Electronic)

Gingeras, T. R. (2008) Mapping the strand-specific transcriptome of fission yeast. Nature Genetics, 40 (8). pp. 935-936. ISSN 1061-4036

Gingeras, T. R. (2007) Origin of phenotypes: Genes and transcripts. Genome Research, 17 (6). pp. 682-690. ISSN 10889051 (ISSN)

Gingeras, T. R. (2006) The multitasking genome. Nature Genetics, 38 (6). pp. 608-609. ISSN 10614036 (ISSN)

Gingeras, T. R., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., Kwoh, D. Y. (1990) Transcription-based amplification system and the detection of its RNA products by the bead-based sandwich hybridization system. In: PCR Protocols and Applications: Laboratory Manual. Academic Press, New York, pp. 245-252.

Gingeras, T. R., Whitfield, K. M., Kwoh, D. Y. (1990) Unique features of the self-sustained sequence replication (3SR) reaction in the in vitro amplification of nucleic acids. Annales de Biologie Clinique, 48 (7). pp. 498-501. ISSN 00033898 (ISSN)

Giuliano, G., Pollock, D., Stapp, H., Scolnik, P. A. (1988) A Genetic-Physical Map of the Rhodobacter-Capsulatus Carotenoid Biosynthesis Gene Cluster. Molecular & General Genetics, 213 (1). pp. 78-83. ISSN 0026-8925

Greenberg, M. E., Mathews, M. B. (1997) Effects of heterologous downstream sequences on the activity of the HIV-1 promoter and its response to Tat. Nucleic Acids Research, 25 (24). pp. 5017-24. ISSN 0305-1048

Greenberg, M. E., Ostapenko, D. A., Mathews, M. B. (1997) Potentiation of human immunodeficiency virus type 1 Tat by human cellular proteins. Journal of Virology, 71 (9). pp. 7140-4. ISSN 0022-538X (Print)

Grewal, S. I. S. (2000) Transcriptional silencing in fission yeast. Journal of Cellular Physiology, 184 (3). pp. 311-318. ISSN 0021-9541

Grodzicker, T., Spector, D. L., Stewart, D., Stillman, B. (2010) Nuclear Organization & Function. In: Cold Spring Harbor Symposia on Quantitative Biology LXXV: Nuclear Organization and Function, June 2–June 7, 2010.

Gunnery, S., Ma, Y., Mathews, M. B. (1999) Termination sequence requirements vary among genes transcribed by RNA polymerase III. Journal of Molecular Biology, 286 (3). pp. 745-57. ISSN 0022-2836 (Print)

Gunnery, S., Mathews, M. B. (1995) Functional mRNA can be generated by RNA polymerase III. Mol Cell Biol, 15 (7). pp. 3597-607. ISSN 0270-7306 (Print)

Gupta, G. P., Perk, J., Acharyya, S., de Candia, P., Mittal, V., Todorova-Manova, K., Gerald, W. L., Brogi, E., Benezra, R., Massague, J. (2007) ID genes mediate tumor reinitiation during breast cancer lung metastasis. Proc Natl Acad Sci U S A, 104 (49). pp. 19506-11. ISSN 1091-6490 (Electronic)

H

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145 (4). pp. 622-34. ISSN 0092-8674

Hamaguchi, M., O'Connor, E. A., Chen, T., Parnell, L., McCombie, R. W., Wigler, M. H. (1998) Rapid isolation of cDNA by hybridization. Proceedings of the National Academy of Sciences of the United States of America, 95 (7). pp. 3764-9. ISSN 0027-8424

Hammell, M., Long, D., Zhang, L., Lee, A., Carmack, C. S., Han, M., Ding, Y., Ambros, V. (2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nature Methods, 5 (9). pp. 813-9. ISSN 1548-7091 (Print)1548-7091

Hammond, S. M., Bernstein, E., Beach, D., Hannon, G. J. (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 404 (6775). pp. 293-296. ISSN 00280836 (ISSN)

Han, C. D., Derby, R. J., Schnable, P. S., Martienssen, R. A. (1995) Characterization of the plastids affected by class-ii albino mutations of maize at the morphological and transcript levels. Maydica, 40 (1). pp. 13-22. ISSN 0025-6153

He, L., He, X., Lowe, S. W., Hannon, G. J. (2007) microRNAs join the p53 network - another piece in the tumour-suppression puzzle. Nat Rev Cancer, 7 (11). pp. 819-822. ISSN 1474-1768 (Electronic)

Henderson, B. R., Tansey, W. P., Phillips, S. M., Ramshaw, I. A., Kefford, R. F. (1992) Transcriptional and posttranscriptional activation of urokinase plasminogen activator gene expression in metastatic tumor cells. Cancer Res, 52 (9). pp. 2489-96. ISSN 0008-5472 (Print)0008-5472 (Linking)

Henry, R. W., Ford, E., Mital, R., Mittal, V., Hernandez, N. (1998) Crossing the line between RNA polymerases: transcription of human snRNA genes by RNA polymerases II and III. Cold Spring Harbor Symposia on Quantitative Biology, 63. pp. 111-20. ISSN 00917451 (ISSN)

Henry, R. W., Mittal, V., Ma, B., Kobayashi, R., Hernandez, N. (1998) SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III. Genes and Development, 12 (17). pp. 2664-72. ISSN 08909369 (ISSN)

Herbst, A., Hemann, M. T., Tworkowski, K. A., Salghetti, S. E., Lowe, S. W., Tansey, W. P. (2005) A conserved element in Myc that negatively regulates its proapoptotic activity. EMBO Rep, 6 (2). pp. 177-83. ISSN 1469-221X (Print)

Hernandez, N. (2001) Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. Journal of Biological Chemistry, 276 (29). pp. 26733-26736. ISSN 0021-9258

Hernandez, N. (1993) TBP, a universal eukaryotic transcription factor? Genes Dev, 7 (7B). pp. 1291-308. ISSN 0890-9369 (Print)

Hernandez, N., Lobo, S., Lister, J., Ifill, S., Ratnasabapathy, R., Sheldon, M., Johal, L. (1990) Transcription of the human U2 and U6 RNA genes. Mol Biol Rep, 14 (2-3). p. 167. ISSN 0301-4851 (Print)0301-4851 (Linking)

Hernandez, N., Lucito, R. (1988) Elements required for transcription initiation of the human U2 snRNA gene coincide with elements required for snRNA 3' end formation. Embo J, 7 (10). pp. 3125-34.

Hernandez, N., Sadowski, C. L., Henry, R. W., Mital, R., Lobo, S. (1994) Rna-Polymerase-Ii and Rna-Polymerase-Iii Transcription of the Human Snrna Genes. Journal of Cellular Biochemistry. p. 5. ISSN 0730-2312

Herr, W. (1991) Regulation of Eukaryotic Rna Polymerase Ii Transcription by Sequence-Specific DNA-Binding Proteins. In: The hormonal control of gene transcription. Molecular aspects of cellular regulation, 6 . Elsevier Science Publishers, Amsterdam, pp. 25-26. ISBN 0444802258

Herr, W. (1993) The Sv40 Enhancer - Transcriptional Regulation through a Hierarchy of Combinatorial Interactions. Seminars in Virology, 4 (1). pp. 3-13. ISSN 1044-5773

Herr, W. (1998) The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation. Cold Spring Harbor Symposia on Quantitative Biology, 63. pp. 599-607. ISSN 00917451 (ISSN)

Herr, W., Aurora, R., Cleary, M., Das, G., Stern, S., Tanaka, M. (1991) Mechanisms of Transcriptional Activation by Pou Homeodomain Proteins Oct-1 and Oct-2. Journal of Cellular Biochemistry, 47 (Suppl ). p. 162.

Herr, W., Cleary, M. A. (1995) The POU domain: versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. Genes Dev, 9 (14). pp. 1679-93. ISSN 0890-9369 (Print)

Hogan, Megan S, Parfitt, David-Emlyn, Zepeda-Mendoza, Cinthya J, Shen, Michael M, Spector, David L (2015) Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation. Cell Stem Cell, 16 (3). pp. 275-288. ISSN 1934-5909

Hohmann, A. F., Martin, L. J., Minder, J. L., Roe, J. S., Shi, J., Steurer, S., Bader, G., McConnell, D., Pearson, M., Gerstberger, T., Gottschamel, T., Thompson, D., Suzuki, Y., Koegl, M., Vakoc, C. R. (2016) Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition. Nat Chem Biol, 12 (9). pp. 672-9. ISSN 1552-4469 (Electronic)1552-4450 (Linking)

Hong, W., Nakazawa, M., Chen, Y. Y., Kori, R., Vakoc, C. R., Rakowski, C., Blobel, G. A. (2005) FOG-1 recruits the NuRD repressor complex to mediate transcriptional repression by GATA-1. Embo Journal, 24 (13). pp. 2367-2378. ISSN 0261-4189

Hossain, M., Stillman, B. (2016) Opposing roles for DNA replication initiator proteins ORC1 and CDC6 in control of Cyclin E gene transcription. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking)

Hsu, H. C., Stillman, B., Xu, R. M. (2005) Structural basis for origin recognition complex 1 protein-silence information regulator 1 protein interaction in epigenetic silencing. Proc Natl Acad Sci U S A, 102 (24). pp. 8519-24. ISSN 0027-8424 (Print)

Hu, P., Samudre, K., Wu, S., Sun, Y., Hernandez, N. (2004) CK2 phosphorylation of Bdp1 executes cell cycle-specific RNA polymerase III transcription repression. Mol Cell, 16 (1). pp. 81-92. ISSN 1097-2765 (Print)

Hu, P., Wu, S., Hernandez, N. (2004) A role for beta-actin in RNA polymerase III transcription. Genes Dev, 18 (24). pp. 3010-5. ISSN 0890-9369 (Print)

Hu, J., Levin, P., Winkler, M. (2010) MOLECULAR GENETICS OF BACTERIA & PHAGES. In: 2010 meeting of MOLECULAR GENETICS OF BACTERIA & PHAGES, August 24–August 28, 2010, Cold Spring Harbor Laboratory.

Hua, Y. M., Vickers, T. A., Baker, B. F., Bennett, C. F., Krainer, A. R. (2007) Enhancement of SMN2 Exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biology, 5 (4). e73. ISSN 1544-9173

Huang, C. C., Herr, W. (1996) Differential control of transcription by homologous homeodomain coregulators. Mol Cell Biol, 16 (6). pp. 2967-76. ISSN 0270-7306 (Print)

Huang, C. H., Lujambio, A., Zuber, J., Tschaharganeh, D. F., Doran, M. G., Evans, M. J., Kitzing, T., Zhu, N., de Stanchina, E., Sawyers, C. L., Armstrong, S. A., Lewis, J. S., Sherr, C. J., Lowe, S. W. (2014) CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. Genes and Development, 28 (16). pp. 1800-1814. ISSN 15495477 (ISSN)

Huarte, M., Lan, F., Kim, T. H., Vaughn, M. W., Zaratiegui, B. M., Martienssen, R. A., Buratowski, S., Shi, Y. (2007) The fission yeast Jmj2 reverses histone H3 lysine 4 trimethylation. Journal of Biological Chemistry, 282 (30). pp. 21662-21670. ISSN 0021-9258

Hubner, M. R., Eckersley-Maslin, M. A., Spector, D. L. (2013) Chromatin organization and transcriptional regulation. Current Opinion in Genetics & Development, 23 (2). pp. 89-95. ISSN 0959-437X

Hubner, M. R., Spector, D. L. (2010) Role of H3K27 Demethylases Jmjd3 and UTX in Transcriptional Regulation. Cold Spring Harbor Symposia on Quantitative Biology, 75. pp. 43-49. ISSN 00917451 (ISSN)

I

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q. (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proceedings of the National Academy of Sciences, 96 (6). pp. 2891-5. ISSN 0027-8424 (Print)

J

Jackson, D. P., Culianez-Macia, F., Prescott, A. G., Roberts, K., Martin, C. (1991) Expression patterns of myb genes from Antirrhinum flowers. Plant Cell, 3 (2). pp. 115-125. ISSN 1040-4651 (Print)1040-4651 (Linking)

Javelle, M., Vernoud, V., Depège-Fargeix, N., Arnould, C., Oursel, D., Domergue, F., Sarda, X., Rogowsky, P. M. (2010) Overexpression of the epidermis-specific homeodomain-leucine zipper IV transcription factor OUTER CELL LAYER1 in maize identifies target genes involved in lipid metabolism and cuticle biosynthesis. Plant Physiology, 154 (1). pp. 273-286.

Jiang, C., Xuan, Z. Y., Zhao, F., Zhang, M. Q. (2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res, 35 (Databa). D137-D140. ISSN 0305-1048

Jiang, F., Guo, M., Yang, F., Duncan, K., Jackson, D., Rafalski, A., Wang, S., Li, B. (2012) Mutations in an AP2 transcription factor-like gene affect internode length and leaf shape in maize. PLoS ONE, 7 (5). Article no.e37040.

Jiang, W., Sordella, R., Chen, G. C., Hakre, S., Roy, A. L., Settleman, J. (2005) An FF domain-dependent protein interaction mediates a signaling pathway for growth factor-induced gene expression. Molecular Cell, 17 (1). pp. 23-35. ISSN 1097-2765

Jimenez-Garcia, L. F., Spector, D. L. (1993) In vivo evidence that transcription and splicing are coordinated by a recruiting mechanism. Cell, 73 (1). pp. 47-59. ISSN 0092-8674

Johnston, I. M., Allison, S. J., Morton, J. P., Schramm, L., Scott, P. H., White, R. J. (2002) CK2 forms a stable complex with TFIII3 and activates RNA polymerase III transcription in human cells. Molecular and Cellular Biology, 22 (11). pp. 3757-3768. ISSN 0270-7306

Jung, S. K., Jeong, D. G., Chung, S. J., Kim, J. H., Park, B. C., Tonks, N. K., Ryu, S. E., Kim, S. J. (2010) Crystal structure of ED-Eya2: insight into dual roles as a protein tyrosine phosphatase and a transcription factor. FASEB J., 24 (2). pp. 560-569. ISSN 0892-6638

K

Kaiserli, E., Paldi, K., O'Donnell, L., Batalov, O., Pedmale, U. V., Nusinow, D. A., Kay, S. A., Chory, J. (2015) Integration of Light and Photoperiodic Signaling in Transcriptional Nuclear Foci. Dev Cell, 35 (3). pp. 311-21. ISSN 1534-5807

Kannabiran, C., Morris, G. F., Labrie, C., Mathews, M. B. (1993) The Adenovirus-E1a 12s Product Displays Functional Redundancy in Activating the Human Proliferating Cell Nuclear Antigen Promoter. Journal of Virology, 67 (1). pp. 507-515. ISSN 0022-538X

Kannabiran, C., Morris, G. F., Mathews, M. B. (1999) Dual action of the adenovirus E1A 243R oncoprotein on the human proliferating cell nuclear antigen promoter: repression of transcriptional activation by p53. Oncogene, 18 (54). pp. 7825-33. ISSN 0950-9232 (Print)

Kannanganattu, P. K. V., Sacco-Bubulya, P. A., Spector, D. L. (2001) Sequential entry of transcription/RNA processing factors into post-mitotic daughter nuclei. Molecular Biology of the Cell, 12. 101A-101A. ISSN 1059-1524

Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. A., Gingeras, T. R. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296 (5569). pp. 916-919. ISSN 00368075 (ISSN)

Kapranov, P., Drenkow, J., Cheng, J., Long, J., Helt, G., Dike, S., Gingeras, T. R. (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research, 15 (7). pp. 987-997. ISSN 10889051 (ISSN)

Kapranov, P., Willingham, A. T., Gingeras, T. R. (2007) Genome-wide transcription and the implications for genomic organization. Nature Reviews Genetics, 8 (6). pp. 413-423. ISSN 14710056 (ISSN)

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.

Kaufman, P. D., Botchan, M. R. (1994) Assembly of nucleosomes: do multiple assembly factors mean multiple mechanisms? Curr Opin Genet Dev, 4 (2). pp. 229-35. ISSN 0959-437X (Print)

Kazzaz, J. A., Helfman, D. M. (1991) Transcriptional Regulation of the Beta Tropomyosin Gene. Journal of Cellular Biochemistry, 47 (Suppl ). p. 74.

Kel, A. E., Kel-Margoulis, O. V., Farnham, P. J., Bartley, S. M., Wingender, E., Zhang, M. Q. (2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology, 309 (1). pp. 99-120. ISSN 0022-2836

Kessler, M., Gunnery, S., Mathews, M. B. (1992) The Role of Tat in Transcriptional Initiation and Elongation. Aids Research and Human Retroviruses, 8 (5). p. 868. ISSN 0889-2229

Kessler, M., Mathews, M. B. (1992) Premature termination and processing of human immunodeficiency virus type 1-promoted transcripts. J Virol, 66 (7). pp. 4488-96. ISSN 0022-538X (Print)0022-538X (Linking)

Keyes, W. M., Mills, A. A. (2003) Inducible systems see the light. Trends in Biotechnology, 21 (2). pp. 53-55. ISSN 0167-7799

Kilpatrick, B. A., Gelinas, R. E., Broker, T. R., Chow, L. T. (1979) Comparison of late mRNA splicing among class B and class C adenoviruses. Journal of Virology, 30 (3). pp. 899-912. ISSN 0022-538X

Kim, S. Y., Herbst, A., Tworkowski, K. A., Salghetti, S. E., Tansey, W. P. (2003) Skp2 regulates Myc protein stability and activity. Molecular Cell, 11 (5). pp. 1177-1188. ISSN 1097-2765

Kim, Y. C., Jung, Y. C., Xuan, Z., Dong, H., Zhang, M. Q., Wang, S. M. (2006) Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters, 580 (28-29). pp. 6721-6729. ISSN 0014-5793

Kinney, J. B. (2008) Biophysical models of transcriptional regulation from sequence data. PhD thesis, Princeton University.

Kinney, J. B. (2011) Talk from Justin Kinney at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Kinney, J. B., Murugan, A., Callan, C. G., Cox, E. C. (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proceedings of the National Academy of Sciences of the United States of America, 107 (20). pp. 9158-9163. ISSN 0027-8424

Klar, A. J. S., Strathern, J. N., Broach, J. R., Hicks, J. B. (1981) Regulation of transcription in expressed and unexpressed mating type cassettes of yeast. Nature, 289 (5795). pp. 239-244. ISSN 00280836 (ISSN)

Klejman, M. P., Zhao, X. M., van Schaik, F. M. A., Herr, W., Timmers, H. T. M. (2005) Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants. Nucleic Acids Research, 33 (17). pp. 5426-5436. ISSN 0305-1048

Knott, S. R., Viggiani, C. J., Aparicio, O. M. (2009) To promote and protect: coordinating DNA replication and transcription for genome stability. Epigenetics, 4 (6). pp. 362-5. ISSN 1559-2294

Knott, S. R. V., Peace, J. M., Ostrow, A. Z., Gan, Y., Rex, A. E., Viggiani, C. J., Tavaré, S., Aparicio, O. M. (2012) Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell, 148 (1-2). pp. 99-111. ISSN 00928674 (ISSN)

Kolman, J. L., Taylor, N., Marshak, D. R., Miller, G. (1993) Serine-173 of the Epstein-Barr-Virus Zebra Protein Is Required for DNA-Binding and Is a Target for Casein Kinase-Ii Phosphorylation. Proc Natl Acad Sci U S A, 90 (21). pp. 10115-10119. ISSN 0027-8424

Koumenis, C., Alarcon, R., Hammond, E., Sutphin, P., Hoffman, W., Murphy, M., Derr, J., Taya, Y., Lowe, S. W., Kastan, M., Giaccia, A. (2001) Regulation of p53 by hypoxia: Dissociation of transcriptional repression and apoptosis from p53-dependent transactivation. Molecular and Cellular Biology, 21 (4). pp. 1297-1310. ISSN 0270-7306

Kowalczyk, M. S., Higgs, D. R., Gingeras, T. R. (2012) Molecular biology: RNA discrimination. Nature, 482 (7385). pp. 310-1. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Kraus, V. B., Moran, E., Nevins, J. R. (1992) Promoter-Specific Transactivation by the Adenovirus-E1a12s Product Involves Separate E1a Domains. Molecular and Cellular Biology, 12 (10). pp. 4391-4399. ISSN 0270-7306

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

Kumar, P. R., Yu, Y., Sternglanz, R., Johnston, S. A., Joshua-Tor, L. (2008) NADP regulates the yeast GAL induction system. Science, 319 (5866). pp. 1090-2. ISSN 1095-9203 (Electronic)

Kumaran, R. I., Spector, D. L. (2008) A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. Journal of Cell Biology, 180. pp. 51-65. ISSN 0021-9525

Kurland, J. F., Tansey, W. P. (2008) Myc-mediated transcriptional repression by recruitment of histone deacetylase. Cancer Res, 68 (10). pp. 3624-9.

Kwoh, D. Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichelle, L. J., Gingeras, T. R. (1989) Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proceedings of the National Academy of Sciences of the United States of America, 86 (4). pp. 1173-1177. ISSN 00278424 (ISSN)

Kwoh, D. Y., Gingeras, T. R. (1988) The use of transcription-based amplification systems in the diagnosis of HIV-1 infections. In: Applied virology research. Springer. ISBN 9780306446689

Kwoh, D. Y., Kwoh, T. J., Gingeras, T. R. (1991) Transcription-based amplification system. In: Methods in Gene Technology. Jai Press, London, pp. 285-299. ISBN 9781559382632

Kwoh, T. J., Zipser, D., Wigler, M. H. (1983) Mutational analysis of the cloned chicken thymidine kinase gene. J Mol Appl Genet, 2 (2). pp. 191-200. ISSN 0271-6801 (Print)

L

Labrie, C., Morris, G. F., Mathews, M. B. (1993) A complex promoter element mediates transactivation of the human proliferating cell nuclear antigen promoter by the 243-residue adenovirus E1A oncoprotein. Mol Cell Biol, 13 (3). pp. 1697-707. ISSN 0270-7306 (Print)

Lai, J. S., Cleary, M. A., Herr, W. (1992) A single amino acid exchange transfers VP16-induced positive control from the Oct-1 to the Oct-2 homeo domain. Genes Dev, 6 (11). pp. 2058-65. ISSN 0890-9369 (Print)0890-9369 (Linking)

Lai, J. S., Herr, W. (1997) Interdigitated residues within a small region of VP16 interact with Oct-1, HCF, and DNA. Molecular and Cellular Biology, 17 (7). pp. 3937-46. ISSN 0270-7306 (Print)

Lan, Fei, Zaratiegui, Mikel, Villen, Judit, Vaughn, Matthew W., Verdel, Andre, Huarte, Maite, Shi, Yujiang, Gygi, Steven P., Moazed, Danesh, Martienssen, Robert A., Shi, Yang (2007) S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Mol Cell, 26 (1). pp. 89-8101. ISSN 1097-2765

Lasa, I., Toledo-Arana, A., Gingeras, T. R. (2012) An effort to make sense of antisense transcription in bacteria. RNA Biology, 9 (8). pp. 1039-1044. ISSN 1547-6286

Laspia, M. F. (1993) Transcriptional Activation by Hiv-1 Tat in a Cell-Free System - Mechanism of Action and the Role of Cellular Proteins. Journal of Cellular Biochemistry, 53 (17E). p. 50. ISSN 0730-2312

Laspia, M. F., Rice, A. P., Mathews, M. B. (1990) Regulation of Hiv-1 Transcription at Multiple Levels Effects of Hiv-1 Tat and Adenovirus E1a on Transcriptional Initiation and Elongation. Journal of Cellular Biochemistry, 44 (S14D). p. 122.

Laspia, M. F., Rice, A. P., Mathews, M. B. (1990) Synergy between HIV-1 Tat and adenovirus E1A is principally due to stabilization of transcriptional elongation. Genes Dev, 4 (12B). pp. 2397-408. ISSN 0890-9369 (Print)0890-9369 (Linking)

Laspia, M. F., Rice, A. P., Mathews, M. B. (1991) Transactivation Hiv-1 Gene Expression by Tat Is Due to Stimulation of Both Transcriptional Initiation and Elongation. AIDS Research & Human Retroviruses, 7 (2). pp. 173-174.

Laspia, M. F., Wendel, P., Mathews, M. B. (1993) HIV-1 Tat overcomes inefficient transcriptional elongation in vitro. J Mol Biol, 232 (3). pp. 732-46. ISSN 0022-2836 (Print)

Lavy, T., Kumar, P. R., He, H. Z., Joshua-Tor, L. (2012) The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation. Genes & Development, 26 (3). pp. 294-303. ISSN 0890-9369

Lee, D. Y., Ezhkova, E., Li, B., Pattenden, S. G., Tansey, W. P., Workman, J. L. (2005) The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators. Cell, 123 (3). pp. 423-436. ISSN 0092-8674

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S., Li, C., Amamoto, R., Peters, D. T., Turczyk, B. M., Marblestone, A. H., Inverso, S. A., Bernard, A., Mali, P., Rios, X., Aach, J., Church, G. M. (2014) Highly multiplexed subcellular RNA sequencing in situ. Science, 343 (6177). pp. 1360-3. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Lee, S., Herr, W. (2001) Stabilization but not the transcriptional activity of herpes simplex virus VP16-induced complexes is evolutionarily conserved among HCF family members. Journal of Virology, 75 (24). pp. 12402-12411. ISSN 0022-538X

Lee, S., Horn, V., Julien, E., Liu, Y., Wysocka, J., Bowerman, B., Hengartner, M. O., Herr, W. (2007) Epigenetic Regulation of Histone H3 Serine 10 Phosphorylation Status by HCF-1 Proteins in C. elegans and Mammalian Cells. PLoS ONE, 2 (11). e1213. ISSN 1932-6203 (Electronic)

Leung, A., Geng, F., Daulny, A., Collins, G. A., Guzzardo, P. M., Tansey, W. P. (2008) Transcriptional control and the ubiquitin-proteasome system. Ernst Schering Found Symp Proc (1). pp. 75-97.

Li, G., Ruan, X. A., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P. C., Poh, H. M., Goh, Y., Lim, J., Zhang, J., Sim, H. S., Peh, S. Q., Mulawadi, F. H., Ong, C. T., Orlov, Y. L., Hong, S., Zhang, Z., Landt, S. G., Raha, D., Euskirchen, G., Wei, C-L., Ge, W., Wang, H., Davis, C. A., Fisher-Aylor, K. I., Mortazavi, A., Gerstein, M., Gingeras, T. R., Wold, B., Sun, Yi, Fullwood, M. J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y. (2012) Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell, 148 (1–2). pp. 84-98. ISSN 0092-8674

Li, L., Zhang, Q., Pedmale, U. V., Nito, K., Fu, W., Lin, L., Hazen, S. P., Chory, J. (2014) PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. Mol Plant, 7 (10). pp. 1582-5. ISSN 1674-2052

Li, T., Huang, J., Jiang, Y., Zeng, Y., He, F., Zhang, M. Q., Han, Z., Zhang, X. (2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics, 93 (3). pp. 235-242.

Li, Y., Lee, J., Mak, G., Ross, J., Franza, B. R. Jr (1991) The Role of the Human Rel Oncogene Product in Control of Transcription by the Human Immunodeficiency Virus Long-Terminal Repeat Hiv1-Ltr Kappab Elements. Journal of Cellular Biochemistry, 47 (Suppl ). p. 58.

Li, Y., Mak, G., Franza, B. R. (1994) In vitro study of functional involvement of Sp1, NF-kappa B/Rel, and AP1 in phorbol 12-myristate 13-acetate-mediated HIV-1 long terminal repeat activation. J Biol Chem, 269 (48). pp. 30616-9. ISSN 0021-9258 (Print)

Li, Y. C., Niu, G., Franza, B. R. (1994) Transcriptional Activation of Human Cdc2 Gene by an Oncogene, E1a 12s. Journal of Cellular Biochemistry. p. 34. ISSN 0730-2312

Li, Y. C., Ross, J., Scheppler, J. A., Franza, B. R. (1991) An in vitro transcription analysis of early responses of the human immunodeficiency virus type 1 long terminal repeat to different transcriptional activators. Mol Cell Biol, 11 (4). pp. 1883-93. ISSN 0270-7306 (Print)0270-7306 (Linking)

Lin, S., Lin, Y., Nery, J. R., Urich, M. A., Breschi, A., Davis, C. A., Dobin, A., Zaleski, C., Beer, M. A., Chapman, W. C., Gingeras, T. R., Ecker, J. R., Snyder, M. P. (2014) Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America, 111 (48). pp. 17224-17229. ISSN 0027-8424

Livi, G. P., Hicks, J. B., Klar, A. J. S. (1990) The sum1-1 mutation affects silent mating-type gene transcription in Saccharomyces cerevisiae. Molecular and Cellular Biology, 10 (1). pp. 409-412. ISSN 02707306 (ISSN)

Lobo, S. M., Ifill, S., Hernandez, N. (1990) cis-acting elements required for RNA polymerase II and III transcription in the human U2 and U6 snRNA promoters. Nucleic Acids Res, 18 (10). pp. 2891-9. ISSN 0305-1048 (Print)0305-1048 (Linking)

Lobo, S. M., Lister, J., Sullivan, M. L., Hernandez, N. (1991) The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro. Genes Dev, 5 (8). pp. 1477-89. ISSN 0890-9369 (Print)0890-9369 (Linking)

Lobo, S. M., Tanaka, M., Sullivan, M. L., Hernandez, N. (1992) A Tbp Complex Essential for Transcription from Tata-Less but Not Tata-Containing Rna Polymerase-Iii Promoters Is Part of the Tfiiib Fraction. Cell, 71 (6). pp. 1029-1040. ISSN 0092-8674

Lucito, R., Schneider, R. J. (1992) Hepatitis B virus X protein activates transcription factor NF-kappa B without a requirement for protein kinase C. J Virol, 66 (2). pp. 983-91.

Lucito, R., Schneider, R. J. (1993) Transcriptional activation by the hepatitis B virus X protein. In: Regulation of gene expression in animal viruses. Plenum Press, New York, pp. 67-80. ISBN 0306444089

Luo, W., Hankenson, K. D., Woolf, P. J. (2008) Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics, 9. p. 467.

Luo,  W., Woolf, P. J. (2010) Reconstructing transcriptional regulatory networks using three-way mutual information and Bayesian networks. In: Methods Mol Biol. Springer Science+Business Media, pp. 401-18. ISBN 1940-6029 (Electronic) 1064-3745 (Linking)

Lyon, Gholson J. (2016) New human neurologic and intellectual disability syndromes involving transcription, translation, and protein degradation. In: Columbia Child Neurology and Institute of Genomic Medicine, Columbia University, New York, NY. (Unpublished)

Lyon, Gholson J. (2016) New human neurologic and intellectual disability syndromes involving transcription, translation, and protein degradation. In: Computational Genomics Seminar Series, Icahn School of Medicine at Mount Sinai, NY. (Unpublished)

Lyon, Gholson J. (2015) Optimized sequencing leading to new human genetic syndromes involving transcription, translation, and protein degradation. In: The 24th KOGO Annual Conference 2015 & The 10th Asian Epigenomics Meeting, The Korea Science and Technology Center, Seoul, Korea. (Unpublished)

Lyon, Gholson J. (2015) Optimized sequencing leading to new human genetic syndromes involving transcription, translation, and protein degradation. In: Seminar, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. (Unpublished)

M

Ma, B., Hernandez, N. (2001) A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc. Journal of Biological Chemistry, 276 (7). pp. 5027-5035. ISSN 0021-9258

Ma, B. C., Hernandez, N. (2002) Redundant cooperative interactions for assembly of a human U6 transcription initiation complex. Molecular and Cellular Biology, 22 (22). pp. 8067-8078. ISSN 0270-7306

Maki, R. G., Old, L. J., Srivastava, P. K. (1990) Human homologue of murine tumor rejection antigen gp96: 5'-regulatory and coding regions and relationship to stress-induced proteins. Proc Natl Acad Sci U S A, 87 (15). pp. 5658-62. ISSN 0027-8424 (Print)0027-8424 (Linking)

Manak, J. R., Dike, S., Sementchenko, V., Kapranov, P., Biemar, F., Long, J., Cheng, J., Bell, I., Ghosh, S., Piccolboni, A., Gingeras, T. R. (2006) Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nature Genetics, 38 (10). pp. 1151-1158. ISSN 10614036 (ISSN)

Mangone, M., Myers, M. P., Herr, W. (2010) Role of the HCF-1 Basic Region in Sustaining Cell Proliferation. PLoS ONE, 5 (2). e9020. ISSN 1932-6203 (Electronic) 1932-6203 (Linking)

Mao, Y. S., Sunwoo, H., Zhang, B., Spector, D. L. (2011) Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nature Cell Biology, 13 (1). pp. 95-9101. ISSN 1465-7392

Maran, A., Mathews, M. B. (1988) Characterization of the double-stranded RNA implicated in the inhibition of protein synthesis in cells infected with a mutant adenovirus defective for VA RNA. Virology, 164 (1). pp. 106-13. ISSN 0042-6822

Maroney, P. A., Hannon, G. J., Nilsen, T. W. (1990) Transcription and cap trimethylation of a nematode spliced leader RNA in a cell-free system. Proceedings of the National Academy of Sciences of the United States of America, 87 (2). pp. 709-713. ISSN 00278424 (ISSN)

Masuda, H. P., Cabral, L. M., De Veylder, L., Tanurdzic, M., de Almeida Engler, J., Geelen, D., Inze, D., Martienssen, R. A., Ferreira, P. C., Hemerly, A. S. (2008) ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription. EMBO Journal, 27 (20). pp. 2746-56. ISSN 1460-2075 (Electronic)0261-4189 (Linking)

McKay, R. (1979) Probing eukaryotic gene control. Nature, 282 (5739). pp. 556-7. ISSN 0028-0836 (Print)0028-0836 (Linking)

McVey, D., Ray, S., Gluzman, Y., Berger, L., Wildeman, A. G., Marshak, D. R., Tegtmeyer, P. (1993) Cdc2 Phosphorylation of Threonine 124 Activates the Origin-Unwinding Functions of Simian-Virus 40-T Antigen. Journal of Virology, 67 (9). pp. 5206-5215. ISSN 0022-538X

Mellits, K. H., Pe'ery, T., Manche, L., Robertson, H. D., Mathews, M. B. (1990) Removal of double-stranded contaminants from RNA transcripts: synthesis of adenovirus VA RNAI from a T7 vector. Nucleic Acids Res, 18 (18). pp. 5401-6. ISSN 0305-1048 (Print)0305-1048 (Linking)

Misteli, T., Cáceres, J. F., Clement, J. Q., Krainer, A. R., Wilkinson, M. F., Spector, D. L. (1998) Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo. Journal of Cell Biology, 143 (2). pp. 297-307. ISSN 0021-9525

Misteli, T., Cáceres, J. F., Krainer, A. R., Spector, D. L. (1997) The control of splicing factor recruitment to sites of transcription in-vivo. Molecular Biology of the Cell, 8. p. 597. ISSN 1059-1524

Mital, R., Kobayashi, R., Hernandez, N. (1996) RNA polymerase III transcription from the human U6 and adenovirus type 2 VAI promoters has different requirements for human BRF, a subunit of human TFIIIB. Molecular and Cellular Biology, 16 (12). pp. 7031-42. ISSN 0270-7306

Mittal, V., Hernandez, N. (1997) Role for the amino-terminal region of human TBP in U6 snRNA transcription. Science, 275 (5303). pp. 1136-40. ISSN 0036-8075 (Print)

Mittal, V., Ma, B., Hernandez, N. (1999) SNAP(c): a core promoter factor with a built-in DNA-binding damper that is deactivated by the Oct-1 POU domain. Genes & Development, 13 (14). pp. 1807-21. ISSN 0890-9369

Miyoshi, G., Young, A., Petros, T., Karayannis, T., McKenzie Chang, M., Lavado, A., Iwano, T., Nakajima, M., Taniguchi, H., Huang, Z. J., Heintz, N., Oliver, G., Matsuzaki, F., Machold, R. P., Fishell, G. (2015) Prox1 Regulates the Subtype-Specific Development of Caudal Ganglionic Eminence-Derived GABAergic Cortical Interneurons. J Neurosci, 35 (37). pp. 12869-89. ISSN 1529-2401 (Electronic)0270-6474 (Linking)

Mizukami, Y., Ma, H. (1997) Determination of Arabidopsis floral meristem identity by AGAMOUS. Plant Cell, 9 (3). pp. 393-408. ISSN 1040-4651 (Print)

Moran, E. (1991) Cycles within cycles. Curr Biol, 1 (5). pp. 281-3. ISSN 0960-9822 (Print)0960-9822 (Linking)

Mori, N., Tajima, Y., Sakaguchi, H., Vandenbergh, D. J., Nawa, H., Salvaterra, P. M. (1993) Partial Cloning of the Rat Choline-Acetyltransferase Gene and Insitu Localization of Its Transcripts in the Cell Body of Cholinergic Neurons in the Brain-Stem and Spinal-Cord. Molecular Brain Research, 17 (1-2). pp. 101-111. ISSN 0169-328X

Morikawa, H., Ohkura, N., Vandenbon, A., Itoh, M., Nagao-Sato, S., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R., Standley, D. M., Date, H., Sakaguchi, S., FANTOM Consortium, (2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America, 111 (14). pp. 5289-94. ISSN 0027-8424

Morris, G. F., Bischoff, J. R., Mathews, M. B. (1996) Transcriptional activation of the human proliferating-cell nuclear antigen promoter by p53. Proceedings of the National Academy of Sciences, 93 (2). pp. 895-9. ISSN 0027-8424 (Print)

Muratani, Masafumi, Kung, Charles, Shokat, Kevan M., Tansey, William P. (2005) The F box protein Dsg1/Mdm30 is a transcriptional coactivator that stimulates Gal4 turnover and cotranscriptional mRNA processing. Cell, 120 (6). pp. 887-899. ISSN 0092-8674

Muratani, Masafumi, Tansey, William P. (2003) How the ubiquitin-proteasome system controls transcription. Nature Reviews Molecular Cell Biology, 4 (3). pp. 192-201. ISSN 1471-0072

Muratani, M., Gerlich, D., Janicki, S. M., Gebhard, M., Eils, R., Spector, D. L. (2002) Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nature Cell Biology, 4. pp. 106-110. ISSN 1465-7392

Murchison, E. P., Stein, P., Xuan, Z. Y., Pan, H., Zhang, M. Q., Schultz, R. M., Hannon, G. J. (2007) Critical roles for Dicer in the female germline. Genes Dev, 21 (6). pp. 682-93. ISSN 0890-9369 (Print)

Murchison, E. P., Tovar, C., Hsu, A., Bender, H. S., Kheradpour, P., Rebbeck, C. A., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, C. A., Pyecroft, S., Kreiss, A., Kellis, M., Stark, A., Harkins, T. T., Marshall Graves, J. A., Woods, G. M., Hannon, G. J., Papenfuss, A. T. (2010) The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science, 327 (5961). pp. 84-7. ISSN 1095-9203 (Electronic) 1095-9203 (Linking)

Muñoz, A., Santos Muñoz, D., Zimin, A., Yorke, J. A. (2016) Evolution of transcriptional networks in yeast: Alternative teams of transcriptional factors for different species. BMC Genomics, 17 (Suppl ). p. 826. ISSN 1471-2164

N

Nahreini, P., Mathews, M. B. (1995) Effects of the simian virus 40 origin of replication on transcription from the human immunodeficiency virus type 1 promoter. J Virol, 69 (2). pp. 1296-301. ISSN 0022-538X (Print)

Nakayama, J., Allshire, R. C., Klar, A. J. S., Grewal, S. I. S. (2001) Role for DNA polymerase alpha in epigenetic control of transcriptional silencing in fission yeast. Embo Journal, 20 (11). pp. 2857-2866. ISSN 0261-4189

Natesan, S., Gilman, M. (1993) Regulation of C-Fos Transcription by DNA Bending Mediated by P62dbf/Yy1. Journal of Cellular Biochemistry, 53 (17B). p. 85. ISSN 0730-2312

Natesan, S., Gilman, M. Z. (1993) DNA bending and orientation-dependent function of YY1 in the c-fos promoter. Genes Dev, 7 (12B). pp. 2497-509. ISSN 0890-9369 (Print)

Niida, A., Smith, A. D., Imoto, S., Tsutsumi, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics, 9. p. 404.

Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R. I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S., Saijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R. A., Babina, M., Baillie, J. K., Barnett, T. C., Beckhouse, A. G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A. J., Clevers, H. C., Davis, C. A., Detmar, M., Dohi, T., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M. C., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L. M., Fujita, R., Furusawa, J. I., Geijtenbeek, T. B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K. J., Hume, D. A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y. I., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klein, S., Klinken, S. P., Knox, A. J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A., Mackay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K. J., Motohashi, H. (2017) FANTOM5 CAGE profiles of human and mouse samples. Sci Data, 4. p. 170112. ISSN 2052-4463

O

Oliver, T. G., Mercer, K. L., Sayles, L. C., Burke, J. R., Mendus, D., Lovejoy, K. S., Cheng, M. H., Subramanian, A., Mu, D., Powers, S., Crowley, D., Bronson, R. T., Whittaker, C. A., Bhutkar, A., Lippard, S. J., Golub, T., Thomale, J., Jacks, T., Sweet-Cordero, E. A. (2010) Chronic cisplatin treatment promotes enhanced damage repair and tumor progression in a mouse model of lung cancer. Genes & Development, 24 (8). pp. 837-852. ISSN 0890-9369

P

Para, A., Li, Y., Marshall-Colon, A., Varala, K., Francoeur, N. J., Moran, T. M., Edwards, M. B., Hackley, C., Bargmann, B. O., Birnbaum, K. D., McCombie, W. R., Krouk, G., Coruzzi, G. M. (2014) Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 111 (28). pp. 10371-10378. ISSN 0027-8424

Paterson, B. M., Roberts, B. E., Mathews, M. B. (1979) Assignment of the Adenovirus-2 Messenger-Rna Transcripts to Their Respective Viral Polypeptides. Journal of Supramolecular Structure, 12 (S3). p. 71. ISSN 0091-7419

Pautler, M., Eveland, A. L., LaRue, T., Yang, F., Weeks, R., Lunde, C., Je, B. I., Meeley, R., Komatsu, M., Vollbrecht, E., Sakai, H., Jackson, D. (2015) FASCIATED EAR4 Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize. Plant Cell, 27 (1). pp. 104-120. ISSN 1040-4651

Pawlak, G., Helfman, D. M. (2002) Post-transcriptional down-regulation of ROCKI/Rho-kinase through an MEK-dependent pathway leads to cytoskeleton disruption in Ras-transformed fibroblasts. Molecular Biology of the Cell, 13 (1). pp. 336-347. ISSN 1059-1524

Paz, S., Krainer, A. R., Caputi, M. (2014) HIV-1 transcription is regulated by splicing factor SRSF1. Nucleic Acids Research, 42 (22). pp. 13812-13823. ISSN 0305-1048

Pendergrast, P. S., Hernandez, N. (1997) RNA-targeted activators, but not DNA-targeted activators, repress the synthesis of short transcripts at the human immunodeficiency virus type 1 long terminal repeat. Journal of Virology, 71 (2). pp. 910-7. ISSN 0022-538X

Pendergrast, P. S., Morrison, D., Tansey, W. P., Hernandez, N. (1996) Mutations in the carboxy-terminal domain of TBP affect the synthesis of human immunodeficiency virus type 1 full-length and short transcripts similarly. Journal of Virology, 70 (8). pp. 5025-34. ISSN 0022-538X

Perales, R., King, D. M., Aguirre-Chen, C., Hammell, C. M. (2014) LIN-42, the Caenorhabditis elegans PERIOD homolog, Negatively Regulates MicroRNA Transcription. PLoS Genetics, 10 (7). e1004486. ISSN 15537390 (ISSN)

Pessler, F., Hernandez, N. (1998) The HIV-1 inducer of short transcripts activates the synthesis of 5,6-dichloro-1-beta-D-benzimidazole-resistant short transcripts in vitro. Journal of Biological Chemistry, 273 (9). pp. 5375-84. ISSN 0021-9258 (Print)

Pessler, F., Pendergrast, P. S., Hernandez, N. (1997) Purification and characterization of FBI-1, a cellular factor that binds to the human immunodeficiency virus type 1 inducer of short transcripts. Molecular and Cellular Biology, 17 (7). pp. 3786-98. ISSN 0270-7306 (Print)

Petsch, K. A., Chonglie, M., Scanlon, M. J., Jorgensen, R. A. (2010) Targeted forward mutagenesis by transitive RNAi. The Plant Journal, 61 (5). pp. 873-882.

Peunova, N., Enikolopov, G. (1993) Amplification of calcium-induced gene transcription by nitric oxide in neuronal cells. Nature, 364 (6436). pp. 450-453. ISSN 0028-0836

Phares, W., Franza, B. R., Herr, W. (1992) The Kb Enhancer Motifs in Human-Immunodeficiency-Virus Type-1 and Simian Virus-40 Recognize Different Binding Activities in Human Jurkat and H9 T-Cells - Evidence for Nf-Kb-Independent Activation of the Kb Motif. Journal of Virology, 66 (12). pp. 7490-7498. ISSN 0022-538X

Phares, W., Franza, R., Herr, W. (1990) Relationship between the Kb Sites in the Hiv and Sv-40 Transcriptional Enhancers. Journal of Cellular Biochemistry, 44 (S14D). p. 125.

Pinto, S., Quintana, D. G., Smith, P., Mihalek, R. M., Hou, Z. H., Boynton, S., Jones, C. J., Hendricks, M., Velinzon, K., Wohlschlegel, J. A., Austin, R. J., Lane, W. S., Tully, T., Dutta, A. (1999) latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant. Neuron, 23 (1). pp. 45-54. ISSN 0896-6273 (Print)

Pistritto, G., Jost, M., Srinivasula, S. M., Baffa, R., Poyet, J. L., Kari, C., Lazebnik, Y., Rodeck, U., Alnemri, E. S. (2002) Expression and transcriptional regulation of caspase-14 in simple and complex epithelia. Cell Death and Differentiation, 9 (9). pp. 995-991006. ISSN 1350-9047

Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, Md, Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., Kawai, J., Daub, C. O., Hayashizaki, Y., Gustincich, S., Carninci, P. (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7 (7). pp. 528-34. ISSN 15487091 (ISSN)

Prasanth, K. V. , Prasanth, S. G., Xuan, Z. Y., Hearn, S., Freier, S. M., Bennett, C. F., Zhang, M. Q., Spector, D. L. (2005) Regulating gene expression through RNA nuclear retention. Cell, 123 (2). pp. 249-263. ISSN 0092-8674

Ptashne, M., Gann, A. (2001) Transcription initiation: imposing specificity by localization. In: Regulation of Gene Expression. Essays in Biochemistry, 37 . Portland Press Ltd, London, pp. 1-15. ISBN 0071-1365

Ptashne, M., Gann, A. A. (1990) Activators and targets. Nature, 346 (6282). pp. 329-31. ISSN 0028-0836 (Print)0028-0836

Ptashne, Mark, Gann, Alexander (1997) Transcriptional activation by recruitment. Nature, 386 (6625). pp. 569-577.

R

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (2009) High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biology, 10 (9). R101. ISSN 1474-7596

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

Rathert, P., Roth, M., Neumann, T., Muerdter, F., Roe, J. S., Muhar, M., Deswal, S., Cerny-Reiterer, S., Peter, B., Jude, J., Hoffmann, T., Boryn, L. M., Axelsson, E., Schweifer, N., Tontsch-Grunt, U., Dow, L. E., Gianni, D., Pearson, M., Valent, P., Stark, A., Kraut, N., Vakoc, C. R., Zuber, J. (2015) Transcriptional plasticity promotes primary and acquired resistance to BET inhibition. Nature, 525. pp. 543-547. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Raychaudhuri, P., Bagchi, S., Devoto, S. H., Kraus, V. B., Moran, E., Nevins, J. R. (1991) Domains of the adenovirus E1A protein required for oncogenic activity are also required for dissociation of E2F transcription factor complexes. Genes & Development, 5 (7). pp. 1200-1211. ISSN 0890-9369

Reilly, P. T., Herr, W. (2002) Spontaneous reversion of tsBN67 cell proliferation and cytokinesis defects in the absence of HCF-1 function. Experimental Cell Research, 277 (1). pp. 119-130. ISSN 0014-4827

Ren, J., Castel, S. E., Martienssen, R. A. (2015) Dicer in action at replication-transcription collisions. Mol Cell Oncol, 2 (3). e991224. ISSN 2372-3556 (Electronic)2372-3556 (Linking)

Ren, J., Wang, C. L., Sternglanz, R. (2010) Promoter strength influences the S phase requirement for establishment of silencing at the Saccharomyces cerevisiae silent mating type loci. Genetics, 186 (2). pp. 551-560.

Riabowol, K., Schiff, J., Gilman, M. Z. (1992) Transcription Factor Ap-1 Activity Is Required for Initiation of DNA Synthesis and Is Lost During Cellular Aging. Proceedings of the National Academy of Sciences of the United States of America, 89 (1). pp. 157-161. ISSN 0027-8424

Rice, A. P., Mathews, M. B. (1988) Transcriptional but not translational regulation of HIV-1 by the tat gene product. Nature, 332 (6164). pp. 551-3. ISSN 0028-0836

Roche, B., Arcangioli, B., Martienssen, R. A. (2017) Transcriptional reprogramming in cellular quiescence. RNA Biol, 14 (7). pp. 843-853. ISSN 1547-6286

Roe, J. S., Vakoc, C. R. (2017) The Essential Transcriptional Function of BRD4 in Acute Myeloid Leukemia. Cold Spring Harb Symp Quant Biol, 81. pp. 61-66. ISSN 0091-7451

Roe, Jae-Seok, Mercan, Fatih, Rivera, Keith, Pappin, Darryl J, Vakoc, Christopher R (2015) BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Molecular Cell, 58 (6). pp. 1028-1036. ISSN 1097-2765

Rothstein, J. L., Johnson, D., Jessee, J., Skowronski, J., Deloia, J. A., Solter, D., Knowles, B. B. (1993) Construction of Primary and Subtracted Cdna Libraries from Early Embryos. In: Guide to Techniques in Mouse Development (Methods in Enzymology. Methods in Enzymology, 225 . Academic Press Inc, San Diego, pp. 587-610. ISBN 0076-6879

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L. J., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., Candeias, R., Carlson, J. W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M. Y., Will, S., Alekseyenko, A. A., Artieri, C., Booth, B. W., Brooks, A. N., Dai, Q., Davis, C. A., Duff, M. O., Feng, X., Gorchakov, A. A., Gu, T. T., Henikoff, J. G., Kapranov, P., Li, R. H., MacAlpine, H. K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S. K., Riddle, N. C., Sakai, A., Samsonova, A., Sandler, J. E., Schwartz, Y. B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K. H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S. E., Brent, M. R., Cherbas, L., Elgin, S. C. R., Gingeras, T. R., Grossman, R., Hoskins, R. A., Kaufman, T. C., Kent, W., Kuroda, M. I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J. W., Ren, B., Russell, S., Cherbas, P., Graveley, B. R., Lewis, S., Micklem, G., Oliver, B., Park, P. J., Celniker, S. E., Henikoff, S., Karpen, G. H., Lai, E. C., MacAlpine, D. M., Stein, L. D., White, K. P., Kellis, M. (2010) Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. Science, 330 (6012). pp. 1787-1797. ISSN 0036-8075

Rozowsky, J., Wu, J., Lian, Z., Nagalakshmi, U., Korbel, J. O., Kapranov, P., Zheng, D., Dyke, S., Newburger, P., Miller, P., Gingeras, T. R., Weissman, S., Gerstein, M., Snyder, M. (2006) Novel transcribed regions in the human genome. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 111-116. ISSN 00917451 (ISSN)

Rozowsky, J. S., Newburger, D., Sayward, F., Wu, J., Jordan, G., Korbel, J. O., Nagalakshmi, U., Yang, J., Zheng, D., Guigó, R., Gingeras, T. R., Weissman, S., Miller, P., Snyder, M., Gerstein, M. B. (2007) The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Research, 17 (6). pp. 732-745. ISSN 10889051 (ISSN)

S

Sabin, L. R., Delas, M. J., Hannon, G. J. (2013) Dogma derailed: the many influences of RNA on the genome. Molecular Cell, 49 (5). pp. 783-94. ISSN 1097-2765

Sacco-Bubulya, P. A., Spector, D. L. (2001) Interchromatin granule clusters are essential for coordinating transcription and pre-mRNA splicing. Molecular Biology of the Cell, 12. 103A-103A. ISSN 1059-1524

Sachidanandam, Ravi (2005) RNAi as a bioinformatics consumer. Brief Bioinform, 6 (2). pp. 146-62. ISSN 1467-5463 (Print)

Sadowski, C. L., Henry, R. W., Kobayashi, R., Hernandez, N. (1996) The SNAP45 subunit of the small nuclear RNA (snRNA) activating protein complex is required for RNA polymerase II and III snRNA gene transcription and interacts with the TATA box binding protein. Proceedings of the National Academy of Sciences, 93 (9). pp. 4289-93. ISSN 0027-8424 (Print)

Sadowski, C. L., Henry, R. W., Lobo, S. M., Hernandez, N. (1993) Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE. Genes Dev, 7 (8). pp. 1535-48. ISSN 0890-9369 (Print)

Sadowski, Henry B., Gilman, Michael Z. (1993) Cell-free activation of a DNA-binding protein by epidermal growth factor. Nature, 362 (6415). pp. 79-83.

Salghetti, S. E., Caudy, A. A., Chenoweth, J. G., Tansey, W. P. (2001) Regulation of transcriptional activation domain function by ubiquitin. Science, 293 (5535). pp. 1651-1653. ISSN 0036-8075

Salghetti, S. E., Muratani, M., Wijnen, H., Futcher, B., Tansey, W. P. (2000) Functional overlap of sequences that activate transcription and signal ubiquitin-mediated proteolysis. Proceedings of the National Academy of Sciences of the United States of America, 97 (7). pp. 3118-3123. ISSN 0027-8424

Schalch, T., Job, G., Shanker, S., Partridge, J. F., Joshua-Tor, L. (2011) The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS. Nature Structural and Molecular Biology, 18 (12). pp. 1351-1357. ISSN 15459993 (ISSN)

Schatz, M. C. (2010) The missing graphical user interface for genomics. Genome Biology, 11 (8). p. 128. ISSN 14656914 (ISSN)

Schlesinger, F., Smith, A. D., Gingeras, T. R., Hannon, G. J., Hodges, E. (2013) De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Research, 23 (10). pp. 1601-1614. ISSN 10889051 (ISSN)

Sendoel, A., Kohler, I., Fellmann, C., Lowe, S. W., Hengartner, M. O. (2010) HIF-1 antagonizes p53-mediated apoptosis through a secreted neuronal tyrosinase. Nature, 465 (7298). 577-U69. ISSN 0028-0836

Sepehri, S., Hernandez, N. (1997) The largest subunit of human RNA polymerase III is closely related to the largest subunit of yeast and trypanosome RNA polymerase III. Genome Research, 7 (10). pp. 1006-19. ISSN 1088-9051

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)

Sheltzer, J. M., Torres, E. M., Dunham, M. J., Amon, A. (2012) Transcriptional consequences of aneuploidy. Proc Natl Acad Sci U S A, 109 (31). pp. 12644-9. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Shepard, A., Clarke, J., Herr, W. (1988) Simian virus 40 Revertant Enhancers Exhibit Restricted Host Ranges for Enhancer Function. Journal of Virology, 62 (9). pp. 3364-3370. ISSN 0022-538X

Sherman, Mara H, Yu, Ruth T, Engle, Dannielle D, Ding, Ning, Atkins, Annette R, Tiriac, Herve, Collisson, Eric A, Connor, Frances, Van Dyke, Terry, Kozlov, Serguei, Martin, Philip, Tseng, Tiffany W, Dawson, David W, Donahue, Timothy R, Masamune, Atsushi, Shimosegawa, Tooru, Apte, Minoti V, Wilson, Jeremy S, Ng, Beverly, Lau, Sue Lynn, Gunton, Jenny E, Wahl, Geoffrey M, Hunter, Tony, Drebin, Jeffrey A, O’Dwyer, Peter J, Liddle, Christopher, Tuveson, David A, Downes, Michael, Evans, Ronald M (2014) Vitamin D Receptor-Mediated Stromal Reprogramming Suppresses Pancreatitis and Enhances Pancreatic Cancer Therapy. Cell, 159 (1). pp. 80-93. ISSN 0092-8674

Sinclair, A. M., Rogers, N., Busse, L., Archibeque, I., Brown, W., Kassner, P. D., Watson, J. E. V., Arnold, G. E., Nguyen, K. C. Q., Powers, S., Elliott, S. (2008) Erythropoietin receptor transcription is neither elevated nor predictive of surface expression in human tumour cells. British Journal of Cancer, 98 (6). pp. 1059-1067. ISSN 0007-0920

Singh, Dinesh K., Kollipara, Rahul K., Vemireddy, Vamsidara, Yang, Xiao-Li, Sun, Yuxiao, Regmi, Nanda, Klingler, Stefan, Hatanpaa, Kimmo J., Raisanen, Jack, Cho, Steve K., Sirasanagandla, Shyam, Nannepaga, Suraj, Piccirillo, Sara, Mashimo, Tomoyuki, Wang, Shan, Humphries, Caroline G., Mickey, Bruce, Maher, Elizabeth A., Zheng, Hongwu, Kim, Ryung S., Kittler, Ralf, Bachoo, Robert M. (2017) Oncogenes Activate an Autonomous Transcriptional Regulatory Circuit That Drives Glioblastoma. Cell Reports, 18 (4). pp. 961-976. ISSN 2211-1247

Skowronska-Krawczyk, D., Ma, Q., Schwartz, M., Scully, K., Li, W., Liu, Z., Taylor, H., Tollkuhn, J., Ohgi, K. A., Notani, D., Kohwi, Y., Kohwi-Shigematsu, T., Rosenfeld, M. G. (2014) Required enhancer-matrin-3 network interactions for a homeodomain transcription program. Nature, 514 (7521). pp. 257-61. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Smith, A. D., Sumazin, P., Zhang, M. Q. (2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

Sobczyk, A., Svoboda, K. (2007) Activity-dependent plasticity of the NMDA-receptor fractional Ca2+ current. Neuron, 53 (1). pp. 17-24. ISSN 0896-6273 (Print)

Song, J. J., Joshua-Tor, L. (2006) Argonaute and RNA--getting into the groove. Curr Opin Struct Biol, 16 (1). pp. 5-11. ISSN 0959-440X (Print)

Speck, N. A., Vakoc, C. R. (2010) PAF Is in the Cabal of MLL1-Interacting Proteins that Promote Leukemia. Cancer Cell, 17 (6). pp. 531-532.

Spector, D. L., Sovak, M. (1989) 3-Dimensional Distribution of Small Nuclear Rnps and Reorganization of Small Nuclear Rnp-Enriched Nuclear Regions Upon Alterations in the Level of Transcription. Journal of Cell Biology, 109 (4 PART). 39A. ISSN 0021-95251540-8140

Spector, D. L. (2007) Nuclear retained rnas regulating gene expression. Faseb Journal, 21 (5). A97. ISSN 0892-6638

Spector, D. L., O'Keefe, R. T., Landon, S., Jimenez Garcia, L. F. (1994) Coordination of Transcription and Pre-Messenger-Rna Splicing within the Cell-Nucleus. Journal of Cellular Biochemistry, 56 (S18C). p. 85. ISSN 0730-2312

Spector, D. L., O'Keefe, R. T., Jimenez-Garcia, L. F. (1993) Dynamics of transcription and pre-mRNA splicing within the mammalian cell nucleus. Cold Spring Harbor Symposia on Quantitative Biology, 58. pp. 799-805. ISSN 00917451 (ISSN)

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

Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Hodges, E., Hinrichs, A. S., Caspi, A., Park, S. W., Han, M. V., Maeder, M. L., Polansky, B. J., Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M. W., Park, Y., Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J., Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M., Kellis, M. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450 (7167). pp. 219-232. ISSN 0028-0836

Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S. E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T. R., Gonzalez, D., Grimmond, S. M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T. J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M. H., Searle, S. M. J., Solorzano, N. D., Solovyev, V., Stanke, M., Stevenson, B. J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B. J., Wu, J., Wu, T. D., Zeller, G., Zerbino, D., Zhang, M. Q. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. ISSN 15487091 (ISSN)

Stern, S., Herr, W. (1991) Interactions of the Transcriptional Transactivator Vp16 with the Oct-1 Homeodomain DNA and Hcf. Journal of Biomolecular Structure & Dynamics, 8 (6). A217.

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

Sturm, R. A., Cassady, J. L., Das, G., Romo, A., Evans, G. A. (1993) Chromosomal Structure and Expression of the Human Otf1 Locus Encoding the Oct-1 Protein. Genomics, 16 (2). pp. 333-341. ISSN 0888-7543

Sturm, R. A., Dalton, S., Wells, J. R. E. (1988) Conservation of Histone H2a-H2b Intergene Regions a Role for the H2b Specific Element in Divergent Transcription. Nucleic Acids Research, 16 (17). pp. 8571-8586. ISSN 0305-1048

Szymanski, P., Stenlund, A. (1991) Regulation of early gene expression from the bovine papillomavirus genome in transiently transfected C127 cells. J Virol, 65 (11). pp. 5710-20. ISSN 0022-538x

T

Tanaka, M. (1996) Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo. Proceedings of the National Academy of Sciences of the United States of America, 93 (9). pp. 4311-5. ISSN 0027-8424

Tanaka, M., Clouston, W. M., Herr, W. (1994) The Oct-2 glutamine-rich and proline-rich activation domains can synergize with each other or duplicates of themselves to activate transcription. Mol Cell Biol, 14 (9). pp. 6046-55. ISSN 0270-7306 (Print)

Tanaka, M., Herr, W. (1990) Differential transcriptional activation by Oct-1 and Oct-2: interdependent activation domains induce Oct-2 phosphorylation. Cell, 60 (3). pp. 375-86. ISSN 0092-8674 (Print)0092-8674 (Linking)

Tanaka, M., Herr, W. (1994) Reconstitution of transcriptional activation domains by reiteration of short peptide segments reveals the modular organization of a glutamine-rich activation domain. Mol Cell Biol, 14 (9). pp. 6056-67. ISSN 0270-7306 (Print)

Tansey, W. P. (2001) Transcriptional activation: risky business. Genes & Development, 15 (9). pp. 1045-1050. ISSN 0890-9369

Tansey, W. P. (2004) Transcriptional control and the ubiquitin/proteasome system. Molecular Biology of the Cell, 15 (Suppl.). 119A. ISSN 1059-1524

Tansey, W. P. (2000) Transcriptional regulation: RUPture in the ER. Nature Cell Biology, 2 (10). E175-E177. ISSN 1465-7392

Tansey, W. P., Ejkova, E., Kim, S. Y., Herbst, A., Muratani, M., Salghetti, S. E., Tworkowski, K. A. (2003) Transcriptional control and the ubiquitin-proteasome system. Faseb Journal, 17 (5). A1184-A1184 Part 2 Supp. S. ISSN 0892-6638

Tansey, W. P., Herr, W. (1994) In-Vivo Analysis of the Human Tata-Binding Protein - Surfaces Required for Activated Transcription in Human-Cells. Journal of Cellular Biochemistry, Supp (18C). p. 38. ISSN 0730-2312

Tansey, W. P., Herr, W. (1997) TAFs: guilt by association? Cell, 88 (6). pp. 729-32. ISSN 0092-8674

Tansey, W. P., Herr, W. (1995) The ability to associate with activation domains in vitro is not required for the TATA box-binding protein to support activated transcription in vivo. Proc Natl Acad Sci U S A, 92 (23). pp. 10550-4. ISSN 0027-8424 (Print)

Tansey, W. P. , Ezhkova, E. (2004) Transcriptional control and the ubiquitin-proteasome system. Faseb Journal, 18 (8). C315-C315 Suppl S.. ISSN 0892-6638

Tansey, William P., Herr, Winship (1997) Selective use of TBP and TFIIB revealed by a TATA-TBP-TFIIB array with altered specificity. Science, 275 (5301). pp. 829-31. ISSN 0036-8075 (Print)

Tansey, William P., Ruppert, Siegfried, Tjian, Robert, Herr, Winship (1994) Multiple regions of TBP participate in the response to transcriptional activators in vivo. Genes Dev, 8 (22). pp. 2756-69. ISSN 0890-9369 (Print)

Taylor, D. R., Mathews, M. B. (1993) Transcription by SP6 RNA polymerase exhibits an ATP dependence that is influenced by promoter topology. Nucleic Acids Res, 21 (8). pp. 1927-33. ISSN 0305-1048 (Print)

Theriault, G., Roy, P. H., Howard, K. A., Benner, J. S., Brooks, J. E., Waters, A. F., Gingeras, T. R. (1985) Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Research, 13 (23). pp. 8441-8461. ISSN 03051048 (ISSN)

Thomann, W., Herr, W. (1993) Transcriptional Activation of Messenger-Rna Promoters by the Octamer Motif in Nonlymphoid Cells. Journal of Cellular Biochemistry, 53 (17A). p. 94. ISSN 0730-2312

Tice-Baldwin, K., Fink, G. R., Arndt, K. T. (1989) BAS1 has a Myb motif and activates HIS4 transcription only in combination with BAS2. Science, 246 (4932). pp. 931-5. ISSN 0036-8075

Tonelli, C., Chio, I. I. C., Tuveson, D. A. (2017) Transcriptional regulation by Nrf2. Antioxid Redox Signal. ISSN 1523-0864

Tripathi, V., Song, D. Y., Zong, X., Shevtsov, S. P., Hearn, S., Fu, X. D., Dundr, M., Prasanth, K. V. (2012) SRSF1 modulates the organization of splicing factors in nuclear speckles and regulates transcription. Mol Biol Cell, 23 (18). pp. 3694-3706. ISSN 1939-4586 (Electronic)1059-1524 (Linking)

Tripic, T., Deng, W., Cheng, Y., Zhang, Y., Vakoc, C. R., Gregory, G. D., Hardison, R. C., Blobel, G. A. (2009) SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood, 113 (10). pp. 2191-2201. ISSN 00064971 (ISSN)

Tyagi, S., Chabes, A. L., Wysocka, J., Herr, W. (2007) E2F Activation of S Phase Promoters via Association with HCF-1 and the MLL Family of Histone H3K4 Methyltransferases. Molecular Cell, 27 (1). pp. 107-119. ISSN 1097-2765

Tyers, M., Tokiwa, G., Futcher, B. (1993) Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. Embo J, 12 (5). pp. 1955-68. ISSN 0261-4189 (Print)

Tyler, D. M., Okamura, K., Chung, W. J., Hagen, J. W., Berezikov, E., Hannon, G. J., Lai, E. C. (2008) Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes and Development, 22 (1). pp. 26-36. ISSN 08909369 (ISSN)

V

Vakoc, C. R. (2012) Talk from Chris Vakoc at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Vakoc, C. R., Mandat, S. A., Olenschock, B. A., Blobel, G. A. (2005) Histone H3 lysine 9 methylation and HP1 gamma are associated with transcription elongation through mammalian chromatin. Blood, 106 (11). 493A-493A. ISSN 0006-4971

Van Aalten, D. M. F., Grotewold, E., Joshua-Tor, L. (1998) Essential dynamics from NMR clusters: Dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant. Methods, 14 (3). pp. 318-328. ISSN 10462023 (ISSN)

Van Scoy, S., Watakabe, I., Krainer, A. R., Hearing, J. (2000) Human p32: A coactivator for Epstein-Barr virus nuclear antigen-1-mediated transcriptional activation and possible role in viral latent cycle DNA replication. Virology, 275 (1). pp. 145-157. ISSN 0042-6822

W

Wanner, L. A., Li, G., Ware, D., Somssich, I. E., Davis, K. R. (1995) The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana. Plant Mol Biol, 27 (2). pp. 327-38. ISSN 0167-4412 (Print)

Willingham, A. T., Dike, S., Cheng, J., Manak, J. R., Bell, I., Cheung, E., Drenkow, J., Dumais, E., Duttagupta, R., Ganesh, M., Ghosh, S., Helt, G., Nix, D., Piccolboni, A., Sementchenko, V., Tammana, H., Kapranov, P., Gingeras, T. R. (2006) Transcriptional landscape of the human and fly genomes: Nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harbor Symposia on Quantitative Biology, 71. pp. 101-110. ISSN 00917451 (ISSN)

Willy, P. J., Kobayashi, R., Kadonaga, J. T. (2000) A basal transcription factor that activates or represses transcription. Science, 290 (5493). pp. 982-984. ISSN 0036-8075

Wilson, A. C., Cleary, M. A., Lai, J. S., LaMarco, K., Peterson, M. G., Herr, W. (1993) Combinatorial control of transcription: the herpes simplex virus VP16-induced complex. Cold Spring Harb Symp Quant Biol, 58. pp. 167-78. ISSN 0091-7451 (Print)

Wilson, A. C., LaMarco, K., Peterson, M. G., Herr, W. (1993) The VP16 accessory protein HCF is a family of polypeptides processed from a large precursor protein. Cell, 74 (1). pp. 115-25. ISSN 0092-8674 (Print)

Wilusz, J. E., Sunwoo, H., Spector, D. L. (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes & Development, 23 (13). pp. 1494-1504. ISSN 0890-9369

Wong, M. W., Henry, R. W., Ma, B., Kobayashi, R., Klages, N., Matthias, P., Strubin, M., Hernandez, N. (1998) The large subunit of basal transcription factor SNAPc is a Myb domain protein that interacts with Oct-1. Molecular and Cellular Biology, 18 (1). pp. 368-77. ISSN 0270-7306 (Print)

Wu, H., Sun, S., Tu, K., Gao, Y., Xie, B., Krainer, A. R., Zhu, J. (2010) A Splicing-Independent Function of SF2/ASF in MicroRNA Processing. Molecular Cell, 38 (1). pp. 67-77.

X

Xu, C., Park, S. J., Van Eck, J., Lippman, Z. B. (2016) Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators. Genes Dev, 30 (18). pp. 2048-2061. ISSN 0890-9369 (Print)0890-9369 (Linking)

Xu, M.X., Jackson, D. (2012) Cell-to-cell Movement of Homeodomain Transcription Factors: Yesterday, Today and Tomorrow. In: Short and Long Distance Signaling. Advances in Plant Biology, 3 (3). Springer, pp. 87-98. ISBN 978-1-4419-1531-3

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)

Xu, X. M., Wang, J., Xuan, Z. Y., Goldshmidt, A., Borrill, P. G. M., Hariharan, N., Kim, J. Y., Jackson, D. P. (2011) Chaperonins Facilitate KNOTTED1 Cell-to-Cell Trafficking and Stem Cell Function. Science, 333 (6046). pp. 1141-1144. ISSN 1095-9203

Xu, Y., Vakoc, C. R. (2017) Targeting Cancer Cells with BET Bromodomain Inhibitors. Cold Spring Harb Perspect Med, 7 (7). ISSN 2157-1422

Xuan, Z. Y., Zhao, F., Wang, J., Chen, G., Zhang, M. Q. (2005) Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology, 6 (8). R72. ISSN 1465-6906

Y

Yang, L. V., Wan, J., Ge, Y., Fu, Z., Kim, S. Y., Fujiwara, Y., Taub, J. W., Matherly, L. H., Eliason, J., Li, L. (2006) The GATA site-dependent hemogen promoter is transcriptionally regulated by GATA1 in hematopoietic and leukemia cells. Leukemia, 20 (3). pp. 417-425. ISSN 08876924

Yang, Z., Jiang, H., Zhao, F., Shankar, D. B., Sakamoto, K. M., Zhang, M. Q., Lin, S. (2007) A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish. Bmc Developmental Biology, 7. ISSN 1471-213X

Yin, Hong, Wang, Michelle D., Svoboda, Karel, Landick, Robert, Block, Steven M., Gelles, Jeff (1995) Transcription against an applied force. Science, 270 (5242). pp. 1653-7. ISSN 0036-8075

Yu, Y., Gu, J., Jin, Y., Luo, Y., Preall, J. B., Ma, J., Czech, B., Hannon, G. J. (2015) Panoramix enforces piRNA-dependent cotranscriptional silencing. Science, 350 (6258). pp. 339-42. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Yuan, C. C., Zhao, X., Florens, L., Swanson, S. K., Washburn, M. P., Hernandez, N. (2007) CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription. Mol Cell Biol, 27 (24). pp. 8729-8738. ISSN 0270-7306 (Print)

Z

Zhang, M. Q. (2005) Using CorePromoter to find human core promoters. Curr Protoc Bioinformatics, Chapte. Unit 2.9. ISSN 1934-340X (Electronic)

Zhang, M. Q. (1998) A discrimination study of human core-promoters. Pacific Symposium on Biocomputing. pp. 240-51.

Zhang, Qiang, Zeng, Lei, Shen, Chen, Ju, Ying, Konuma, Tsuyoshi, Zhao, Chengcheng, Vakoc, Christopher R, Zhou, Ming-Ming (2016) Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4. Structure. ISSN 0969-2126

Zhang, X., Lian, Z., Padden, C., Gerstein, M. B., Rozowsky, J., Snyder, M., Gingeras, T. R., Kapranov, P., Weissman, S. M., Newburger, P. E. (2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood, 113 (11). pp. 2526-34. ISSN 1528-0020 (Electronic)

Zhang, B., Arun, G., Mao, Y. S., Lazar, Z., Hung, G., Bhattacharjee, G., Xiao, X., Booth, C. J., Wu, J., Zhang, C., Spector, D. L. (2012) The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Reports, 2 (1). pp. 111-123. ISSN 2211-1247

Zhao, F., Xuan, Z., Liu, L., Zhang, M. Q. (2005) TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Res, 33 (Databa). D103-107. ISSN 1362-4962 (Electronic)

Zhao, Xi., Xuan, Z. Y., Zhang, M. Q. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol, 8 (2). R17. ISSN 1465-6914 (Electronic)

Zhao, Z. Y., Fang, L., Chen, N. S., Johnsen, R. C., Stein, L., Baillie, D. L. (2005) Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans. Journal of Biological Chemistry, 280 (46). pp. 38787-38794. ISSN 0021-9258

Zhao, R., Bodnar, M. S., Spector, D. L. (2009) Nuclear neighborhoods and gene expression. Current Opinion in Genetics & Development, 19 (2). pp. 172-179. ISSN 0959-437X

Zhao, R., Nakamura, T., Fu, Y., Lazar, Z., Spector, D. L. (2011) Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nature Cell Biology, 13 (11). 1295-1304 . ISSN 1465-7392

Zhu, G. F., Spellman, P. T., Volpe, T., Brown, P. O., Botstein, D., Davis, T. N., Futcher, B. (2000) Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature, 406 (6791). pp. 90-94. ISSN 0028-0836

This list was generated on Mon Oct 23 13:38:01 2017 EDT.
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving