Items where Subject is "transcription"

A

Abuhashem, Abderhman, Chivu, Alexandra, Zhao, Yixin, Rice, Edward, Siepel, Adam, Danko, Charles, Hadjantonakis, Anna-Katerina (2022) RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. bioRxiv. (Submitted)

Abuhashem, Abderhman, Chivu, Alexandra G, Zhao, Yixin, Rice, Edward J, Siepel, Adam, Danko, Charles G, Hadjantonakis, Anna-Katerina (August 2022) RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes and Development. ISSN 0890-9369

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. (November 2011) Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Research, 21 (11). pp. 1788-1799. ISSN 10889051 (ISSN)

Alexander, Katherine A, Coté, Allison, Nguyen, Son C, Zhang, Liguo, Gholamalamdari, Omid, Agudelo-Garcia, Paula, Lin-Shiao, Enrique, Tanim, KMA, Lim, Joan, Biddle, Nicolas, Dunagin, Margaret C, Good, Charly R, Mendoza, Mariel R, Little, Shawn C, Belmont, Andrew, Joyce, Eric F, Raj, Arjun, Berger, Shelley L (April 2021) p53 mediates target gene association with nuclear speckles for amplified RNA expression. Molecular Cell, 81 (8). 1666-1681.e6. ISSN 1097-2765

Alexandre, C., Gilman, M. (January 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. (February 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. (April 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. (May 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. (February 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. (October 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. (April 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. (October 2001) LAF1, a MYB transcription activator for phytochrome A signaling. Genes & Development, 15 (19). pp. 2613-2625. ISSN 0890-9369

Ballouz, Sara, Kawaguchi, Risa Karakida, Pena, Maria T, Fischer, Stephan, Crow, Megan, French, Leon, Knight, Frank M, Adams, Linda B, Gillis, Jesse (November 2023) The transcriptional legacy of developmental stochasticity. Nature Communications, 14 (1). p. 7226. ISSN 2041-1723 (Public Dataset)

Banerjee, N., Zhang, M. Q. (June 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. (January 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. (January 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. (February 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, P. J., Gingeras, T. R. (December 2017) Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife, 6. ISSN 2050-084x

Batut, Philippe (April 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. (August 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. (April 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. (December 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. (February 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. (December 1993) Yeast origin recognition complex functions in transcription silencing and DNA replication. Science, 262 (5141). pp. 1844-9. ISSN 0036-8075 (Print)

Belliveau, N. M., Barnes, S. L., Ireland, W. T., Jones, D. L., Sweredoski, M. J., Moradian, A., Hess, S., Kinney, J. B., Phillips, R. (May 2018) Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A, 115 (21). E4796-e4805. ISSN 0027-8424

Belliveaul, N. M., Barnes, S. L., Ireland, W. T., Beeler, S. M., Kinney, J. B., Phillip, R. (February 2018) A Systematic and Scalable Approach for Dissecting the Molecular Mechanisms of Transcriptional Regulation in Bacteria. Biophysical Journal, 114 (3; Sup). 151A-151A. ISSN 0006-3495

Benitah, S. A., Valeron, P. F., Van Aelst, L., Marshall, C. J., Lacal, J. C. (December 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

Benoit, M. (August 2020) The Great Escape: How a Plant DNA Virus Hijacks an Imprinted Host Gene to Avoid Silencing. Plant Cell, 32 (10). pp. 3051-3052. ISSN 1040-4651

Berezikov, E., Liu, N., Flynt, A. S., Hodges, E., Rooks, M., Hannon, G. J., Lai, E. C. (January 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. (December 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. (March 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. (December 2009) A Reconfigured Pattern of MLL Occupancy within Mitotic Chromatin Promotes Rapid Transcriptional Reactivation Following Mitotic Exit. Molecular Cell, 36 (6). pp. 970-983.

Breschi, A., Muñoz-Aguirre, M., Wucher, V., Davis, C. A., Garrido-Martín, D., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Reverter, F., Snyder, M. P., Gingeras, T. R., Guigó, R. (July 2020) A limited set of transcriptional programs define major cell types. Genome Res, 30 (7). pp. 1047-1059. ISSN 1088-9051 (Print)1088-9051

Broach, J. R., Atkins, J. F., McGill, C., Chow, L. (April 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.

Broker, T. R., Chow, L. T. (July 1980) Patterns and Consequences of Adenoviral Rna Splicing - Ex-Pluribus-Unum - Ex-Uno-Plura. Trends in Biochemical Sciences, 5 (7). pp. 174-177.

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)

Burko, Y., Seluzicki, A., Zander, M., Pedmale, U., Ecker, J.R., Chory, J. (February 2020) Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism. Plant Cell. ISSN 1040-4651

C

Caceres, J. F., Krainer, A. R., Kornblihtt, A. R. (August 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. (February 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. (June 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)

Cao, Zhendong, Budinich, Krista A, Huang, Hua, Ren, Diqiu, Lu, Bin, Zhang, Zhen, Chen, Qingzhou, Zhou, Yeqiao, Huang, Yu-Han, Alikarami‬, Fatemeh, Kingsley, Molly C, Lenard, Alexandra K, Wakabayashi, Aoi, Khandros, Eugene, Bailis, Will, Qi, Jun, Carroll, Martin P, Blobel, Gerd A, Faryabi, Robert B, Bernt, Kathrin M, Berger, Shelley L, Shi, Junwei (August 2021) ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Molecular Cell. ISSN 1097-2765

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. (November 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. (February 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. (September 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 (October 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)

Catizone, Allison N, Good, Charly Ryan, Alexander, Katherine A, Berger, Shelley L, Sammons, Morgan A (April 2019) Comparison of genotoxic versus nongenotoxic stabilization of p53 provides insight into parallel stress-responsive transcriptional networks. Cell Cycle, 18 (8). pp. 809-823. ISSN 1538-4101

Chang, K., Elledge, S. J., Hannon, G. J. (September 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. (February 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. (December 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. (May 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, H., Capponi, S., Wakeling, E., Marchi, E., Li, Q., Zhao, M., Weng, C., Stefan, P. G., Ahlfors, H., Kleyner, R., Rope, A., Lumaka, A., Lukusa, P., Devriendt, K., Vermeesch, J., Posey, J. E., Palmer, E. E., Murray, L., Leon, E., Diaz, J., Worgan, L., Mallawaarachchi, A., Vogt, J., de Munnik, S. A., Dreyer, L., Baynam, G., Ewans, L., Stark, Z., Lunke, S., Goncalves, A. R., Soares, G., Oliveira, J., Fassi, E., Willing, M., Waugh, J. L., Faivre, L., Riviere, J. B., Moutton, S., Mohammed, S., Payne, K., Walsh, L., Begtrup, A., Guillen Sacoto, M. J., Douglas, G., Alexander, N., Buckley, M. F., Mark, P. R., Ades, L. C., Sandaradura, S. A., Lupski, J. R., Roscioli, T., Agrawal, P. B., Kline, A. D., Wang, K., Timmers, H. T. M., Lyon, G. J. (October 2019) Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity. Hum Mutat. ISSN 1059-7794

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) (Public Dataset)

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 (November 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) (Public Dataset)

Chiodi, I., Corioni, M., Giordano, M., Valgardsdottir, R., Ghigna, C., Cobianchi, F., Xu, R. M., Riva, S., Biamonti, G. (August 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. (September 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. (November 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. (October 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. (October 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. (July 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. (July 2011) The reality of pervasive transcription. Plos Biology, 9 (7). ISSN 15449173 (Public Dataset)

Cleary, M. A., Pendergrast, P. S., Herr, W. (August 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. (January 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. (March 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. (October 2009) Gal4 turnover and transcription activation. Nature, 461 (7265). E7-E7.

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

Connelly, Carla J, Vidal-Cardenas, Sofia, Goldsmith, Stephanie, Greider, Carol W (November 2021) The Bur1 cyclin-dependent kinase regulates telomere length in Saccharomyces cerevisiae. Yeast. ISSN 0749-503X

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

Coté, Allison, O'Farrell, Aoife, Dardani, Ian, Dunagin, Margaret, Coté, Chris, Wan, Yihan, Bayatpour, Sareh, Drexler, Heather L, Alexander, Katherine A, Chen, Fei, Wassie, Asmamaw T, Patel, Rohan, Pham, Kenneth, Boyden, Edward S, Berger, Shelly, Phillips-Cremins, Jennifer, Churchman, L Stirling, Raj, Arjun (April 2024) Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife, 12. ISSN 2050-084X (Public Dataset)

Croston, G. E., Kerrigan, L. A., Lira, L. M., Marshak, D. R., Kadonaga, J. T. (February 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

Dachet, Fabien, Brown, James B, Valyi-Nagy, Tibor, Narayan, Kunwar D, Serafini, Anna, Boley, Nathan, Gingeras, Thomas R, Celniker, Susan E, Mohapatra, Gayatry, Loeb, Jeffrey A (March 2021) Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Scientific Reports, 11 (1). p. 6078. ISSN 2045-2322

Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L., Siepel, A. (January 2018) Dynamic evolution of regulatory element ensembles in primate CD4(+) T cells. Nat Ecol Evol. pp. 1-12. ISSN 2397-334x

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., Kraus, W. L. (April 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. (May 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. (June 2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol, 2. pp. 2006-2029. ISSN 1744-4292 (Electronic)

Das, G., Herr, W. (November 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, P. P., Shao, Z., Beyaz, S., Apostolou, E., Pinello, L., Angeles, A. L., O'Brien, K., Atsma, J. M., Fujiwara, Y., Nguyen, M., Ljuboja, D., Guo, G., Woo, A., Yuan, G. C., Onder, T., Daley, G., Hochedlinger, K., Kim, J., Orkin, S. H. (January 2014) Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell, 53 (1). pp. 32-48. ISSN 1097-4164 (Electronic)1097-2765 (Linking)

Das, R., Yu, J., Zhang, Z., Gygi, M. P., Krainer, A. R., Gygi, S. P., Reed, R. (June 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. (December 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. (April 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. (July 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. (September 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) (Public Dataset)

Devlin, C., Tice-Baldwin, K., Shore, D., Arndt, K. T. (July 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. (April 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. (November 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. (September 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. (January 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. (June 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. (November 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. (October 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. (October 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. (February 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. (September 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)

Dukler, N., Booth, G. T., Huang, Y. F., Tippens, N., Waters, C. T., Danko, C. G., Lis, J. T., Siepel, A. (November 2017) Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Res, 27 (11). pp. 1816-1829. ISSN 1088-9051

Dukler, Noah, Booth, Gregory, Huang, Yi-Fei, Tippens, Nathaniel, Danko, Charles, Lis, John, Siepel, Adam (March 2017) Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. BioRxiv. (Unpublished)

Dunn, A. R., Hassell, J. A. (1977) A Novel Method to Map Transcripts Evidence for Homology between an Adenovirus Messenger Rna and Discrete Multiple Regions of the Viral Genome. Cell, 12 (1). pp. 23-36.

Dynan, W. S., Gilman, M. Z. (May 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) (Public Dataset)

Ejkova, Elena, Tansey, William P. (March 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. (May 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)

Engler, J. A., Chow, L. T., Broker, T. R. (1981) Sequences of Human Adenovirus-Ad3 and Adenovirus-Ad7 Dnas Encoding the Promoter and 1st Leader Segment of Late Rnas. Gene, 13 (2). pp. 133-143.

Enikolopov, G., Peunova, N. (March 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. (March 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. (April 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

Flint, S. J., Wewerka-Lutz, Y., Levine, A. S., Sambrook, J., Sharp, P. A. (September 1975) Adenovirus transcription. II. RNA sequences complementary to simian virus 40 and adenovirus 2DNA in AD2+ND1- and AD2+ND3-infected cells. J Virol, 16 (3). pp. 662-73.

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. (April 2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell, 141 (3). pp. 407-418.

Frangeul, Laura, Pouchelon, Gabrielle, Telley, Ludovic, Lefort, Sandrine, Luscher, Christian, Jabaudon, Denis (October 2016) A cross-modal genetic framework for the development and plasticity of sensory pathways. Nature, 538 (7623). pp. 96-98. ISSN 0028-0836

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

Futcher, B. (October 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. (August 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. (September 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. (June 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

Gegenhuber, Bruno (April 2022) Epigenomic organization and activation of brain sex differences. PhD thesis, Cold Spring Harbor Laboratory.

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

Gingeras, T. R. (September 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. (July 1988) A Genetic-Physical Map of the Rhodobacter-Capsulatus Carotenoid Biosynthesis Gene Cluster. Molecular & General Genetics, 213 (1). pp. 78-83. ISSN 0026-8925

Gladman, N., Jiao, Y., Lee, Y. K., Zhang, L., Chopra, R., Regulski, M., Burow, G., Hayes, C., Christensen, S. A., Dampanaboina, L., Chen, J., Burke, J., Ware, D., Xin, Z. (October 2019) Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. Int J Mol Sci, 20 (19). ISSN 1422-0067

Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, JA, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-Ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-Sueki, H, Frith, MC, Abugessaisa, I, Aitken, S, Aken, BL, Alam, I, Alam, T, Alasiri, R, Alhendi, AMN, Alinejad-Rokny, H, Alvarez, MJ, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, AL, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, JK, Bajic, VB, Bajpai, A, Baker, S, Baldarelli, RM, Balic, A, Bansal, M, Batagov, AO, Batzoglou, S, Beckhouse, AG, Beltrami, AP, Beltrami, CA, Bertin, N, Bhattacharya, S, Bickel, PJ, Blake, JA, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, JB, Bult, CJ, Burroughs, AM, Burt, DW, Busch, A, Caglio, G, Califano, A, Cameron, CJ, Cannistraci, CV, Carbone, A, Carlisle, AJ, Carninci, P, Carter, KW, Cesselli, D, Chang, JC, Chen, JC, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, EL, Coskun, M, Dalby, M, Dalla, E, Daub, CO, Davis, CA, de Hoon, MJL, de Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, AD, Dieterich, LC (June 2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1). ISSN 2041-1723 (In Press)

Greenberg, M. E., Mathews, M. B. (December 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. (September 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. (September 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. (June 2010) Nuclear Organization & Function. In: Cold Spring Harbor Symposia on Quantitative Biology LXXV: Nuclear Organization and Function, June 2–June 7, 2010.

Gryder, B. E., Pomella, S., Sayers, C., Wu, X. S., Song, Y., Chiarella, A. M., Bagchi, S., Chou, H. C., Sinniah, R. S., Walton, A., Wen, X., Rota, R., Hathaway, N. A., Zhao, K., Chen, J., Vakoc, C. R., Shern, J. F., Stanton, B. Z., Khan, J. (December 2019) Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nat Genet, 51 (12). pp. 1714-1722. ISSN 1061-4036 (Public Dataset)

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

Guo, Yu, Alexander, Katherine, Clark, Andrew G, Grimson, Andrew, Yu, Haiyuan (November 2016) Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs. RNA: A publication of the RNA Society, 22 (11). pp. 1663-1672. ISSN 1355-8382

Gupta, G. P., Perk, J., Acharyya, S., de Candia, P., Mittal, V., Todorova-Manova, K., Gerald, W. L., Brogi, E., Benezra, R., Massague, J. (December 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. (May 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. (March 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. (September 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

Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712

He, L., He, X., Lowe, S. W., Hannon, G. J. (November 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)

Hegelmeyer, Nuri K, Parkin, Lia A, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C (October 2023) Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria. mBio. e0084123. ISSN 2150-7511

Henderson, B. R., Tansey, W. P., Phillips, S. M., Ramshaw, I. A., Kefford, R. F. (May 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. (September 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. (February 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. (July 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. (July 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. (October 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. (February 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. (February 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. (July 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 (March 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. (September 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) (Public Dataset)

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. (July 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) (Public Dataset)

Hoyt, Savannah J, Storer, Jessica M, Hartley, Gabrielle A, Grady, Patrick GS, Gershman, Ariel, de Lima, Leonardo G, Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J, Gerton, Jennifer L, Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian FA, Straight, Aaron F, Vollger, Mitchell R, Wheeler, Travis J, Schatz, Michael C, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Miga, Karen H, O'Neill, Rachel J (April 2022) From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science, 376 (6588). eabk3112. ISSN 0036-8075

Hsu, H. C., Stillman, B., Xu, R. M. (June 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. (October 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. (December 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. (August 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. (April 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. (June 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. (August 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. (July 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. (April 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)

Hurst, Laurence D, Ghanbarian, Avazeh T, Forrest, Alistair RR, FANTOM consortium, Huminiecki, Lukasz (December 2015) The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology, 13 (12). e1002315. ISSN 1544-9173

I

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q. (March 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. (February 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. (January 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. (May 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. (January 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. (June 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. (February 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. (November 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. (January 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. (December 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. (November 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) (Public Dataset)

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. (June 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. (January 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. (April 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. (May 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

Keller, W., Muller, U., Eicken, I., Wendel, I., Zentgraf, H. (1977) Biochemical and Ultrastructural Analysis of Sv40-Chromatin. Cold Spring Harbor Symposia on Quantitative Biology, 42. pp. 227-244.

Kessler, M., Gunnery, S., Mathews, M. B. (May 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. (July 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. (February 2003) Inducible systems see the light. Trends in Biotechnology, 21 (2). pp. 53-55. ISSN 0167-7799

Khan, Omar, Giles, Josephine R, McDonald, Sierra, Manne, Sasikanth, Ngiow, Shin Foong, Patel, Kunal P, Werner, Michael T, Huang, Alexander C, Alexander, Katherine A, Wu, Jennifer E, Attanasio, John, Yan, Patrick, George, Sangeeth M, Bengsch, Bertram, Staupe, Ryan P, Donahue, Greg, Xu, Wei, Amaravadi, Ravi K, Xu, Xiaowei, Karakousis, Giorgos C, Mitchell, Tara C, Schuchter, Lynn M, Kaye, Jonathan, Berger, Shelley L, Wherry, E John (June 2019) TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature, 571 (7764). pp. 211-218. ISSN 0028-0836

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. (May 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. (December 2006) Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters, 580 (28-29). pp. 6721-6729. ISSN 0014-5793

Kinney, Brian, Sahu, Shubham, Stec, Natalia, Hills-Muckey, Kelly, Adams, Dexter W, Wang, Jing, Jaremko, Matt, Joshua-Tor, Leemor, Keil, Wolfgang, Hammell, Christopher M (August 2023) A circadian-like gene network programs the timing and dosage of heterochronic miRNA transcription during C. elegans development. Developmental Cell. S1534-5807(23)00402. ISSN 1534-5807

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

Kinney, J. B. (November 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. (May 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. (August 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. (January 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. (November 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. (February 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. (February 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. (October 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. (January 2015) On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme. Cell, 160 (4). pp. 644-658. ISSN 0092-8674 (Public Dataset)

Kuhn, C. D., Wilusz, J. E., Zheng, Y., Beal, P. A., Joshua-Tor, L. (July 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. (February 2008) NADP regulates the yeast GAL induction system. Science, 319 (5866). pp. 1090-2. ISSN 1095-9203 (Electronic) (Public Dataset)

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. (May 2008) Myc-mediated transcriptional repression by recruitment of histone deacetylase. Cancer Res, 68 (10). pp. 3624-9.

Kurtz, D. T. (1981) Hormonal Inducibility of Rat Alpha-2u Globulin Genes in Transfected Mouse Cells. Nature (London), 291 (5817). pp. 629-631.

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)

Kwoh, D. Y., Zipser, D. (1981) Identification of the Gin Protein of Bacteriophage-Mu. Virology, 114 (1). pp. 291-296.

L

Labrie, C., Morris, G. F., Mathews, M. B. (March 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. (November 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. (July 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)

Laise, Pasquale, Turunen, Mikko, Maurer, Hans Carlo, Garcia, Alvaro Curiel, Elyada, Ela, Schmierer, Bernhard, Tomassoni, Lorenzo, Worley, Jeremy, Alvarez, Mariano J, Kesner, Jordan, Tan, Xiangtian, Tagore, Somnath, Fernandez, Ester Calvo, Wong, Kelly, Wang, Alexander LE, Ge, Sabrina, Iuga, Alina C, Griffin, Aaron T, Wong, Winston, Manji, Gulam A, Notta, Faiyaz, Tuveson, David A, Olive, Kenneth PP, Califano, Andrea (2022) Pancreatic cancer comprises co-existing transcriptional states regulated by distinct master regulator programs. In: AACR Special Conference on Pancreatic Cancer, 2022 Sep 13-16, Boston, MA.

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

Lanctot, Amy (August 2023) The root of the mystery: The role of long non-coding RNAs in regulating transcription. Plant Physiology. kiad434. ISSN 0032-0889

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

Laspia, M. F. (March 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. (December 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. (August 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. (February 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 (Public Dataset)

Lee, D. Y., Ezhkova, E., Li, B., Pattenden, S. G., Tansey, W. P., Workman, J. L. (November 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. (March 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. (December 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. (November 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. (October 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. (March 2009) Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics, 93 (3). pp. 235-242.

Li, Y., Brooks, M., Yeoh-Wang, J., McCoy, R. M., Rock, T. M., Pasquino, A., Moon, C. I., Patrick, R. M., Tanurdzic, M., Ruffel, S., Widhalm, J. R., McCombie, W. R., Coruzzi, G. M. (October 2019) SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiol. ISSN 0032-0889

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. (December 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. (February 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. (April 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. (November 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

Lin-Shiao, Enrique, Lan, Yemin, Welzenbach, Julia, Alexander, Katherine A, Zhang, Zhen, Knapp, Michael, Mangold, Elisabeth, Sammons, Morgan, Ludwig, Kerstin U, Berger, Shelley L (May 2019) p63 establishes epithelial enhancers at critical craniofacial development genes. Science Advances, 5 (5). ISSN 2375-2548

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. (May 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. (August 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. (December 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. (February 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. (November 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. (February 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. (April 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. (September 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. (September 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. (February 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. (November 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. (August 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) (Public Dataset)

Mangone, M., Myers, M. P., Herr, W. (February 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. (May 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. (October 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)

Mathews, M. B. (1980) Binding of Adenovirus Va Rna to Messenger-Rna - Possible Role in Splicing. Nature, 285 (5766). pp. 575-577.

McKay, R. (December 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. (September 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

Medwig-Kinney, Taylor N, Kinney, Brian A, Martinez, Michael AQ, Yee, Callista, Sirota, Sydney S, Mullarkey, Angelina A, Somineni, Neha, Hippler, Justin, Zhang, Wan, Shen, Kang, Hammell, Christopher, Pani, Ariel M, Matus, David Q (December 2023) Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans. eLife, 12. RP84355. ISSN 2050-084X

Mellits, K. H., Pe'ery, T., Manche, L., Robertson, H. D., Mathews, M. B. (September 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)

Meng, Fei-Long, Du, Zhou, Federation, Alexander, Hu, Jiazhi, Wang, Qiao, Kieffer-Kwon, Kyong-Rim, Meyers, Robin M, Amor, Corina, Wasserman, Caitlyn R, Neuberg, Donna, Casellas, Rafael, Nussenzweig, Michel C, Bradner, James E, Liu, X Shirley, Alt, Frederick W (December 2014) Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell, 159 (7). pp. 1538-48. ISSN 1097-4172

Miller, J. S., Ricciardi, R. P., Roberts, B. E., Paterson, B. M., Mathews, M. B. (1980) Arrangement of Messenger-Rnas and Protein Coding Sequences in the Major Late Transcription Unit of Adenovirus-2. Journal of Molecular Biology, 142 (4). pp. 455-488.

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. (November 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. (December 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. (February 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. (July 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. (September 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. (March 1997) Determination of Arabidopsis floral meristem identity by AGAMOUS. Plant Cell, 9 (3). pp. 393-408. ISSN 1040-4651 (Print)

Moore, J. E., Purcaro, M. J., Pratt, H. E., Epstein, C. B., Shoresh, N., Adrian, J., Kawli, T., Davis, C. A., Dobin, A., Kaul, R., Halow, J., Van Nostrand, E. L., Freese, P., Gorkin, D. U., Shen, Y., He, Y., Mackiewicz, M., Pauli-Behn, F., Williams, B. A., Mortazavi, A., Keller, C. A., Zhang, X. O., Elhajjajy, S. I., Huey, J., Dickel, D. E., Snetkova, V., Wei, X., Wang, X., Rivera-Mulia, J. C., Rozowsky, J., Zhang, J., Chhetri, S. B., Zhang, J., Victorsen, A., White, K. P., Visel, A., Yeo, G. W., Burge, C. B., Lécuyer, E., Gilbert, D. M., Dekker, J., Rinn, J., Mendenhall, E. M., Ecker, J. R., Kellis, M., Klein, R. J., Noble, W. S., Kundaje, A., Guigó, R., Farnham, P. J., Cherry, J. M., Myers, R. M., Ren, B., Graveley, B. R., Gerstein, M. B., Pennacchio, L. A., Snyder, M. P., Bernstein, B. E., Wold, B., Hardison, R. C., Gingeras, T. R., Stamatoyannopoulos, J. A., Weng, Z. (July 2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583 (7818). pp. 699-710. ISSN 0028-0836 (Print)0028-0836

Moran, E. (October 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. (January 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 (April 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. (January 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. (March 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. (March 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. (March 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. (January 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)

Murphy, Kristin E, Shylo, Natalia A, Alexander, Katherine A, Churchill, Angela J, Copperman, Cecilia, García-García, María J (September 2016) The Transcriptional Repressive Activity of KRAB Zinc Finger Proteins Does Not Correlate with Their Ability to Recruit TRIM28. PLoS ONE, 11 (9). e0163555-e0163555. ISSN 1932-6203

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. (February 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. (June 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. (January 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. (December 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. (September 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. (August 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. (April 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

Olson, Andrew J, Ware, Doreen (July 2021) Ranked Choice Voting for Representative Transcripts with TRaCE. Bioinformatics. ISSN 1367-4803

Omary, Moutasem, Gil-Yarom, Naama, Yahav, Chen, Steiner, Evyatar, Hendelman, Anat, Efroni, Idan (March 2022) A conserved superlocus regulates above- and belowground root initiation. Science, 375 (6584). eabf4368. ISSN 0036-8075

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. (June 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. (January 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. (January 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. (November 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. (February 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. (August 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. (July 2014) LIN-42, the Caenorhabditis elegans PERIOD homolog, Negatively Regulates MicroRNA Transcription. PLoS Genetics, 10 (7). e1004486. ISSN 15537390 (ISSN)

Pessler, F., Hernandez, N. (February 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. (July 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. (December 2010) Targeted forward mutagenesis by transitive RNAi. The Plant Journal, 61 (5). pp. 873-882.

Peunova, N., Enikolopov, G. (July 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. (December 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. (May 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. (June 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. (October 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. (July 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.

Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle S, Su, Min, Yin, Zhou, Winkelman, Jared T, Kinney, Justin B, Ebright, Richard H, Nickels, Bryce E (June 2022) Structural and mechanistic basis of σ-dependent transcriptional pausing. Proceedings of the National Academy of Sciences of USA, 119 (23). e2201301119. ISSN 0027-8424

Pukhrambam, Chirangini, Molodtsov, Vadim, Kooshkbaghi, Mahdi, Tareen, Ammar, Vu, Hoa, Skalenko, Kyle S, Su, Min, Zhou, Yin, Winkelman, Jared T, Kinney, Justin B, Ebright, Richard H, Nickels, Bryce E (January 2022) Structural and mechanistic basis of σ-dependent transcriptional pausing. BioRxiv. (Unpublished)

R

Ramani, A. K., Nelson, A. C., Kapranov, P., Bell, I., Gingeras, T. R., Fraser, A. G. (September 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. (August 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. (September 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. (July 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. (July 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. (July 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. (October 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. (January 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. (April 1988) Transcriptional but not translational regulation of HIV-1 by the tat gene product. Nature, 332 (6164). pp. 551-3. ISSN 0028-0836

Roberts, R. J. (November 1976) Restriction endonucleases. CRC Crit Rev Biochem, 4 (2). pp. 123-64.

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

Roe, J. S., Vakoc, C. R. (February 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 (June 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. (December 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. (March 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. (November 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 (June 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. (April 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. (August 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. (March 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. (August 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. (March 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) (Public Dataset)

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. (June 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. (June 2010) HIF-1 antagonizes p53-mediated apoptosis through a secreted neuronal tyrosinase. Nature, 465 (7298). 577-U69. ISSN 0028-0836

Sepehri, S., Hernandez, N. (October 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. (February 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. (July 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. (September 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 (September 2014) Vitamin D Receptor-Mediated Stromal Reprogramming Suppresses Pancreatitis and Enhances Pancreatic Cancer Therapy. Cell, 159 (1). pp. 80-93. ISSN 0092-8674

Siepel, Adam, Zhao, Yixin, Liu, Lingjie (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Research Square. (Submitted)

Siepel, Adam (January 2021) A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data. bioRxiv. (Unpublished)

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. (March 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. (January 2017) Oncogenes Activate an Autonomous Transcriptional Regulatory Circuit That Drives Glioblastoma. Cell Reports, 18 (4). pp. 961-976. ISSN 2211-1247

Skalenko, Kyle, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina, Winkelman, Jared, Cope, Alexander, Taylor, Deanne, Shah, Premal, Ebright, Richard, Kinney, Justin, Zhang, Yu, Nickels, Bryce (April 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. BioRxiv. (Unpublished)

Skalenko, Kyle S, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina O, Winkelman, Jared T, Cope, Alexander L, Taylor, Deanne M, Shah, Premal, Ebright, Richard H, Kinney, Justin B, Zhang, Yu, Nickels, Bryce E (July 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proceedings of the National Academy of Sciences of USA, 118 (27). e2106388118-e2106388118. ISSN 0027-8424

Skalka, Anna Marie (May 1966) Regional and temporal control of genetic transcription in phage lambda. Proceedings of the National Academy of Sciences, 55 (5). pp. 1190-1195.

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. (October 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. (January 2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

Sobczyk, A., Svoboda, K. (January 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. (February 2006) Argonaute and RNA--getting into the groove. Curr Opin Struct Biol, 16 (1). pp. 5-11. ISSN 0959-440X (Print)

Soto-Feliciano, Yadira M, Sánchez-Rivera, Francisco J, Perner, Florian, Barrows, Douglas W, Kastenhuber, Edward R, Ho, Yu-Jui, Carroll, Thomas, Xiong, Yijun, Anand, Disha, Soshnev, Alexey A, Gates, Leah, Beytagh, Mary Clare, Cheon, David, Gu, Shengqing, Liu, X Shirley, Krivtsov, Andrei V, Meneses, Maximiliano, de Stanchina, Elisa, Stone, Richard M, Armstrong, Scott A, Lowe, Scott W, Allis, C David (January 2023) A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition. Cancer Discovery, 13 (1). pp. 146-169. ISSN 2159-8274

Speck, N. A., Vakoc, C. R. (June 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. (November 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. (April 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. (February 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. (May 2000) The essential Mcm7 protein PROLIFERA is localized to the nucleus of dividing cells during the G(1) phase and is required maternally for early Arabidopsis development. Development, 127 (9). pp. 1815-1822. ISSN 0950-1991

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. (November 2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450 (7167). pp. 219-232. ISSN 0028-0836

Stec, N., Doerfel, K., Hills-Muckey, K., Ettorre, V. M., Ercan, S., Keil, W., Hammell, C. M. (December 2020) An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output during C. elegans Development. Curr Biol. ISSN 0960-9822

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. (November 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. (May 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. (September 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

Sun, Yu-Chi, Chen, Xiaoyin, Fischer, Stephan, Lu, Shaina, Zhan, Huiqing, Gillis, Jesse, Zador, Anthony M (May 2021) Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. Nature Neuroscience. ISSN 1097-6256

Szymanski, P., Stenlund, A. (November 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. (April 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. (September 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. (February 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. (September 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. (May 2001) Transcriptional activation: risky business. Genes & Development, 15 (9). pp. 1045-1050. ISSN 0890-9369

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

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

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

Tansey, William P., Herr, Winship (February 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 (November 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)

Tarumoto, Y., Lu, B., Somerville, T. D. D., Huang, Y. H., Milazzo, J. P., Wu, X. S., Klingbeil, O., El Demerdash, O., Shi, J., Vakoc, C. R. (March 2018) LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia. Mol Cell, 69 (6). pp. 1017-1027. ISSN 1097-2765

Taylor, D. R., Mathews, M. B. (April 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)

Tenenbaum, Debora, Inlow, Koe, Friedman, Larry J, Cai, Anthony, Gelles, Jeff, Kondev, Jane (July 2023) RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons. Proceedings of the National Academy of Sciences of USA, 120 (30). e2301402120. ISSN 0027-8424

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. (January 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

Thomas, G. P., Mathews, M. B. (1980) DNA-Replication and the Early to Late Transition in Adenovirus Infection. Cell, 22 (2). pp. 523-533.

Tice-Baldwin, K., Fink, G. R., Arndt, K. T. (November 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. (September 2017) Transcriptional regulation by Nrf2. Antioxid Redox Signal. ISSN 1523-0864

Tran, Thu M, Swentowsky, Kyle W (May 2024) Trehalose or Not-Trehalose: The Question of Direct vs. Indirect Transcriptional Responses to the sugar trehalose-6-phosphate. Plant Physiology. kiae306. ISSN 0032-0889

Tripathi, V., Song, D. Y., Zong, X., Shevtsov, S. P., Hearn, S., Fu, X. D., Dundr, M., Prasanth, K. V. (September 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)

Turcan, Sevin, Makarov, Vladimir, Taranda, Julian, Wang, Yuxiang, Fabius, Armida W. M., Wu, Wei, Zheng, Yupeng, El-Amine, Nour, Haddock, Sara, Nanjangud, Gouri, LeKaye, H. Carl, Brennan, Cameron, Cross, Justin, Huse, Jason T., Kelleher, Neil L., Osten, Pavel, Thompson, Craig B., Chan, Timothy A. (January 2018) Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence. Nature Genetics, 50 (1). pp. 62-72. ISSN 1546-1718

Tyagi, S., Chabes, A. L., Wysocka, J., Herr, W. (July 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. (May 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)

U

Utama, R., Bastian, A., Sadagopan, N., Jin, Y., Antoniou, E., Huang, Y., Lee, P., Atwal, G. (July 2018) Transcriptional landscape of stroma progression in the breast tumor microenvironment. Cancer Research, 78 (13 S). meeting abstract : LB-357. ISSN 0008-5472

V

Vakoc, C. R. (November 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. (November 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. (March 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. (September 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

Varala, K., Marshall-Colon, A., Cirrone, J., Brooks, M. D., Pasquino, A. V., Leran, S., Mittal, S., Rock, T. M., Edwards, M. B., Kim, G. J., Ruffel, S., McCombie, W. R., Shasha, D., Coruzzi, G. M. (May 2018) Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proc Natl Acad Sci U S A. ISSN 0027-8424

W

Wai, D. C., Szyszka, T. N., Campbell, A. E., Kwong, C., Wilkinson-White, L. E., Silva, A. P. G., Low, J. K. K., Kwan, A. H., Gamsjaeger, R., Chalmers, J. N., Patrick, W. M., Lu, B., Vakoc, C. R., Blobel, G., Mackay, J. P. (May 2018) The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. J Biol Chem, 293 (19). pp. 7160-7175. ISSN 0021-9258

Walisko, O., Schorn, A. J., Rolfs, F., Devaraj, A., Miskey, C., Izsvak, Z., Ivics, Z. (February 2008) Transcriptional activities of the Sleeping Beauty transposon and shielding its genetic cargo with insulators. Molecular Therapy, 16 (2). pp. 359-69. ISSN 1525-0016

Wang, X., Chen, Q., Wu, Y., Lemmon, Z. H., Xu, G., Huang, C., Liang, Y., Xu, D., Li, D., Doebley, J. F., Tian, F. (March 2018) Genome-wide analysis of transcriptional variability in a large maize-teosinte population. Mol Plant, 11 (3). pp. 443-459. ISSN 1674-2052

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

Weingartner, B., Keller, W. (1981) Transcription and Processing of Adenoviral Rna by Extracts from Hela-Cells. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences, 78 (7). pp. 4092-4096.

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. (November 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. (June 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. (July 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. (July 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. (January 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, Xiaoli S, Vakoc, Christopher R (May 2023) Made to order tuft cells by an OCA-T1 isoform switch. Science Immunology, 8 (83). eadh3123. ISSN 2470-9468

Wu, H., Sun, S., Tu, K., Gao, Y., Xie, B., Krainer, A. R., Zhu, J. (April 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. (September 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. (October 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. (August 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. (July 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. (August 2007) A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish. Bmc Developmental Biology, 7. p. 97. ISSN 1471-213X

Yang, RS, Xu, F, Wang, YM, Zhong, WS, Dong, L, Shi, YN, Tang, TJ, Sheng, HJ, Jackson, D, Yang, F (December 2021) Glutaredoxins regulate maize inflorescence meristem development via redox control of TGA transcriptional activity. Nature Plants. ISSN 2055-0278

Yin, Hong, Wang, Michelle D., Svoboda, Karel, Landick, Robert, Block, Steven M., Gelles, Jeff (December 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. (October 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. (December 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)

Yuste, R., Hawrylycz, M., Aalling, N., Aguilar-Valles, A., Arendt, D., Arnedillo, R. A., Ascoli, G. A., Bielza, C., Bokharaie, V., Bergmann, T. B., Bystron, I., Capogna, M., Chang, Y., Clemens, A., de Kock, C. P. J., DeFelipe, J., Dos Santos, S. E., Dunville, K., Feldmeyer, D., Fiáth, R., Fishell, G. J., Foggetti, A., Gao, X., Ghaderi, P., Goriounova, N. A., Güntürkün, O., Hagihara, K., Hall, V. J., Helmstaedter, M., Herculano, S., Hilscher, M. M., Hirase, H., Hjerling-Leffler, J., Hodge, R., Huang, J., Huda, R., Khodosevich, K., Kiehn, O., Koch, H., Kuebler, E. S., Kühnemund, M., Larrañaga, P., Lelieveldt, B., Louth, E. L., Lui, J. H., Mansvelder, H. D., Marin, O., Martinez-Trujillo, J., Moradi Chameh, H., Nath, A., Nedergaard, M., Němec, P., Ofer, N., Pfisterer, U. G., Pontes, S., Redmond, W., Rossier, J., Sanes, J. R., Scheuermann, R., Serrano-Saiz, E., Steiger, J. F., Somogyi, P., Tamás, G., Tolias, A. S., Tosches, M. A., García, M. T., Vieira, H. M., Wozny, C., Wuttke, T. V., Yong, L., Yuan, J., Zeng, H., Lein, E. (August 2020) A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci, 23 (12). pp. 1456-1468. ISSN 1097-6256

Ywoh, D. Y., Zipser, D. (1981) Identification of the Gin Protein of Bacterio Phage Mu. Virology, 114 (1). pp. 291-296.

Z

Zhang, M. Q. (July 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 (June 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. (March 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, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam (October 2023) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Research. ISSN 0305-1048

Zhao, Yixin, Liu, Lingjie, Siepel, Adam (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. bioRxiv. (Submitted)

Zhao, F., Xuan, Z., Liu, L., Zhang, M. Q. (January 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. (February 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. (November 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. (April 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. (November 2011) Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nature Cell Biology, 13 (11). 1295-1304 . ISSN 1465-7392

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803

Zhou, Jessica, Guruvayurappan, Karthik, Toneyan, Shushan, Chen, Hsiuyi V, Chen, Aaron R, Koo, Peter, McVicker, Graham (July 2024) Analysis of single-cell CRISPR perturbations indicates that enhancers act multiplicatively and provides limited evidence for epistatic-like interactions. bioRxiv. (Public Dataset) (Submitted)

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