Items where Subject is "transcription"

Paper

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)

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

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.

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. (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

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, 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., 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)

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

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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

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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)

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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)

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Book Section

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.

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.

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

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

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., 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)

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

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

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

Conference or Workshop Item

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.

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.

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.

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.

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)

Book

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

Thesis

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

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.

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

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

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

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

Video

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

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