 | Up a level |
Abraham, S. E., Lobo, S., Yaciuk, P., Wang, H. G., Moran, E. (June 1993) p300, and p300-associated proteins, are components of TATA-binding protein (TBP) complexes. Oncogene, 8 (6). pp. 1639-47. ISSN 0950-9232
Aksoy, O., Chicas, A., Zeng, T., Zhao, Z., McCurrach, M., Wang, X., Lowe, S. W. (July 2012) The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence. Genes Dev, 26 (14). pp. 1546-57. ISSN 1549-5477 (Electronic)0890-9369 (Linking)
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)
Arbiza, L., Gronau, I., Aksoy, B. A., Hubisz, M. J., Gulko, B., Keinan, A., Siepel, A. (July 2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet, 45 (7). pp. 723-9. ISSN 1061-4036
Atanasoski, S., Schreiber, E., Fontana, A., Herr, W. (March 1997) N-Oct 5 is generated by in vitro proteolysis of the neural POU-domain protein N-Oct 3. Oncogene, 14 (11). pp. 1287-94. ISSN 0950-9232 (Print)
Babb, R., Cleary, M. A., Herr, W. (December 1997) OCA-B is a functional analog of VP16 but targets a separate surface of the Oct-1 POU domain. Molecular and Cellular Biology, 17 (12). pp. 7295-305. ISSN 0270-7306 (Print)
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
Banerjee, N., Zhang, M. Q. (December 2003) Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Research, 31 (23). pp. 7024-7031. ISSN 0305-1048
Barnes, S. L., Belliveau, N. M., Ireland, W. T., Kinney, J. B., Phillips, R. (February 2019) Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comput Biol, 15 (2). e1006226. ISSN 1553-734x
Barrot, M., Olivier, J. D. A., Perrotti, L. I., DiLeone, R. J., Berton, O., Eisch, A. J., Impey, S., Storm, D. R., Neve, R. L., Yin, J. C., Zachariou, V., Nestler, E. J. (August 2002) CREB activity in the nucleus accumbens shell controls gating of behavioral responses to emotional stimuli. Proceedings of the National Academy of Sciences of the United States of America, 99 (17). pp. 11435-11440. ISSN 0027-8424
Baumgart, S., Chen, N. M., Siveke, J. T., Konig, A., Zhang, J. S., Singh, S. K., Wolf, E., Bartkuhn, M., Esposito, I., Hessmann, E., Reinecke, J., Nikorowitsch, J., Brunner, M., Singh, G., Fernandez-Zapico, M. E., Smyrk, T., Bamlet, W. R., Eilers, M., Neesse, A., Gress, T. M., Billadeau, D. D., Tuveson, D., Urrutia, R., Ellenrieder, V. (June 2014) Inflammation-Induced NFATc1-STAT3 Transcription Complex Promotes Pancreatic Cancer Initiation by Kras(G12D). Cancer Discovery, 4 (6). pp. 688-701. ISSN 2159-8274
Berkowitz, L. A., Gilman, M. Z. (July 1990) Two distinct forms of active transcription factor CREB (cAMP response element binding protein). Proc Natl Acad Sci U S A, 87 (14). pp. 5258-62. ISSN 0027-8424 (Print)0027-8424 (Linking)
Beyaz, S., Kim, J. H., Pinello, L., Xifaras, M. E., Hu, Y., Huang, J., Kerenyi, M. A., Das, P. P., Barnitz, R. A., Herault, A., Dogum, R., Haining, W. N., Yilmaz, O. H., Passegue, E., Yuan, G. C., Orkin, S. H., Winau, F. (February 2017) The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol, 18 (2). pp. 184-195. ISSN 1529-2916 (Electronic)1529-2908 (Linking)
Bhagwat, A. S., Vakoc, C. R. (September 2015) Targeting Transcription Factors in Cancer. Trends Cancer, 1 (1). pp. 53-65. ISSN 2405-8033 (Print)
Bortiri, E., Chuck, G., Vollbrecht, E., Rocheford, T. R., Martienssen, R. A., Hake, S. (March 2006) ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize. Plant Cell, 18 (3). pp. 574-585. ISSN 10404651
Brodie, C. R., Khaliq, M., Yin, J. C. P., Clark, H. B., Orr, H. T., Boland, L. M. (April 2004) Overexpression of CREB reduces CRE-mediated transcription: behavioral and cellular analyses in transgenic mice. Molecular and Cellular Neuroscience, 25 (4). pp. 602-611. ISSN 1044-7431
Brodie, C. R., Yin, J. C. P., Clarke, H. B., Boland, L. M., Orr, H. T. (2000) Transgenic overexpression of wild-type CREB blocks endogenous CREB function. European Journal of Neuroscience, 12. p. 346. ISSN 0953-816X
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)
Carroll, D. K., Carroll, J. S., Leong, C. O., Cheng, F., Brown, M., Mills, A. A., Brugge, J. S., Ellisen, L. W. (June 2006) p63 regulates an adhesion programme and cell survival in epithelial cells. Nature Cell Biology, 8 (6). pp. 551-561. ISSN 14657392
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., Wheeler, R., Wong, B., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K., Gingeras, T. R. (2004) Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs. Cell, 116 (4). pp. 499-509. ISSN 0092-8674
Cecchini, Katharine, Biasini, Adriano, Yu, Tianxiong, Säflund, Martin, Mou, Haiwei, Arif, Amena, Eghbali, Atiyeh, Colpan, Cansu, Gainetdinov, Ildar, de Rooij, Dirk G, Weng, Zhiping, Zamore, Phillip, Ozata, Deniz M (November 2022) The transcription factor TCFL5 responds to A MYB to elaborate the male meiotic program in mice. Reproduction. REP-22. ISSN 1470-1626
Chen, G., Hata, N., Zhang, M. Q. (2004) Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res, 32 (8). pp. 2362-71. ISSN 1362-4962 (Electronic)
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
Cheng, C., Alexander, R., Min, R. Q., Leng, J., Yip, K. Y., Rozowsky, J., Yan, K. K., Dong, X. J., Djebali, S., Ruan, Y. J., Davis, C. A., Carninci, P., Lassman, T., Gingeras, T. R., Guigo, R., Birney, E., Weng, Z. P., Snyder, M., Gerstein, M. (September 2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research, 22 (9). pp. 1658-1667. ISSN 1088-9051
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)
Chi, P., Chen, Y., Zhang, L., Guo, X., Wongvipat, J., Shamu, T., Fletcher, J. A., Dewell, S., Maki, R. G., Zheng, D., Antonescu, C. R., Allis, C. D., Sawyers, C. L. (October 2010) ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours. Nature, 467 (7317). pp. 849-53. ISSN 1476-4687 (Electronic)0028-0836 (Linking)
Choi, Charlotte P, Tay, Rebecca J, Starostik, Margaret R, Feng, Suhua, Moresco, James J, Montgomery, Brooke E, Xu, Emily, Hammonds, Maya A, Schatz, Michael C, Montgomery, Taiowa A, Yates, John R, Jacobsen, Steven E, Kim, John K (February 2021) SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. eLife, 10. pp. 1-35. ISSN 2050-084X
Chou, S. T., Khandros, E., Bailey, L. C., Nichols, K. E., Vakoc, C. R., Yao, Y., Huang, Z., Crispino, J. D., Hardison, R. C., Blobel, G. A., Weiss, M. J. (July 2009) Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. Blood, 114 (5). pp. 983-994.
Chuck, G., Whipple, C., Jackson, D. P., Hake, S. (2010) The maize SBP-box transcription factor encoded by tasselsheath4 regulates bract development and the establishment of meristem boundaries. Development (Cambridge, England), 137 (8). pp. 1243-1250. ISSN 14779129 (ISSN)
Cleary, M. A., Herr, W. (April 1995) Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain. Mol Cell Biol, 15 (4). pp. 2090-100. ISSN 0270-7306 (Print)
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)
Cohen, D. R., Ferreira, P. C. P., Gentz, R., Franza, B. R., Curran, T. (February 1989) The Product of a Fos-Related Gene, Fra-1, Binds Cooperatively to the Ap-1 Site with Jun - Transcription Factor Ap-1 Is Comprised of Multiple Protein Complexes. Genes & Development, 3 (2). pp. 173-184. ISSN 0890-9369
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)
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)
Dallas, P. B., Pacchione, S., Wilsker, D., Bowrin, V., Kobayashi, R., Moran, E. (May 2000) The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. Molecular and Cellular Biology, 20 (9). pp. 3137-3146. ISSN 0270-7306
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, D., Banerjee, N., Zhang, M. Q. (November 2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci U S A, 101 (46). pp. 16234-9. ISSN 0027-8424 (Print)
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, G., Hinkley, C. S., Herr, W. (April 1995) Basal promoter elements as a selective determinant of transcriptional activator function. Nature, 374 (6523). pp. 657-60. ISSN 0028-0836 (Print)
DeZazzo, J., Sandstrom, D., de Belle, S., Velinzon, K., Smith, P., Grady, L., DelVecchio, M., Ramaswami, M., Tully, T. (July 2000) nalyot, a mutation of the Drosophila Myb-related Adf1 transcription factor, disrupts synapse formation and olfactory memory. Neuron, 27 (1). pp. 145-158. ISSN 0896-6273
DeZazzo, J., Tully, T. (May 1995) Dissection of memory formation: from behavioral pharmacology to molecular genetics. Trends Neurosci, 18 (5). pp. 212-8. ISSN 0166-2236 (Print)
Denissov, S., Van Driel, M., Voit, R., Hekkelman, M., Hulsen, T., Hernandez, N., Grummt, I., Wehrens, R., Stunnenberg, H. (February 2007) Identification of novel functional TBP-binding sites and general factor repertoires. Embo Journal, 26 (4). pp. 944-954. ISSN 0261-4189
Denk, Franziska, Crow, Megan, Didangelos, Athanasios, Lopes, Douglas M, McMahon, Stephen B (May 2016) Persistent Alterations in Microglial Enhancers in a Model of Chronic Pain. Cell Reports, 15 (8). pp. 1771-81. ISSN 2211-1247
Depge-Fargeix, N., Javelle, M., Chambrier, P., Frangne, N., Gerentes, D., Perez, P., Rogowsky, P. M., Vernoud, V. (2011) Functional characterization of the HD-ZIP IV transcription factor OCL1 from maize. Journal of Experimental Botany, 62 (1). pp. 293-305.
Di Como, C. J., Bose, R., Arndt, K. T. (January 1995) Overexpression of SIS2, which contains an extremely acidic region, increases the expression of SWI4, CLN1 and CLN2 in sit4 mutants. Genetics, 139 (1). pp. 95-107. ISSN 0016-6731 (Print)
Ding, J. X., Feng, Y. J., Yao, L. Q., Yu, M., Jin, H. Y., Yin, L. H. (2006) The reinforcement of invasion in epithelial ovarian cancer cells by 17?-Estradiol is associated with up-regulation of Snail. Gynecologic Oncology, 103 (2). pp. 623-630. ISSN 00908258
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.
Emili, A., Shales, M., McCracken, S., Xie, W. J., Tucker, P. W., Kobayashi, R., Blencowe, B. J., Ingles, C. J. (September 2002) Splicing and transcription-associated proteins PSF and p54(nrb)/NonO bind to the RNA polymerase II CTD. RNA, 8 (9). pp. 1102-1111. ISSN 1355-8382
Evans, R., Olefsky, J., Yamamoto, K. (August 2010) NUCLEAR RECEPTORS & DISEASE. In: 2010 meeting on NUCLEAR RECEPTORS & DISEASE, August 31–September 4, 2010.
Fang, F., Fan, S., Zhang, X., Zhang, M. Q. (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics, 22 (18). pp. 2204-2209. ISSN 13674803
Farmer, A. A., Loftus, T. M., Mills, A. A., Sato, K. Y., Neill, J. D., Tron, T., Yang, M., Trumpower, B. L., Stanbridge, E. J. (1994) Extreme evolutionary conservation of QM, a novel c-Jun associated transcription factor. Human Molecular Genetics, 3 (5). pp. 723-728. ISSN 09646906 (ISSN)
Feng, Z., Jin, S., Zupnick, A., Hoh, J., De Stanchina, E., Lowe, S. W., Prives, C., Levine, A. J. (2006) p53 tumor suppressor protein regulates the levels of huntingtin gene expression. Oncogene, 25 (1). pp. 1-7. ISSN 09509232
Filipkowski, R. K., Rydz, M., Kaczmarek, L. (2001) Expression of c-Fos, Fos B, Jun B, and Zif268 transcription factor proteins in rat barrel cortex following apomorphine-evoked whisking behavior. Neuroscience, 106 (4). pp. 679-688. ISSN 0306-4522
Forcier, T. L., Ayaz, A., Gill, M. S., Jones, D., Phillips, R., Kinney, J. B. (December 2018) Measuring cis-regulatory energetics in living cells using allelic manifolds. eLife, 7. ISSN 2050084X (ISSN)
Ford, E., Hernandez, N. (June 1997) Characterization of a trimeric complex containing Oct-1, SNAPc, and DNA. Journal of Biological Chemistry, 272 (25). pp. 16048-55. ISSN 0021-9258
Ford, E., Strubin, M., Hernandez, N. (November 1998) The Oct-1 POU domain activates snRNA gene transcription by contacting a region in the SNAPc largest subunit that bears sequence similarities to the Oct-1 coactivator OBF-1. Genes and Development, 12 (22). pp. 3528-40. ISSN 08909369 (ISSN)
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.
Freiman, R. N., Herr, W. (December 1997) Viral mimicry: common mode of association with HCF by VP16 and the cellular protein LZIP. Genes and Development, 11 (23). pp. 3122-7. ISSN 08909369 (ISSN)
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
Gass, P., Reichardt, H. M., Strekalova, T., Henn, F., Tronche, F. (August 2001) Mice with targeted mutations of glucocorticoid and mineralocorticoid receptors: models for depression and anxiety? Physiol Behav, 73 (5). pp. 811-25. ISSN 0031-9384 (Print)0031-9384 (Linking)
Gaudinier, A., Rodriguez-Medina, J., Zhang, L., Olson, A., Liseron-Monfils, C., Bagman, A. M., Foret, J., Abbitt, S., Tang, M., Li, B., Runcie, D. E., Kliebenstein, D. J., Shen, B., Frank, M. J., Ware, D., Brady, S. M. (October 2018) Transcriptional regulation of nitrogen-associated metabolism and growth. Nature, 563 (7730). pp. 259-264. ISSN 0028-0836
Gilman, M. Z., Berkowitz, L. A., Feramisco, J. R., Franza, B. R., Graham, R. M., Riabowol, K. T., Ryan, W. A. (1988) Intracellular mediators of c-fos induction. Cold Spring Harb Symp Quant Biol, 53 Pt . pp. 761-7. ISSN 0091-7451
Gray, J., Bevan, M., Brutnell, T., Buell, C. R., Cone, K., Hake, S., Jackson, D. P., Kellogg, E., Lawrence, C., McCouch, S., Mockler, T., Moose, S., Paterson, A., Peterson, T., Rokshar, D., Souza, G. M., Springer, N., Stein, N., Timmermans, M. C. P., Wang, G.-L., Grotewold, E. (January 2009) A Recommendation for Naming Transcription Factor Proteins in the Grasses. Plant Physiol., 149 (1). pp. 4-6.
Grotewold, E., Athma, P., Peterson, T. (June 1991) Alternatively spliced products of the maize P gene encode proteins with homology to the DNA-binding domain of myb-like transcription factors. Proc Natl Acad Sci U S A, 88 (11). pp. 4587-91. ISSN 0027-8424 (Print)0027-8424 (Linking)
Grotewold, E., Chamberlin, M., Snook, M., Siame, B., Butler, L., Swenson, J., Maddock, S., Clair, G. S., Bowen, B. (May 1998) Engineering secondary metabolism in maize cells by ectopic expression of transcription factors. Plant Cell, 10 (5). pp. 721-40. ISSN 1040-4651 (Print)
Grueneberg, D. A., Simon, K. J., Brennan, K., Gilman, M. (June 1995) Sequence-specific targeting of nuclear signal transduction pathways by homeodomain proteins. Mol Cell Biol, 15 (6). pp. 3318-26. ISSN 0270-7306 (Print)
Guertin, M. J., Martins, A. L., Siepel, A., Lis, J. T. (2012) Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet, 8 (3). e1002610. ISSN 1553-7390
Halevy, O., Novitch, B. G., Spicer, D. B., Skapek, S. X., Rhee, J., Hannon, G. J., Beach, D., Lassar, A. B. (1995) Correlation of terminal cell cycle arrest of skeletal muscle with induction of p21 by MyoD. Science, 267 (5200). pp. 1018-1021. ISSN 00368075 (ISSN)
Han, J. J., Jackson, D., Martienssen, R. (July 2012) Pod corn is caused by rearrangement at the Tunicate1 locus. The Plant cell, 24 (7). pp. 2733-44. ISSN 1532-298X (Electronic)1040-4651 (Linking)
Hansen, K. R., Burns, G., Mata, J., Volpe, T. A., Martienssen, R. A., Bahler, J., Thon, G. (January 2005) Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Molecular and Cellular Biology, 25 (2). pp. 590-601. ISSN 0270-7306
Hansen, K. R., Hazan, I., Shanker, S., Watt, S., Verhein-Hansen, J., Bahler, J., Martienssen, R. A., Partridge, J. F., Cohen, A., Thon, G. (January 2011) H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases. Plos Genetics, 7 (1). ISSN 1553-7390
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)
Henry, R. W., Sadowski, C. L., Kobayashi, R., Hernandez, N. (April 1995) A TBP-TAF complex required for transcription of human snRNA genes by RNA polymerase II and III. Nature, 374 (6523). pp. 653-6. ISSN 0028-0836 (Print)
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)
Herbst, A., Salghetti, S. E., Kim, S. Y., Tansey, W. P. (May 2004) Multiple cell-type-specific elements regulate Myc protein stability. Oncogene, 23 (21). pp. 3863-71. ISSN 0950-9232 (Print)
Hernandez, N. (July 1993) TBP, a universal eukaryotic transcription factor? Genes Dev, 7 (7B). pp. 1291-308. ISSN 0890-9369 (Print)
Hernando, E., Nahle, Z., Juan, G., Diaz-Rodriguez, E., Alaminos, M., Hemann, M., Michel, L., Mittal, V., Gerald, W., Benezra, R., Lowe, S. W., Cordon-Cardo, C. (August 2004) Rb inactivation promotes genomic instability by uncoupling cell cycle progression from mitotic control. Nature, 430 (7001). pp. 797-802. ISSN 0028-0836
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., Sturm, R. A., Clerc, R. G., Corcoran, L. M., Baltimore, D., Sharp, P. A., Ingraham, H. A., Rosenfeld, M. G., Finney, M., Ruvkun, G. (December 1988) The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. Genes Dev, 2 (12A). pp. 1513-6. ISSN 0890-9369
Hsieh, C. L., Sturm, R., Herr, W., Francke, U. (April 1990) The gene for the ubiquitous octamer-binding protein Oct-1 is on human chromosome 1, region cen-q32, and near Ly-22 and Ltw-4 on mouse chromosome 1. Genomics, 6 (4). pp. 666-672. ISSN 0888-7543
Hsieh, M. C., Das, D., Sambandam, N., Zhang, M. Q., Nahle, Z. (October 2008) Regulation of the PDK4 isozyme by the Rb-E2F1 complex. J Biol Chem, 283 (41). pp. 27410-7.
Hsu, D. S., Acharya, C. R., Balakumaran, B. S., Riedel, R. F., Kim, M. K., Stevenson, M., Tuchman, S., Mukherjee, S., Barry, W., Dressman, H. K., Nevins, J. R., Powers, S., Mu, D., Potti, A. (March 2009) Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer. Proc Natl Acad Sci U S A, 106 (13). pp. 5312-5317. ISSN 0027-8424 (Print)1091-6490 (Electronic)
Hu, P., Wu, S., Hernandez, N. (September 2003) A minimal RNA polymerase III transcription system from human cells reveals positive and negative regulatory roles for CK2. Molecular Cell, 12 (3). pp. 699-709. ISSN 1097-2765
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, H., Tudor, M., Weiss, C. A., Hu, Y., Ma, H. (June 1995) The Arabidopsis MADS-box gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. Plant Mol Biol, 28 (3). pp. 549-67. ISSN 0167-4412 (Print)
Huang, Xiaozhen, Tang, Lingli, Yu, Yuan, Dalrymple, Justin, Lippman, Zachary B., Xu, Cao (May 2018) Control of flowering and inflorescence architecture in tomato by synergistic interactions between ALOG transcription factors. Journal of Genetics and Genomics, 45 (10). pp. 557-560. ISSN 1673-8527
Huang, Z. J., Edery, I., Rosbash, M. (July 1993) PAS is a dimerization domain common to Drosophila period and several transcription factors. Nature, 364 (6434). pp. 259-62. ISSN 0028-0836 (Print)0028-0836
Huilgol, D., Venkataramani, P., Nandi, S., Bhattacharjee, S. (October 2019) Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer. Genes (Basel), 10 (10). ISSN 2073-4425
Husbands, Aman Y, Feller, Antje, Aggarwal, Vasudha, Dresden, Courtney E, Holub, Ashton S, Ha, Taekjip, Timmermans, Marja CP The START domain potentiates HD-ZIPIII transcriptional activity. The Plant Cell. ISSN 1040-4651
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)
Italiano, A., Sung, Y. S., Zhang, L., Singer, S., Maki, R. G., Coindre, J. M., Antonescu, C. R. (March 2012) High prevalence of CIC fusion with double-homeobox (DUX4) transcription factors in EWSR1-negative undifferentiated small blue round cell sarcomas. Genes Chromosomes Cancer, 51 (3). pp. 207-18. ISSN 1098-2264 (Electronic)1045-2257 (Linking)
Jackson, D. P. (2005) Transcription Factor Movement Through Plasmadesmata. In: Plasmodesmata. Blackwell Publishing Ltd, pp. 113-134. ISBN 9780470988572
Jackson, D. P., Hake, S. (1997) Morphogenesis on the move: Cell-to cell trafficking of plant regulatory proteins. Current Opinion in Genetics and Development, 7 (4). pp. 495-500. ISSN 0959437X (ISSN)
Jackson, David (2007) Transcription Factor Movement Through Plasmadesmata. In: Plasmodesmata. Blackwell Publishing Ltd, pp. 113-134. ISBN 9780470988572
Javelle, M., Klein-Cosson, C., Vernoud, V., Boltz, V., Maher, C., Timmermans, M. C. P., Depege-Fargeix, N., Rogowsky, P. M. (October 2011) Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis. Plant Physiology, 157 (2). pp. 790-803. ISSN 0032-0889
Jiang, B., Zhang, M. Q., Zhang, X. (November 2007) OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics, 23 (21). pp. 2823-8. ISSN 1460-2059 (Electronic)
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.
Jing, H., Vakoc, C. R., Ying, L., Mandat, S., Wang, H., Zheng, X., Blobel, G. A. (2008) Exchange of GATA Factors Mediates Transitions in Looped Chromatin Organization at a Developmentally Regulated Gene Locus. Molecular Cell, 29 (2). pp. 232-242. ISSN 10972765 (ISSN)
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
Karakida Kawaguchi, Risa, Tang, Ziqi, Fischer, Stephan, Rajesh, Chandana, Tripathy, Rohit, Koo, Peter K, Gillis, Jesse (December 2022) Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. Briefings in Bioinformatics. bbac541. ISSN 1467-5463
Kato, M., Hata, N., Banerjee, N., Futcher, B., Zhang, M. Q. (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology, 5 (8). ISSN 1465-6914
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, M. M., Jaillais, Y., Pedmale, U. V., Moreno, J. E., Chory, J., Ballare, C. L. (July 2011) Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades. Plant J, 67 (2). pp. 195-207. ISSN 0960-7412
Kerr, J. B., Hutt, K. J, Michalak, E. M., Cook, M., Vandenberg, C. J., Liew, S. H., Bouillet, P., Mills, A., Scott, C. L., Findlay, J. K., Strasser, A. (November 2012) DNA Damage-Induced Primordial Follicle Oocyte Apoptosis and Loss of Fertility Require TAp63-Mediated Induction of Puma and Noxa. Molecular Cell, 48 (3). pp. 343-352. ISSN 1097-2765
Kerschensteiner, D., Liu, H., Cheng, C. W., Demas, J., Cheng, S. H., Hui, C. c., Chow, R. L., Wong, R. O. L. (March 2008) Genetic Control of Circuit Function: Vsx1 and Irx5 Transcription Factors Regulate Contrast Adaptation in the Mouse Retina. J. Neurosci., 28 (10). pp. 2342-2352.
Keyes, W. M., Mills, A. A. (February 2003) Inducible systems see the light. Trends in Biotechnology, 21 (2). pp. 53-55. ISSN 0167-7799
Khalil, D. N., Tansey, W. P. (March 2007) A novel role for Myc in prostate cancer. Journal of Investigative Medicine, 55 (2). S356-S356. ISSN 1081-5589
Kim, M. V., Ouyang, W., Liao, W., Zhang, M. Q., Li, M. O. (August 2013) The transcription factor Foxo1 controls central-memory CD8+ T cell responses to infection. Immunity, 39 (2). pp. 286-97. ISSN 1074-7613
Kim, T. H., Abdullaev, Z. K., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., Ren, B. (March 2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 128 (6). pp. 1231-1245. ISSN 0092-8674
Kim, Y. S., Kim, J. M., Jung, D. L., Kang, J. E., Lee, S., Kim, J. S., Seol, W., Shin, H. C., Kwon, H. S., Van Lint, C., Hernandez, N., Hur, M. W. (June 2005) Artificial zinc finger fusions targeting Sp1-binding sites and the trans-activator-responsive element potently repress transcription and replication of HIV-1. Journal of Biological Chemistry, 280 (22). pp. 21545-21552. ISSN 0021-9258
Kininis, M., Chen, B. S., Diehl, A. G., Isaacs, G. D., Zhang, T., Siepel, A. C., Clark, A. G., Kraus, W. L. (July 2007) Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol, 27 (14). pp. 5090-104. ISSN 0270-7306 (Print)0270-7306
Kirberger, S. E., Ycas, P. D., Johnson, J. A., Chen, C., Ciccone, M. F., Woo, R. W. L., Urick, A. K., Zahid, H., Shi, K., Aihara, H., McAllister, S. D., Kashani-Sabet, M., Shi, J., Dickson, A., Dos Santos, C. O., Pomerantz, W. C. K. (February 2019) Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor. Org Biomol Chem, 17 (2). pp. 2020-2027. ISSN 1477-0520
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
Klemm, J. D., Rould, M. A., Aurora, R., Herr, W., Pabo, C. O. (April 1994) Crystal-Structure of the Oct-1 Pou Domain Bound to an Octamer Site - DNA Recognition with Tethered DNA-Binding Modules. Cell, 77 (1). pp. 21-32. ISSN 0092-8674
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
Koo, PK, Ploenzke, M (February 2020) Deep learning for inferring transcription factor binding sites. Current Opinion in Systems Biology, 19. pp. 16-23. ISSN 2452-3100
Kouros-Mehr, H., Bechis, S. K., Slorach, E. M., Littlepage, L. E., Egeblad, M., Ewald, A. J., Pai, S. Y., Ho, I. C., Werb, Z. (2008) GATA-3 Links Tumor Differentiation and Dissemination in a Luminal Breast Cancer Model. Cancer Cell, 13 (2). pp. 141-152. ISSN 15356108 (ISSN)
Kwoh, D., Zipser, D. (February 1979) Specific binding of mu repressor to DNA. Nature, 277 (5696). pp. 489-91. ISSN 0028-0836 (Print)0028-0836 (Linking)
Labrie, C., Lee, B. H., Mathews, M. B. (September 1995) Transcription factors RFX1/EF-C and ATF-1 associate with the adenovirus E1A-responsive element of the human proliferating cell nuclear antigen promoter. Nucleic Acids Res, 23 (18). pp. 3732-41. ISSN 0305-1048 (Print)
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)
Lakhina, V., Subramanian, L., Huilgol, D., Shetty, A. S., Vaidya, V. A., Tole, S. (October 2013) Seizure evoked regulation of LIM-HD genes and co-factors in the postnatal and adult hippocampus. F1000 Research, 2. p. 205. ISSN 20461402 (ISSN)
Lamonica, J. M., Vakoc, C. R., Blobel, G. A. (2006) Acetylation of GATA-1 is required for chromatin occupancy. Blood, 108 (12). pp. 3736-3738. ISSN 00064971 (ISSN)
Lanctot, Amy (September 2022) At home and away: A mobile transcription factor regulates meristem development in discrete spatial domains. Plant Physiology. kiac453. ISSN 0032-0889
Laska, M. J., Lowe, S. W., Zender, L., Hearn, S. A., Vogel, U., Jensen, U. B., Bric, A., Nexo, B. A. (September 2009) Enforced expression of PPP1R13L increases tumorigenesis and invasion through p53-dependent and p53-independent mechanisms. Mol Carcinog, 48 (9). pp. 832-42.
Lau, B. Y. B., Fogerson, S. M., Walsh, R. B., Morgan, J. R. (December 2013) Cyclic AMP promotes axon regeneration, lesion repair and neuronal survival in lampreys after spinal cord injury. Experimental Neurology, 250. pp. 31-42. ISSN 00144886 (ISSN)
Lee, Young Koung, Kumari, Sunita, Olson, Andrew, Hauser, Felix, Ware, Doreen (August 2022) Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. International Journal of Molecular Sciences, 23 (15). p. 8665. ISSN 1422-0067
Li, X. Y., MacArthur, S., Bourgon, R., Nix, D., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Luengo Hendriks, C. L., Hou, C. C., Ogawa, N., Inwood, W., Sementchenko, V., Beaton, A., Weiszmann, R., Celniker, S. E., Knowles, D. W., Gingeras, T. R., Speed, T. P., Eisen, M. B., Biggin, M. D. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biology, 6 (2). 0365-0388. ISSN 1544-9173
Liao, H. J., Kobayashi, R., Mathews, M. B. (July 1998) Activities of adenovirus virus-associated RNAs: purification and characterization of RNA binding proteins. Proceedings of the National Academy of Sciences, 95 (15). pp. 8514-9. ISSN 0027-8424 (Print)
Liu, M., Lee, B. H., Mathews, M. B. (May 1999) Involvement of RFX1 protein in the regulation of the human proliferating cell nuclear antigen promoter. Journal of Biological Chemistry, 274 (22). pp. 15433-9. ISSN 0021-9258 (Print)
Liu, Y., Hengartner, M. O., Herr, W. (January 1999) Selected elements of herpes simplex virus accessory factor HCF are highly conserved in Caenorhabditis elegans. Molecular and Cellular Biology, 19 (1). pp. 909-15. ISSN 0270-7306 (Print)
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)
Maroney, P. A., Hannon, G. J., Nilsen, T. W. (July 1989) Accurate and efficient RNA polymerase III transcription in a cell-free extract prepared from Ascaris suum embryos. Molecular and Biochemical Parasitology, 35 (3). pp. 277-283. ISSN 01666851
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)
Martinez, M. J., Smith, A. D., Li, B. L., Zhang, M. Q., Harrod, K. S. (January 2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics, 23 (1). pp. 21-29. ISSN 1367-4803
Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan Jr, C. G., Kinney, J. B., Kellis, M., Lander, E. S., Mikkelsen, T. S. (March 2012) Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature Biotechnology, 30 (3). pp. 271-277. ISSN 10870156 (ISSN)
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)
Moran, E. (February 1993) DNA tumor virus transforming proteins and the cell cycle. Curr Opin Genet Dev, 3 (1). pp. 63-70. ISSN 0959-437X (Print)
Moran, E. (July 1993) Interaction of adenoviral proteins with pRB and p53. Faseb J, 7 (10). pp. 880-5. ISSN 0892-6638 (Print)
Morris, G. F., Mathews, M. B. (December 1991) The adenovirus E1A transforming protein activates the proliferating cell nuclear antigen promoter via an activating transcription factor site. J Virol, 65 (12). pp. 6397-406. ISSN 0022-538X (Print)0022-538X (Linking)
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
Mustonen, V., Kinney, J., Callan, C. G., Lassig, M. (August 2008) Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci U S A, 105 (34). pp. 12376-81. ISSN 1091-6490 (Electronic)0027-8424 (Linking)
Muñoz, A., Santos Muñoz, D., Zimin, A., Yorke, J. A. (2016) Evolution of transcriptional networks in yeast: Alternative teams of transcriptional factors for different species. BMC Genomics, 17 (Suppl ). p. 826. ISSN 1471-2164
Nahle, Z., Hsieh, M., Pietka, T., Coburn, C. T., Grimaldi, P. A., Zhang, M. Q., Das, D., Abumrad, N. A. (May 2008) CD36-dependent Regulation of Muscle FoxO1 and PDK4 in the PPAR{delta}/{beta}-mediated Adaptation to Metabolic Stress. J Biol Chem, 283 (21). pp. 14317-26.
Natesan, S., Gilman, M. (November 1995) YY1 facilitates the association of serum response factor with the c-fos serum response element. Mol Cell Biol, 15 (11). pp. 5975-82. ISSN 0270-7306 (Print)
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)
Nogueira, F. T., Madi, S., Chitwood, D. H., Juarez, M. T., Timmermans, M. C. P. (April 2007) Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev, 21 (7). pp. 750-5. ISSN 0890-9369 (Print)
Ohtsu, K., Smith, M. B., Emrich, S. J., Borsuk, L. A., Zhou, R. L., Chen, T. L., Zhang, X. L., Timmermans, M. C. P., Beck, J., Buckner, B., Janick-Buckner, D., Nettleton, D., Scanlon, M. J., Schnable, P. S. (November 2007) Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant Journal, 52 (3). pp. 391-404. ISSN 0960-7412
Ouyang, W., Liao, W., Luo, C. T., Yin, N., Huse, M., Kim, M. V., Peng, M., Chan, P., Ma, Q., Mo, Y., Meijer, D., Zhao, K., Rudensky, A. Y., Atwal, G., Zhang, M. Q., Li, M. O. (November 2012) Novel Foxo1-dependent transcriptional programs control T reg cell function. Nature, 491 (7425). pp. 554-559.
Pai, E. L., Vogt, D., Clemente-Perez, A., McKinsey, G. L., Cho, F. S., Hu, J. S., Wimer, M., Paul, A., Fazel Darbandi, S., Pla, R., Nowakowski, T. J., Goodrich, L. V., Paz, J. T., Rubenstein, J. L. R. (January 2019) Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function. Cell Rep, 26 (5). 1157-1173.e5. ISSN 2211-1247
Pal, B., Chan, N. C., Helfenbaum, L., Tan, K. L., Tansey, W. P., Gething, M. J. (February 2007) SCFCdc4-mediated degradation of the Hac1p transcription factor regulates the unfolded protein response in Saccharomyces cerevisiae. Molecular Biology of the Cell, 18 (2). pp. 426-440. ISSN 1059-1524
Passamaneck, Y. J., Katikala, L., Perrone, L., Dunn, M. P., Oda-Ishii, I., Di Gregorio, A. (November 2009) Direct activation of a notochord cis-regulatory module by Brachyury and FoxA in the ascidian Ciona intestinalis. Development, 136 (21). pp. 3679-89. ISSN 0950-1991
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
Pedmale, U. V., Huang, S. S., Zander, M., Cole, B. J., Hetzel, J., Ljung, K., Reis, P. A., Sridevi, P., Nito, K., Nery, J. R., Ecker, J. R., Chory, J. (January 2016) Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell, 164 (1-2). pp. 233-45. ISSN 0092-8674
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)
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.
Rabinowicz, P. D., Grotewold, E. (November 2000) A novel reverse-genetic approach (SIMF) identifies Mutator insertions in new Myb genes. Planta, 211 (6). pp. 887-893. ISSN 0032-0935
Rada-Iglesias, A., Ameur, A., Kapranov, P., Enroth, S., Komorowski, J., Gingeras, T. R., Wadelius, C. (May 2007) Genome-wide gene regulatory networks for USF1 and USF2 in liver cells - implications for familial combined hyperlipidemia. European Journal of Clinical Investigation, 37 (S1). p. 76. ISSN 0014-2972
Riabowol, K. T., Vosatka, R. J., Ziff, E. B., Lamb, N. J., Feramisco, J. R. (April 1988) Microinjection of fos-specific antibodies blocks DNA synthesis in fibroblast cells. Molecular & Cellular Biology, 8 (4). pp. 1670-6. ISSN 0270-7306
Roe, J. S., Vakoc, C. R. (January 2014) C/EBPalpha: critical at the origin of leukemic transformation. Journal of Experimental Medicine, 211 (1). pp. 1-4. ISSN 0022-1007
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, H. B., Shuai, K., Darnell, J. E., Gilman, M. Z. (September 1993) A common nuclear signal transduction pathway activated by growth factor and cytokine receptors. Science, 261 (5129). pp. 1739-44. ISSN 0036-8075 (Print)
Salghetti, S. E., Kim, S. Y., Tansey, W. P. (February 1999) Destruction of Myc by ubiquitin-mediated proteolysis: cancer-associated and transforming mutations stabilize Myc. Embo Journal, 18 (3). pp. 717-26. ISSN 0261-4189 (Print)
Sanders, C. M., Stenlund, A. (December 1998) Recruitment and loading of the E1 initiator protein: an ATP-dependent process catalysed by a transcription factor. Embo J, 17 (23). pp. 7044-55. ISSN 0261-4189 (Print)
Sanders, C. M., Stenlund, A. (February 2000) Transcription factor-dependent loading of the E1 initiator reveals modular assembly of the papillomavirus origin melting complex. Journal of Biological Chemistry, 275 (5). pp. 3522-3534. ISSN 0021-9258
Saxena, A., Ma, B. C., Schramm, L., Hernandez, N. (November 2005) Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription. Molecular and Cellular Biology, 25 (21). pp. 9406-9418. ISSN 0270-7306
Schones, D. E., Smith, A. D., Zhang, M. Q. (January 2007) Statistical significance of cis-regulatory modules. Bmc Bioinformatics, 8. p. 16. ISSN 1471-2105
Sever, R., Glass, C. K. (March 2013) Signaling by nuclear receptors. Cold Spring Harbor Perspectives in Biology, 5 (3). ISSN 1943-0264 (Electronic)
Shimokawa, T., Mohammed Ferdous-Ur, Rahman, Tostar, U., Sonkoly, E., Ståhle, M., Pivarcsi, A., Palaniswamy, R., Zaphiropoulos, P. G. (February 2013) RNA editing of the GLI1 transcription factor modulates the output of Hedgehog signaling. Rna Biology, 10 (2). pp. 321-333. ISSN 15476286 (ISSN)
Shrestha, Padmina, Jaganathan, Anbalagan, Huilgol, Dhananjay, Ballon, Carlos, Hwangbo, Yon, Mills, Alea A (January 2023) Chd5 regulates the transcription factor Six3 to promote neuronal differentiation. Stem Cells. sxad002. ISSN 1066-5099
Silva, A. J., Fedorov, N., Kogan, J., Frankland, P., Coblentz, J., Lundsten, R., Friedman, E., Smith, A., Cho, Y., Giese, K. P. (1996) Genetic analysis of function and dysfunction in the central nervous system. Cold Spring Harbor Symposia on Quantitative Biology, 61. pp. 239-46. ISSN 0091-7451 (Print)
Soengas, M. S., Lowe, S. W. (December 2000) p53 and p73: seeing double? Nature Genetics, 26 (4). pp. 391-392. ISSN 1061-4036
Solnick, D. (1981) An Adenovirus Mutant Defective in Splicing Rna from Early Region-1a. Nature, 291 (5815). pp. 508-510.
Steger, D. J., Lefterova, M. I., Ying, L., Stonestrom, A. J., Schupp, M., Zhuo, D., Vakoc, A. L., Kim, J. E., Chen, J., Lazar, M. A., Blobel, G. A., Vakoc, C. R. (2008) DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Molecular and Cellular Biology, 28 (8). pp. 2825-2839. ISSN 02707306 (ISSN)
Stern, S., Herr, W. (December 1991) The herpes simplex virus trans-activator VP16 recognizes the Oct-1 homeo domain: evidence for a homeo domain recognition subdomain. Genes Dev, 5 (12B). pp. 2555-66. ISSN 0890-9369 (Print)0890-9369 (Linking)
Sturm, R. A., Herr, W. (December 1988) The POU domain is a bipartite DNA-binding structure. Nature, 336 (6199). pp. 601-4. ISSN 0028-0836
Sumazin, P., Chen, G., Hata, N., Smith, A. D., Zhang, T., Zhang, M. Q. (January 2005) DWE: discriminating word enumerator. Bioinformatics, 21 (1). pp. 31-8. ISSN 1367-4803 (Print)
Sun, P., Dong, P., Dai, K., Hannon, G. J., Beach, D. (December 1998) p53-independent role of MDM2 in TGF-beta1 resistance. Science, 282 (5397). pp. 2270-2. ISSN 0036-8075 (Print)
Sun, Qin, Li, Yunfu, Gong, Dianming, Hu, Aoqing, Zhong, Wanshun, Zhao, Hailiang, Ning, Qiang, Tan, Zengdong, Liang, Kun, Mu, Luyao, Jackson, David, Zhang, Zuxin, Yang, Fang, Qiu, Fazhan (September 2022) A NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination. Nature Communications, 13 (1). p. 5708. ISSN 2041-1723
Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P. P., Mattick, J. S., Spector, D. L. (March 2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Research, 19 (3). pp. 347-359. ISSN 10889051 (ISSN)
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., 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)
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., Catanzaro, D. F. (May 1991) Sp1 and thyroid hormone receptor differentially activate expression of human growth hormone and chorionic somatomammotropin genes. J Biol Chem, 266 (15). pp. 9805-13. ISSN 0021-9258 (Print)0021-9258 (Linking)
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, 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)
Tarumoto, Y., Lin, S., Wang, J., Milazzo, J. P., Xu, Y., Lu, B., Yang, Z., Wei, Y., Polyanskaya, S., Wunderlich, M., Gray, N. S., Stegmaier, K., Vakoc, C. R. (November 2019) Salt-Inducible Kinase inhibition suppresses acute myeloid leukemia progression in vivo. Blood. ISSN 0006-4971
Thome, J., Henn, F. A., Duman, R. S. (May 2002) Cyclic AMP response element-binding protein and depression. Expert Rev Neurother, 2 (3). pp. 347-54. ISSN 1744-8360 (Electronic)1473-7175 (Linking)
Thummel, C., Tjian, R., Grodzicker, T. (1981) Expression of Sv40 T-Antigen under Control of Adenovirus Promoters. Cell, 23 (3). pp. 825-836.
Tramantano, M., Sun, L., Au, C., Labuz, D., Liu, Z., Chou, M., Shen, C., Luk, E. (July 2016) Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. Elife, 5. ISSN 2050-084X (Electronic)2050-084X (Linking)
Tsaniras, S. C., Delinasios, G. J., Petropoulos, M., Panagopoulos, A., Anagnostopoulos, A. K., Villiou, M., Vlachakis, D., Bravou, V., Stathopoulos, G. T., Taraviras, S. (November 2019) DNA Replication Inhibitor Geminin and Retinoic Acid Signaling Participate in Complex Interactions Associated With Pluripotency. Cancer Genomics Proteomics, 16 (6). pp. 593-601. ISSN 1109-6535
Tubon, T. C., Tansey, W. P., Herr, W. (April 2004) A nonconserved surface of the TFIIB zinc ribbon domain plays a direct role in RNA polymerase II recruitment. Molecular and Cellular Biology, 24 (7). pp. 2863-2874. ISSN 0270-7306
Vakoc, C. R., Kentsis, A. (August 2018) Disabling an oncogenic transcription factor by targeting of control kinases. Oncotarget, 9 (64). pp. 32276-32277. ISSN 19492553 (ISSN)
Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., Blobel, G. A. (2005) Proximity among distant regulatory elements at the β-globin locus requires GATA-1 and FOG-1. Molecular Cell, 17 (3). pp. 453-462. ISSN 10972765 (ISSN)
Vignais, M. L., Gilman, M. (May 1999) Distinct mechanisms of activation of Stat1 and Stat3 by platelet-derived growth factor receptor in a cell-free system. Molecular and Cellular Biology, 19 (5). pp. 3727-35. ISSN 0270-7306 (Print)
Wagner, A. J., Malinowska-Kolodziej, I., Morgan, J. A., Qin, W., Fletcher, C. D., Vena, N., Ligon, A. H., Antonescu, C. R., Ramaiya, N. H., Demetri, G. D., Kwiatkowski, D. J., Maki, R. G. (February 2010) Clinical activity of mTOR inhibition with sirolimus in malignant perivascular epithelioid cell tumors: targeting the pathogenic activation of mTORC1 in tumors. J Clin Oncol, 28 (5). pp. 835-40. ISSN 1527-7755 (Electronic)0732-183X (Linking)
Wang, E., Kawaoka, S., Roe, J. S., Shi, J., Hohmann, A. F., Xu, Y., Bhagwat, A. S., Suzuki, Y., Kinney, J. B., Vakoc, C. R. (April 2015) The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. Elife, 4. ISSN 2050-084X (Electronic)2050-084X (Linking)
Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., Bussemaker, H. J., Quaid, M. D., Bulyk, M. L., Stolovitzky, G., Hughes, T. R., Agius, P., Arvey, A., Bucher, P., Callan Jr, C. G., Chang, C. W., Chen, C. Y., Chen, Y. S., Chu, Y. W., Grau, J., Grosse, I., Jagannathan, V., Keilwagen, J., Kiebasa, S. M., Kinney, J. B., Klein, H., Kursa, M. B., Lähdesmäki, H., Laurila, K., Lei, C., Leslie, C., Linhart, C., Murugan, A., Myšičková, A., Noble, W. S., Nykter, M., Orenstein, Y., Posch, S., Ruan, J., Rudnicki, W. R., Schmid, C. D., Shamir, R., Sung, W. K., Vingron, M., Zhang, Z. (February 2013) Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology, 31 (2). pp. 126-134. ISSN 10870156 (ISSN)
Welch, J. J., Watts, J. A., Vakoc, C. R., Yao, Y., Wang, H., Hardison, R. C., Blobel, G. A., Chodosh, L. A., Weiss, M. J. (2004) Global regulation of erythroid gene expression by transcription factor GATA-1. Blood, 104 (10). pp. 3136-3147. ISSN 00064971 (ISSN)
Wijnen, H., Landman, A., Futcher, B. (June 2002) The G(1) cyclin Cln3 promotes cell cycle entry via the transcription factor Swi6. Molecular and Cellular Biology, 22 (12). pp. 4402-4418. ISSN 0270-7306
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., Freiman, R. N., Goto, H., Nishimoto, T., Herr, W. (October 1997) VP16 targets an amino-terminal domain of HCF involved in cell cycle progression. Molecular and Cellular Biology, 17 (10). pp. 6139-46. ISSN 0270-7306
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)
Wilson, A. C., Parrish, J. E., Massa, H. F., Nelson, D. L., Trask, B. J., Herr, W. (January 1995) The gene encoding the VP16-accessory protein HCF (HCFC1) resides in human Xq28 and is highly expressed in fetal tissues and the adult kidney. Genomics, 25 (2). pp. 462-8. ISSN 0888-7543 (Print)
Wilson, A. C., Peterson, M. G., Herr, W. (October 1995) The HCF repeat is an unusual proteolytic cleavage signal. Genes Dev, 9 (20). pp. 2445-58. ISSN 0890-9369 (Print)
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)
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, R. M., Koch, C., Liu, Y., Horton, J. R., Knapp, D., Nasmyth, K., Cheng, X. (March 1997) Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis. Structure, 5 (3). pp. 349-58. ISSN 0969-2126 (Print)
Xuan, Z., Zhang, M. Q. (January 2005) From worm to human: bioinformatics approaches to identify FOXO target genes. Mech Ageing Dev, 126 (1). pp. 209-15. ISSN 0047-6374 (Print)
Yordanov, Georgi Nenov (July 2019) Myc and Spdef: two transcription factors hijacked by pancreatic cancer. PhD thesis, Cold Spring Harbor.
Zhang, C., Xuan, Z., Otto, S., Hover, J. R., McCorkle, S. R., Mandel, G., Zhang, M. Q. (2006) A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res, 34 (8). pp. 2238-46. ISSN 1362-4962 (Electronic)
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.
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)
Zhu, J., Zhang, M. Q. (July 1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15 (7-8). pp. 607-11. ISSN 1367-4803 (Print)
Zilfou, J. T., Spector, M. S., Lowe, S. W. (November 2005) Slugging it out: fine tuning the p53-PUMA death connection. Cell, 123 (4). pp. 545-8. ISSN 0092-8674 (Print)
