Items where Subject is "gene regulation"

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Aguirre-Chen, C., Hammell, C. M. (2014) Cell death machinery makes life more robust. Elife, 3. e05816. ISSN 2050-084X (Electronic)2050-084X (Linking)

Akhade, V. S., Arun, G., Donakonda, S., Satyanarayana Rao, M. R. (October 2014) Genome wide chromatin occupancy of mrhl RNA and its role in gene regulation in mouse spermatogonial cells. RNA Biol, 11 (10). pp. 1262-79. ISSN 1547-6286

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

Antonescu, C. R., Viale, A., Sarran, L., Tschernyavsky, S. J., Gonen, M., Segal, N. H., Maki, R. G., Socci, N. D., DeMatteo, R. P., Besmer, P. (May 2004) Gene expression in gastrointestinal stromal tumors is distinguished by KIT genotype and anatomic site. Clin Cancer Res, 10 (10). pp. 3282-90. ISSN 1078-0432 (Print)1078-0432 (Linking)

Ariazi, E. A., Taylor, J. C., Black, M. A., Nicolas, E., Slifker, M. J., Azzam, D. J., Boyd, J. (2017) A new role for ERα: Silencing via DNA methylation of basal, stem cell, and EMT genes. Molecular Cancer Research, 15 (2). pp. 152-164. ISSN 1541-7786

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Bakken, Trygve, Jorstad, Nikolas, Hu, Qiwen, Lake, Blue, Tian, Wei, Kalmbach, Brian, Crow, Megan, Hodge, Rebecca, Krienen, Fenna, Sorensen, Staci, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian, Aldridge, Andrew, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa, Crichton, Kirsten, Daigle, Tanya, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas, Herb, Brian, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang Eric, Liu, Christine, Liu, Hanqing, Lucero, Jacinta, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy, Moussa, Marmar, Nery, Joseph, Nicovich, Philip, Orvis, Joshua, Osteen, Julia, Owen, Scott, Palmer, Carter, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora, Rimorin, Christine, Rivkin, Angeline, Romanow, William, Sedeño-Cortés, Adriana, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna Marie, Zhang, Renee, Ament, Seth, Behrens, Margarita, Bravo, Hector Corrada, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick, Höllt, Thomas, Horwitz, Gregory, Keene, Dirk, Kharchenko, Peter, Ko, Andrew, Lelieveldt, Boudewijn, Luo, Chongyuan, Mukamel, Eran, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard, Smith, Kimberly, Spain, William, White, Owen, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan, McCarroll, Steven, Ting, Jonathan, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph, Linnarsson, Sten, Lein, Ed (April 2020) Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse. BioRxiv. (Unpublished)

Bar-Sagi, D. (April 1992) Mechanisms of signal transduction by Ras. Semin Cell Biol, 3 (2). pp. 93-8. ISSN 1043-4682 (Print)1043-4682 (Linking)

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

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

Benoit, M. (May 2020) Shooting for the STARRs: A Modified STARR-seq Assay for Rapid Identification and Evaluation of Plant Regulatory Sequences in Tobacco Leaves. Plant Cell. ISSN 1040-4651

Bodnar, M. S. (March 2013) The Dynamics of Pluripotency Genes Upon Differentiation of Mouse Embryonic Stem Cells. PhD thesis, Cold Spring Harbor Laboratory.

Bommert, P., Je, B. I., Goldshmidt, A., Jackson, D. (September 2013) The maize G alpha gene COMPACT PLANT2 functions in CLAVATA signalling to control shoot meristem size. Nature, 502 (7472). pp. 555-558. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Broach, J. R. (June 1979) Galactose regulation in Saccharomyces cerevisiae. The enzymes encoded by the GAL7, 10, 1 cluster are co-ordinately controlled and separately translated. J Mol Biol, 131 (1). pp. 41-53. ISSN 0022-2836 (Print)0022-2836 (Linking)

Brown, J., Sundaresan, V. (April 1992) Genetic study of the loss and restoration of Mutator transposon activity in maize: evidence against dominant-negative regulator associated with loss of activity. Genetics, 130 (4). pp. 889-98. ISSN 0016-6731 (Print)0016-6731 (Linking)

Busch, H., Reddy, R., Henning, D., Spector, D. L., Epstein, P., Domae, N., Liu, M. H., Subrahmanyam, C. S., Schrier, W. H., Rothblum, L. (1982) Small nuclear RNPs and RNA processing. In: Gene Regulation: proceedings of the symposium on gene regulation held March 28-April 4, 1982, Keystone, Colorado. UCLA symposia on molecular and cellular biology, 26 . Academic Press, New York, pp. 167-187. ISBN 0125259603

Byrd, C., Turner, G. C., Varshavsky, A. (1998) The N-end rule pathway controls the import of peptides through degradation of a transcriptional repressor. Embo Journal, 17 (1). pp. 269-277. ISSN 02614189 (ISSN)

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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)

Cano, Alejandro V, Rozhoňová, Hana, Stoltzfus, Arlin, McCandlish, David M, Payne, Joshua L (February 2022) Mutation bias shapes the spectrum of adaptive substitutions. Proceedings of the National Academy of Sciences of USA, 119 (7). e2119720119-e2119720119. ISSN 0027-8424

Chang, K. C., Diermeier, S. D., Yu, A. T., Brine, L. D., Russo, S., Bhatia, S., Alsudani, H., Kostroff, K., Bhuiya, T., Brogi, E., Pappin, D. J., Bennett, C. F., Rigo, F., Spector, D. L. (December 2020) MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression. Nat Commun, 11 (1). p. 6438. ISSN 2041-1723

Cheng, D. K., Oni, T. E., Park, Y., Thalappillil, J. S, Ting, H.-C., Alagesan, B., Prasad, N. V., Rivera, K. D., Pappin, D. J., Van Aelst, L., Tuveson, D. A. (September 2020) Oncogenic KRAS engages an RSK1/NF1 complex in pancreatic cancer. BioRxiv. (Unpublished)

Choi, K., Zhao, X., Tock, A. J., Lambing, C., Underwood, C. J., Hardcastle, T. J., Serra, H., Kim, J., Cho, H. S., Kim, J., Ziolkowski, P. A., Yelina, N. E., Hwang, I., Martienssen, R. A., Henderson, I. R. (April 2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res, 28 (4). pp. 532-546. ISSN 1088-9051

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.

Christensen, S. A., Nemchenko, A., Borrego, E., Murray, I., Sobhy, I. S., Bosak, L., Deblasio, S., Erb, M., Robert, C. A., Vaughn, K. A., Herrfurth, C., Tumlinson, J., Feussner, I., Jackson, D., Turlings, T. C., Engelberth, J., Nansen, C., Meeley, R., Kolomiets, M. V. (April 2013) The maize lipoxygenase, ZmLOX10, mediates green leaf volatile, jasmonate and herbivore-induced plant volatile production for defense against insect attack. Plant Journal, 74 (1). pp. 59-73. ISSN 09607412 (ISSN)

Ciren, Danielle, Zebell, Sophia, Lippman, Zachary B (December 2023) Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. bioRxiv. (Submitted)

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)

Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (November 2020) Coexpression reveals conserved mechanisms of transcriptional cell identity. BioRxiv. (Unpublished)

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Dalton, J. E., Fear, J. M., Knott, S., Baker, B. S., McIntyre, L. M., Arbeitman, M. N. (September 2013) Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains. BMC Genomics, 14. ISSN 1471-2164 (Public Dataset)

Dampanaboina, L., Jiao, Y., Chen, J., Gladman, N., Chopra, R., Burow, G., Hayes, C., Christensen, S. A., Burke, J., Ware, D., Xin, Z. (October 2019) Sorghum MSD3 Encodes an omega-3 Fatty Acid Desaturase that Increases Grain Number by Reducing Jasmonic Acid Levels. Int J Mol Sci, 20 (21). ISSN 1422-0067 (Public Dataset)

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

Das, D., Zhang, M. Q. (2007) Predictive models in gene regulation. Methods Mol Biol, 377. pp. 95-110. ISSN 978-1-59745-390-5

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)

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

Dow, L. E., Nasr, Z., Saborowski, M., Ebbesen, S. H., Manchado, E., Tasdemir, N., Lee, T., Pelletier, J., Lowe, S. W. (April 2014) Conditional Reverse Tet-Transactivator Mouse Strains for the Efficient Induction of TRE-Regulated Transgenes in Mice. PLoS ONE, 9 (4). e95236. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

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)

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Eckersley-Maslin, M. A., Spector, D. L. (June 2014) Random monoallelic expression: Regulating gene expression one allele at a time. Trends in Genetics, 30 (6). pp. 237-244. ISSN 13624555

Efrat, S., Teitelman, G., Anwar, M., Ruggiero, D., Hanahan, D. (September 1988) Glucagon gene regulatory region directs oncoprotein expression to neurons and pancreatic alpha cells. Neuron, 1 (7). pp. 605-13. ISSN 0896-6273

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

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Feigman, M.J., Moss, M.A., Chen, C., Cyrill, S.L., Cicone, M.F., Trousdell, M.C., Yang, S.-T., Frey, W.D., Wilkinson, J.E., Dos Santos, C. O. (May 2020) Pregnancy Reprograms the Epigenome of Mammary Epithelial Cells and Blocks the Development of Premalignant Lesions. Nat Commun, 11 (1). p. 2649. ISSN 2041-1723

Flanagan, C. A., Hu, Y., Ma, H. (August 1996) Specific expression of the AGL1 MADS-box gene suggests regulatory functions in Arabidopsis gynoecium and ovule development. Plant Journal, 10 (2). pp. 343-53. ISSN 0960-7412

Foster, Toshi M, Timmermans, Marja C. P. (2009) Axial Patterning of the Maize Leaf. In: Handbook of Maize: Its Biology. Springer New York, pp. 161-178. ISBN 978-0-387-79417-4

Frey, W. D., Chaudhry, A., Slepicka, P. F., Ouellette, A. M., Kirberger, S. E., Pomerantz, W. C. K., Hannon, G. J., Dos Santos, C. O. (July 2017) BPTF Maintains Chromatin Accessibility and the Self-Renewal Capacity of Mammary Gland Stem Cells. Stem Cell Reports, 9 (1). pp. 23-31. ISSN 2213-6711 (Public Dataset)

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Gann, A. (June 1992) Classical sex education. Current biology, 2 (6). pp. 282-4. ISSN 0960-9822 (Print)0960-9822

Gegenhuber, B, Wu, MV, Bronstein, R, Tollkuhn, J (May 2022) Gene regulation by gonadal hormone receptors underlies brain sex differences. Nature. ISSN 0028-0836

Goldie, S. J., Mulder, K. W., Tan, D. W., Lyons, S. K., Sims, A. H., Watt, F. M. (July 2012) FRMD4A upregulation in human squamous cell carcinoma promotes tumor growth and metastasis and is associated with poor prognosis. Cancer Res, 72 (13). pp. 3424-36. ISSN 1538-7445 (Electronic)0008-5472 (Linking)

Greenberg, M. E., Bronson, S., Lock, M., Neumann, M., Pavlakis, G. N., Skowronski, J. (December 1997) Co-localization of HIV-1 Nef with the AP-2 adaptor protein complex correlates with Nef-induced CD4 down-regulation. Embo Journal, 16 (23). pp. 6964-76. ISSN 0261-4189

Greenberg, M. E., Iafrate, A. J., Skowronski, J. (May 1998) The SH3 domain-binding surface and an acidic motif in HIV-1 Nef regulate trafficking of class I MHC complexes. Embo Journal, 17 (10). pp. 2777-89. ISSN 0261-4189

Gryder, B. E., Wachtel, M., Chang, K., El Demerdash, O., Aboreden, N.G., Mohammed, W., Ewert, W., Pomella, S., Rota, R., Wei, J.S., Song, Y., Stanton, B. Z., Schafer, B., Vakoc, C.R., Khan, J. (May 2020) Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience, 23 (5). p. 101103. ISSN 2589-0042

Gutschner, T., Hammerle, M., Eissmann, M., Hsu, J., Kim, Y., Hung, G. N., Revenko, A., Arun, G., Stentrup, M., Gross, M., Zornig, M., MacLeod, A. R., Spector, D. L., Diederichs, S. (April 2013) The long non-coding RNA MALAT1 is an essential gene regulator for lung cancer metastasis in a novel human knockout model. Cancer Research, 73 (8 (Sup). p. 1121. ISSN 0008-5472

Gutschner, T., Hammerle, M., Eißmann, M., Hsu, J., Kim, Y., Hung, G., Revenko, A., Arun, G., Stentrup, M., Groß, M., Zörnig, M., MacLeod, A. R., Spector, D. L., Diederichs, S. (February 2013) The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Research, 73 (3). pp. 1180-1189. ISSN 00085472 (ISSN)

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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

Howarth, Dianella G, Dunn, Matthew P (2016) Phylogenetic Approach to Studying Developmental Evolution: A Model Clade Approach. In: Encyclopedia of Evolutionary Biology. Academic Press, Waltham, Massachusetts, USA, pp. 246-253.

Hu, Y, Tareen, A., Sheu, Y. J., Ireland, W. T., Speck, C., Li, H., Joshua-Tor, L., Kinney, J. B., Stillman, B. (October 2020) Evolution of DNA replication origin specification and gene silencing mechanisms. Nature Communications, 11 (1). p. 5175. ISSN 2041-1723

Huang, Y. H., Klingbeil, O., He, X. Y., Wu, X. S., Arun, G., Lu, B., Somerville, T. D. D., Milazzo, J. P., Wilkinson, J. E., Demerdash, O. E., Spector, D. L., Egeblad, M., Shi, J., Vakoc, C. R. (July 2018) POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer. Genes Dev, 32 (13-14). pp. 915-928. ISSN 0890-9369

Husbands, A. Y., Benkovics, A. H., Nogueira, F. T., Lodha, M., Timmermans, M. C. (December 2015) The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 27 (12). pp. 3321-3335. ISSN 1532-298X (Electronic)1040-4651 (Linking)

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Ireland, William T, Beeler, Suzannah M, Flores-Bautista, Emanuel, McCarty, Nicholas S, Röschinger, Tom, Belliveau, Nathan M, Sweredoski, Michael J, Moradian, Annie, Kinney, Justin B, Phillips, Rob (September 2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife, 9. pp. 1-76. ISSN 2050-084X

Ireland, William Thornton, Beeler, Suzannah, Flores-Bautista, Emanuel, Belliveau, Nathan, Sweredoski, Michael, Moradian, Annie, Kinney, Justin Block, Phillips, Robert (January 2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. BioRxiv. (Unpublished)

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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)

Johansen, Nelson J, Kempynck, Niklas, Zemke, Nathan R, Somasundaram, Saroja, Winter, Seppe De, Hooper, Marcus, Dwivedi, Deepanjali, Lohia, Ruchi, Wehbe, Fabien, Li, Bocheng, Abaffyová, Darina, Armand, Ethan J, Man, Julie De, Eksi, Eren Can, Hecker, Nikolai, Hulselmans, Gert, Konstantakos, Vasilis, Mauduit, David, Mich, John K, Partel, Gabriele, Daigle, Tanya L, Levi, Boaz P, Zhang, Kai, Tanaka, Yoshiaki, Gillis, Jesse, Ting, Jonathan T, Ben-Simon, Yoav, Miller, Jeremy, Ecker, Joseph R, Ren, Bing, Aerts, Stein, Lein, Ed S, Tasic, Bosiljka, Bakken, Trygve E (August 2024) Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. bioRxiv. (Submitted)

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

Ketting, R. F., Fischer, S. E. J., Bernstein, E., Sijen, T., Hannon, G. J., Plasterk, R. H. A. (October 2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes and Development, 15 (20). pp. 2654-2659. ISSN 0890-9369

Kirik, Ufuk, Cifani, Paolo, Albrekt, Ann-Sofie, Lindstedt, Malin, Heyden, Anders, Levander, Fredrik (May 2012) Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation. Journal of Proteome Research, 11 (5). pp. 2955-2967. ISSN 1535-3893

Kirschner, K., Samarajiwa, S. A., Cairns, J. M., Menon, S., Perez-Mancera, P. A., Tomimatsu, K., Bermejo-Rodriguez, C., Ito, Y., Chandra, T., Narita, M., Lyons, S. K., Lynch, A. G., Kimura, H., Ohbayashi, T., Tavare, S., Narita, M. (March 2015) Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet, 11 (3). e1005053. ISSN 1553-7390

Klar, A. J., Fogel, S., Macleod, K. (September 1979) MAR1-a Regulator of the HMa and HMalpha Loci in SACCHAROMYCES CEREVISIAE. Genetics, 93 (1). pp. 37-50. ISSN 0016-6731 (Print)0016-6731 (Linking)

Klein, Harry, Gallagher, Joseph, Demesa-Arevalo, Edgar, Abraham-Juárez, María Jazmín, Heeney, Michelle, Feil, Regina, Lunn, John E, Xiao, Yuguo, Chuck, George, Whipple, Clinton, Jackson, David, Bartlett, Madelaine (January 2022) Recruitment of an ancient branching program to suppress carpel development in maize flowers. Proceedings of the National Academy of Sciences of USA, 119 (2). e2115871119-e2115871119. ISSN 0027-8424

Knott, S., Mostafavi, S., Mousavi, P. (2010) A neural network based modeling and validation approach for identifying gene regulatory networks. Neurocomputing, 73 (13-15). pp. 2419-2429.

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Lachke, S. A., Alkuraya, F. S., Kneeland, S. C., Ohn, T., Aboukhalil, A., Howell, G. R., Saadi, I., Cavallesco, R., Yue, Y. Z., Tsai, A. C. H., Nair, K. S., Cosma, M. I., Smith, R. S., Hodges, E., AlFadhli, S. M., Al-Hajeri, A., Shamseldin, H. E., Behbehani, A., Hannon, G. J., Bulyk, M. L., Drack, A. V., Anderson, P. J., John, S. W. M., Maas, R. L. (March 2011) Mutations in the RNA Granule Component TDRD7 Cause Cataract and Glaucoma. Science, 331 (6024). pp. 1571-1576. ISSN 0036-8075

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)

Lanctot, Amy (December 2022) A lotus by any other color: Gene regulation divergence in lotus petal development. Plant Physiology. kiac596. ISSN 0032-0889

Lavy, Tali, Prakash, Rajesh K, He, Hongzhen, Joshua-Tor, Leemor (2011) The GAL regulon in S. CEREVISIAE: the Gal3p/Gal80p interaction. In: Acta Crystallographica.

Lee, YK, Olson, A, Kim, K, Ohme-Takagi, M, Ware, D (January 2023) HB31 and HB21 regulate floral architecture through miRNA396/GRF modules in Arabidopsis. Plant Biotechnology Reports. ISSN 1863-5466

Lee, Seung Cho, Martienssen, Robert A (September 2021) Regulation of retrotransposition in Arabidopsis. Biochemical Society Transactions. ISSN 0300-5127

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, C. I., Livi, G. P., Ivy, J. M., Klar, A. J. (June 1990) Extragenic suppressors of mar2(sir3) mutations in Saccharomyces cerevisiae. Genetics, 125 (2). pp. 321-31. ISSN 0016-6731 (Print)0016-6731 (Linking)

Lindbäck, Louise N, Hu, Yuzhao, Ackermann, Amanda, Artz, Oliver, Pedmale, Ullas V (June 2022) UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth. Current Biology. ISSN 0960-9822

Liseron-Monfils, Christophe, Ware, Doreen (December 2015) Revealing gene regulation and associations through biological networks. Current Plant Biology, 3-4. pp. 30-39. ISSN 2214-6628

Lodha, M., Marco, C. F., Timmermans, M. C. (March 2013) The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes & Development, 27 (6). pp. 596-601. ISSN 0890-9369

Lohia, Ruchi, Fox, Nathan, Gillis, Jesse (November 2022) A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships. Genome Biology, 23 (1). p. 238. ISSN 1474-760X

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. (August 2011) Three periods of regulatory innovation during vertebrate evolution. Science, 333 (6045). pp. 1019-24. ISSN 0036-8075

Lu, Guang-An, Zhang, Jinning, Zhao, Yixin, Chen, Qingjian, Lin, Pei, Tang, Tian, Tang, Zhixiong, Wen, Haijun, Liufu, Zhongqi, Wu, Chung-I (January 2023) Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed. Molecular Biology and Evolution, 40 (1). msad005. ISSN 0737-4038

Luo, W. J., Friedman, M. S., Hankenson, K. D., Woolf, P. J. (May 2011) Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. BMC Systems Biology, 5 (82). ISSN 1752-0509

Luo, Y., Yang, Y., Liu, M., Wang, D., Wang, F., Bi, Y., Ji, J., Li, S., Liu, Y., Chen, R., Huang, H., Wang, X., Swidnicka-Siergiejko, A. K., Janowitz, T., Beyaz, S., Wang, G., Xu, S., Bialkowska, A. B., Luo, C. K., Pin, C. L., Liang, G., Lu, X., Wu, M., Shroyer, K. R., Wolff, R. A., Plunkett, W., Ji, B., Li, Z., Li, E., Li, X., Yang, V. W., Logsdon, C. D., Abbruzzese, J. L., Lu, W. (July 2019) Oncogenic KRAS Reduces Expression of FGF21 in Acinar Cells to Promote Pancreatic Tumorigenesis in Mice on a High-Fat Diet. Gastroenterology, 157 (5). ISSN 0016-5085

Lyon, Gholson J. (June 2013) The Chaperone-Like Protein HYPK Acts Together with NatA in Cotranslational N-Terminal Acetylation and Prevention of Huntingtin Aggregation. Journal Club. (Unpublished)

M

Macleod, K. F., Sherry, N., Hannon, G., Beach, D., Tokino, T., Kinzler, K., Vogelstein, B., Jacks, T. (1995) p53-Dependent and independent expression of p21 during cell growth, differentiation, and DNA damage. Genes and Development, 9 (8). pp. 935-944. ISSN 08909369

Madlung, A., Tyagi, A. P., Watson, B., Jiang, H. M., Kagochi, T., Doerge, R. W., Martienssen, R. A., Comai, L. (January 2005) Genomic changes in synthetic Arabidopsis polyploids. Plant Journal, 41 (2). pp. 221-230. ISSN 0960-7412

Maestro, R., Dei Tos, A. P., Hamamori, Y., Krasnokutsky, S., Sartorelli, V., Kedes, L., Doglioni, C., Beach, D. H., Hannon, G. J. (September 1999) Twist is a potential oncogene that inhibits apoptosis. Genes and Development, 13 (17). pp. 2207-17. ISSN 0890-9369

Maia-Silva, Diogo (March 2023) MECHANISMS OF GENE TRANSCRIPTION BY TP63 AND THE MEDIATOR COMPLEX IN SQUAMOUS PANCREATIC CANCER. PhD thesis, Cold Spring Harbor Laboratory.

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)

Mariani, R., Skowronski, J. (June 1993) CD4 down-regulation by nef alleles isolated from human immunodeficiency virus type 1-infected individuals. Proc Natl Acad Sci U S A, 90 (12). pp. 5549-53. ISSN 0027-8424 (Print)

Marshall, M., Mahoney, D., Rose, A., Hicks, J. B., Broach, J. R. (1987) Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Molecular and Cellular Biology, 7 (12). pp. 4441-4452. ISSN 02707306 (ISSN)

Maturana, Carola J, Verpeut, Jessica L, Kooshkbaghi, Mahdi, Engel, Esteban A (June 2021) Novel tool to quantify with single-cell resolution the number of incoming AAV genomes co-expressed in the mouse nervous system. Gene Therapy (Basingstoke). ISSN 0969-7128

McClintock, B. (February 1956) Intranuclear systems controlling gene action and mutation. Brookhaven Symp Biol, 8 (8). pp. 58-74. ISSN 0068-2799 (Print)0068-2799 (Linking)

McClintock, B. (November 1984) The significance of responses of the genome to challenge. Science, 226 (4676). pp. 792-801. ISSN 0036-8075 (Print)0036-8075 (Linking)

McClintock, Barbara (December 1964) Aspects of gene regulation in maize. In: Carnegie Institution of Washington Year Book No. 63, 1963-1964. Carnegie Institution of Washington, Washington, D.C., pp. 592-602.

McClintock, Barbara (April 1965) Attempts to Separate Ds from neighboring gene loci. Maize Genetics Cooperation News Letter, 39. pp. 45-51.

McClintock, Barbara (December 1965) Components of action of the regulators Spm and Ac. In: Carnegie Institution of Washington Year Book 64, 1964-1965. Carnegie Institution of Washington, Washington, D.C., pp. 527-536.

McClintock, Barbara (1957) Continued Study of Stability of Location of Spm. Maize Genetics Cooperation News Letter, 31. pp. 31-36.

McClintock, Barbara (December 1963) Further studies of gene-control systems in maize. In: Carnegie Institution of Washington Year Book No. 62, 1962-1963. Carnegie Institution of Washington, Washington, D.C., pp. 486-493.

McClintock, Barbara (1956) Further study of the a1m-1 Spm system. Maize Genetics Cooperation News Letter, 9. p. 9.

McClintock, Barbara (1968) Genetic systems regulating gene expression during development. In: Developmental Biology. Supplement 1: The 26th symposium of the society for developmental biology. Developmental Biology. Supplement 1: The 26th Symposium of the Society for Developmental Biology (June, 1967), Control Mechanisms in Developmental Processes . Academic Press, New York, pp. 84-112.

McClintock, Barbara (November 1953) Induction of instability at selected loci in maize. Genetics, 38 (6). pp. 579-599.

McClintock, Barbara (April 1965) Restoration of A1 gene action by crossing over. Maize Genetics Cooperation News Letter, 39. pp. 42-45.

McClintock, Barbara (September 1961) Some parallels between gene control systems in maize and in bacteria. American Naturalist, 95 (884). pp. 265-277.

McClintock, Barbara (December 1962) Topographical relations between elements of control systems in maize. In: Carnegie Institution of Washington Year Book No. 61, 1961-1962. Carnegie Institution of Washington, Washington, D.C., pp. 448-461.

McClintock, Barbara (June 1965) The control of gene action in maize. Brookhaven Symposia in Biology, 18. pp. 162-184.

McClintock, Barbara (December 1967) The states of a gene locus in maize. In: Carnegie Institution of Washington Year Book 66, 1966-1967. Carnegie Institution of Washington, Washington, D.C., pp. 664-672.

McClintock, Barbara (December 1958) The suppressor-mutator system of control of gene action in maize. In: Annual Report of the Director of the Department of Genetics Carnegie Institution of Washington Year Book No. 57, 1957-1958. Carnegie Institution of Washington, Washington, D.C., pp. 452-456.

McClintock, Barbara (1955) A suppressor-mutator system of control of genic action and mutational change. Maize Genetics Cooperation News Letter, 29. p. 17.

McJunkin, K. (2010) Inducible RNAi targeting essential genes. PhD thesis, Cold Spring Harbor Laboratory.

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

Mizukami, Y., Huang, H., Tudor, M., Hu, Y., Ma, H. (May 1996) Functional domains of the floral regulator AGAMOUS: characterization of the DNA binding domain and analysis of dominant negative mutations. Plant Cell, 8 (5). pp. 831-45. ISSN 1040-4651 (Print)

Mizukami, Y., Ma, H. (August 1995) Separation of AG function in floral meristem determinacy from that in reproductive organ identity by expressing antisense AG RNA. Plant Mol Biol, 28 (5). pp. 767-84. ISSN 0167-4412 (Print)

Morris, G. F., Mathews, M. B. (1990) Regulation of the Proliferating Cell Nuclear Antigen by Adenovirus E1 Products. Journal of Cellular Biochemistry, 44 (S14B). p. 134.

Muratani, M. (April 2005) Regulation of Gene Expression by the Ubiquitin-Proteasome System. PhD thesis, Cold Spring Harbor Laboratory.

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

Paszkowski, J., Martienssen, R. A. (November 2012) Cell signaling and gene regulation. Current Opinion in Plant Biology, 15 (5). pp. 493-495. ISSN 1369-5266

Paul, A., Cai, Y., Atwal, G. S., Huang, Z. J. (June 2012) Developmental Coordination of Gene Expression between Synaptic Partners During GABAergic Circuit Assembly in Cerebellar Cortex. Frontiers in Neural Circuits, 6. p. 37. ISSN 1662-5110 (Electronic)1662-5110 (Linking)

Pautler, Michael (August 2013) Meristem size and determinacy in Maize. PhD thesis, Cold Spring Harbor Laboratory.

Plavskin, Y., Timmermans, M. C. (January 2013) Small RNA-Regulated Networks and the Evolution of Novel Structures in Plants. Cold Spring Harbor Symposia on Quantitative Biology, 77. ISSN 00917451 (ISSN)

Powers, S., Gonzales, E., Christensen, T., Cubert, J., Broek, D. (June 1991) Functional cloning of BUD5, a CDC25-related gene from S. cerevisiae that can suppress a dominant-negative RAS2 mutant. Cell, 65 (7). pp. 1225-31. ISSN 0092-8674 (Print)0092-8674

Prakash, S., Sarran, L., Socci, N., DeMatteo, R. P., Eisenstat, J., Greco, A. M., Maki, R. G., Wexler, L. H., LaQuaglia, M. P., Besmer, P., Antonescu, C. R. (April 2005) Gastrointestinal stromal tumors in children and young adults: a clinicopathologic, molecular, and genomic study of 15 cases and review of the literature. J Pediatr Hematol Oncol, 27 (4). pp. 179-87. ISSN 1077-4114 (Print)1077-4114 (Linking)

Ptashne, M., Gann, A. (1999) Imposing specificity by localization: mechanism and evolvability. Evolution as Computation: Dimacs Workshop, Princeton, January 1999 . Springer Berlin Heidelberg. ISBN 9783540667094

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

R

Rafi, Abdul Muntakim, Nogina, Daria, Penzar, Dmitry, Lee, Dohoon, Lee, Danyeong, Kim, Nayeon, Kim, Sangyeup, Kim, Dohyeon, Shin, Yeojin, Kwak, Il-Youp, Meshcheryakov, Georgy, Lando, Andrey, Zinkevich, Arsenii, Kim, Byeong-Chan, Lee, Juhyun, Kang, Taein, Vaishnav, Eeshit Dhaval, Yadollahpour, Payman, Random Promoter DREAM Challenge Consortium, Kim, Sun, Albrecht, Jake, Regev, Aviv, Gong, Wuming, Kulakovskiy, Ivan V, Meyer, Pablo, de Boer, Carl G (October 2024) A community effort to optimize sequence-based deep learning models of gene regulation. Nature Biotechnology. ISSN 1087-0156 (Public Dataset)

Rappaport, A. R. (2011) Dissecting tumor suppressor and tumor maintenance genes in poor prognosis AML. PhD thesis, Cold Spring Harbor Laboratory.

S

Schwab, R., Maizel, A., Ruiz-Ferrer, V., Garcia, D., Bayer, M., Crespi, M., Voinnet, O., Martienssen, R. A. (June 2009) Endogenous TasiRNAs mediate non-cell autonomous effects on gene regulation in Arabidopsis thaliana. PloS one, 4 (6). e5980. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Shi, J., Whyte, W. A., Zepeda-Mendoza, C. J., Milazzo, J. P., Shen, C., Roe, J. S., Minder, J. L., Mercan, F., Wang, E., Eckersley-Maslin, M. A., Campbell, A. E., Kawaoka, S., Shareef, S., Zhu, Z., Kendall, J., Muhar, M., Haslinger, C., Yu, M., Roeder, R. G., Wigler, M. A., Blobel, G. A., Zuber, J., Spector, D. L., Young, R. A., Vakoc, C. R. (November 2013) Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes and Development, 27 (24). pp. 264-273. ISSN 08909369 (ISSN)

Singh, R., Low, E. T., Ooi, L. C., Ong-Abdullah, M., Nookiah, R., Ting, N. C., Marjuni, M., Chan, P. L., Ithnin, M., Manaf, M. A., Nagappan, J., Chan, K. L., Rosli, R., Halim, M. A., Azizi, N., Budiman, M. A., Lakey, N., Bacher, B., Van Brunt, A., Wang, C., Hogan, M., He, D., MacDonald, J. D., Smith, S. W., Ordway, J. M., Martienssen, R. A., Sambanthamurthi, R. (June 2014) The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB. Nature Communications, 5. p. 4106. ISSN 20411723

Singh, R., Low, E. T. L., Ooi, L. C. L., Ong-Abdullah, M., Ting, N. C., Nagappan, J., Nookiah, R., Amiruddin, M. D., Rosli, R., Manaf, M. A. A., Chan, K. L., Halim, M. A., Azizi, N., Lakey, N., Smith, S. W., Budiman, M. A., Hogan, M., Bacher, B., Van Brunt, A., Wang, C., Ordway, J. M., Sambanthamurthi, R., Martienssen, R. A. (August 2013) The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature, 500 (7462). pp. 340-344. ISSN 00280836

Somerville, T. D. D., Xu, Y., Wu, X. S., Maia-Silva, D., Hur, S. K., de Almeida, L. M. N., Preall, J. B., Koo, P. K., Vakoc, C. R. (May 2020) ZBED2 is an antagonist of interferon regulatory factor 1 and modifies cell identity in pancreatic cancer. Proc Natl Acad Sci U S A, 117 (21). pp. 11471-11482. ISSN 0027-8424 (Print)0027-8424

Souza, G. M., Van Sluys, M. A., Lembke, C. G., Lee, H., Margarido, G. R. A., Hotta, C. T., Gaiarsa, J. W., Diniz, A. L., Oliveira, M. M., Ferreira, S. S., Nishiyama, M. Y., Ten-Caten, F., Ragagnin, G. T., Andrade, P. M., de Souza, R. F., Nicastro, G. G., Pandya, R., Kim, C., Guo, H., Durham, A. M., Carneiro, M. S., Zhang, J., Zhang, X., Zhang, Q., Ming, R., Schatz, M. C., Davidson, B., Paterson, A. H., Heckerman, D. (December 2019) Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience, 8 (12). giz129. ISSN 2047-217x (Public Dataset)

Spector, M. S., Desnoyers, S., Hoeppner, D. J., Hengartner, M. O. (February 1997) Interaction between the C. elegans cell-death regulators CED-9 and CED-4. Nature, 385 (6617). pp. 653-6. ISSN 0028-0836 (Print)

Spector, D. L. (2003) The dynamics of chromosome organization and gene regulation. Annual Review of Biochemistry, 72. pp. 573-608. ISSN 0066-4154

Stec, Natalia, Doerfel, Katja, Hills-Muckey, Kelly, Ettorre, Victoria M, Ercan, Sevinc, Keil, Wolfgang, Hammell, CM (September 2020) An Epigenetic Priming Mechanism Mediated by Nutrient Sensing Regulates Transcriptional Output. BioRxiv. (Unpublished)

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)

Sun, Yonghao, Dong, Liang, Zhang, Ying, Lin, Da, Xu, Weize, Ke, Changxiong, Han, Linqian, Deng, Lulu, Li, Guoliang, Jackson, David, Li, Xingwang, Yang, Fang (June 2020) 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize. Genome Biology, 21 (1). p. 143. ISSN 1474-760X

Suresh, Hamsini, Crow, Megan, Jorstad, Nikolas, Hodge, Rebecca, Lein, Ed, Dobin, Alexander, Bakken, Trygve, Gillis, Jesse (September 2023) Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nature Ecology and Evolution. ISSN 2397-334X

T

Takao, Sumiko, Forbes, Lauren, Uni, Masahiro, Cheng, Shuyuan, Pineda, Jose Mario Bello, Tarumoto, Yusuke, Cifani, Paolo, Minuesa, Gerard, Chen, Celine, Kharas, Michael G, Bradley, Robert K, Vakoc, Christopher R, Koche, Richard P, Kentsis, Alex (February 2021) Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia. eLife, 10. pp. 1-46. ISSN 2050-084X

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)

Tareen, Ammar, Kinney, Justin (November 2019) Biophysical models of cis-regulation as interpretable neural networks. BioRxiv. (Unpublished)

Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T. W., Gaudinier, A., Young, N. F., Trabucco, G. M., Veling, M. T., Lamothe, R., Handakumbura, P. P., Xiong, G., Wang, C., Corwin, J., Tsoukalas, A., Zhang, L., Ware, D., Pauly, M., Kliebenstein, D. J., Dehesh, K., Tagkopoulos, I., Breton, G., Pruneda-Paz, J. L., Ahnert, S. E., Kay, S. A., Hazen, S. P., Brady, S. M. (January 2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 517 (7536). pp. 571-575. ISSN 0028-0836

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

Toneyan, Shushan, Koo, Peter K (July 2023) Interpreting Cis -Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. bioRxiv. (Submitted)

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)

Tu, H., Barr, M., Dong, D. L., Wigler, M. H. (October 1997) Multiple regulatory domains on the Byr2 protein kinase. Mol Cell Biol, 17 (10). pp. 5876-87. ISSN 0270-7306 (Print)

Turner, G. C., Du, F., Varshavsky, A. (2000) Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature, 405 (6786). pp. 579-583. ISSN 00280836 (ISSN)

Turner, Tychele N, Hormozdiari, Fereydoun, Duyzend, Michael H, McClymont, Sarah A, Hook, Paul W, Iossifov, Ivan, Raja, Archana, Baker, Carl, Hoekzema, Kendra, Stessman, Holly A, Zody, Michael C, Nelson, Bradley J, Huddleston, John, Sandstrom, Richard, Smith, Joshua D, Hanna, David, Swanson, James M, Faustman, Elaine M, Bamshad, Michael J, Stamatoyannopoulos, John, Nickerson, Deborah A, McCallion, Andrew S, Darnell, Robert, Eichler, Evan E (January 2016) Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. The American Journal of Human Genetics, 98 (1). pp. 58-74. ISSN 0002-9297

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)

V

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

Van Aelst, L., Hohmann, S., Bulaya, B., Dekoning, W., Sierkstr, L., Neves, M. J., Luyten, K., Alijo, R., Ramos, J., Coccetti, P., Martegani, E., Demagalhaesrocha, N. M., Brandao, R. L., Vandijck, P., Vanhalewyn, M., Durnez, P., Jans, A. W. H., Thevelein, J. M. (May 1993) Molecular-Cloning of a Gene Involved in Glucose Sensing in the Yeast Saccharomyces-Cerevisiae. Molecular Microbiology, 8 (5). pp. 927-943. ISSN 0950-382X

van Oordt, W. V., Diaz-Meco, M. T., Lozano, J., Krainer, A. R., Moscat, J., Caceres, J. F. (April 2000) The MKK3/6-p38-signaling cascade alters the subcellular distribution of hnRNP A1 and modulates alternative splicing regulation. Journal of Cell Biology, 149 (2). pp. 307-316. ISSN 0021-9525

W

Wang, X., Trotman, L. C., Koppie, T., Alimonti, A., Chen, Z., Gao, Z., Wang, J., Erdjument-Bromage, H., Tempst, P., Cordon-Cardo, C., Pandolfi, P. P., Jiang, X. (January 2007) NEDD4-1 Is a Proto-Oncogenic Ubiquitin Ligase for PTEN. Cell, 128 (1). pp. 129-139. ISSN 00928674 (ISSN)

Wang, Y., Xu, H. P., Riggs, M., Rodgers, L., Wigler, M. H. (July 1991) byr2, a Schizosaccharomyces pombe gene encoding a protein kinase capable of partial suppression of the ras1 mutant phenotype. Molecular & Cellular Biology, 11 (7). pp. 3554-63. ISSN 0270-7306

Wang, Xingang, Aguirre, Lyndsey, Rodríguez-Leal, Daniel, Hendelman, Anat, Benoit, Matthias, Lippman, Zachary B (April 2021) Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nature Plants, 7 (4). pp. 419-427. ISSN 2055-026X

Webb, C. P., Van Aelst, L., Wigler, M. H., Woude, G. F. (July 1998) Signaling pathways in Ras-mediated tumorigenicity and metastasis. Proc Natl Acad Sci U S A, 95 (15). pp. 8773-8. ISSN 0027-8424 (Print)

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)

Wigler, M. H., Mishra, B. (May 2002) Genetics. Wild by nature. Science, 296 (5572). pp. 1407-1408. ISSN 0036-8075

Wigler, M. H., Xu, H. P., Vanaelst, L., Jung, V., Marcus, S., Polverino, T., Oneill, K., Chang, E., Camonis, J., Nicolette, C., White, M., Ballester, R. (April 1993) Evolution of Ras Signal Transduction Pathways. Faseb Journal, 7 (7). A1124-A1124. ISSN 0892-6638

Won, K. A., Baumann, H. (1991) NF-AB, a liver-specific and cytokine-inducible nuclear factor that interacts with the interleukin-1 response element of the rat alpha 1-acid glycoprotein gene. Molecular & Cellular Biology, 11 (6). pp. 3001-3008.

Won, K. A., Xiong, Y., Beach, D., Gilman, M. Z. (October 1992) Growth-regulated expression of D-type cyclin genes in human diploid fibroblasts. Proc Natl Acad Sci U S A, 89 (20). pp. 9910-4. ISSN 0027-8424 (Print)0027-8424 (Linking)

X

Xing, Z., Ma, W. K., Tran, E. J. (December 2018) The DDX5/Dbp2 subfamily of DEAD-box RNA helicases. Wiley Interdiscip Rev RNA, 10 (2). e1519. ISSN 1757-7004

Xue, B., Krishnamurthy, K., Allred, D. C., Muthuswamy, S. K. (2013) Loss of Par3 promotes breast cancer metastasis by compromising cell-cell cohesion. Nature Cell Biology, 15 (2). pp. 189-200. ISSN 1465-7392

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., Zhang, J., Luo, W. J., Hicks, J., Zender, L., Wang, X. W., Powers, S., Wigler, M., Lowe, S. W. (May 2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109 (21). pp. 8212-8217. ISSN 0027-8424

Xue, W., Krasnitz, A., Lucito, R., Sordella, R., Van Aelst, L., Cordon-Cardo, C., Singer, S., Kuehnel, F., Wigler, M. H., Powers, S., Zender, L., Lowe, S. W. (June 2008) DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma. Genes & Development, 22 (11). pp. 1439-44. ISSN 0890-9369

Y

Yajnik, V., Paulding, C., Sordella, R., McClatchey, A. I., Saito, M., Wahrer, D. C., Reynolds, P., Bell, D. W., Lake, R., van den Heuvel, S., Settleman, J., Haber, D. A. (March 2003) DOCK4, a GTPase activator, is disrupted during tumorigenesis. Cell, 112 (5). pp. 673-84. ISSN 0092-8674 (Print)

Yordanov, Georgi Nenov (July 2019) Myc and Spdef: two transcription factors hijacked by pancreatic cancer. PhD thesis, Cold Spring Harbor.

Yu, A., Saudemont, B., Bouteiller, N., Elvira-Matelot, E., Lepere, G., Parent, J. S., Morel, J. B., Cao, J., Elmayan, T., Vaucheret, H. (August 2015) Second site mutagenesis of a hypomorphic ago1 allele identifies SKI3 as an endogenous suppressor of PTGS. Plant Physiol, 169 (2). pp. 1266-1274. ISSN 1532-2548 (Electronic)0032-0889 (Linking)

Yu, Duonan, dos Santos, Camila O, Zhao, Guowei, Jiang, Jing, Amigo, Julio D, Khandros, Eugene, Dore, Louis C, Yao, Yu, D'Souza, Janine, Zhang, Zhe, Ghaffari, Saghi, Choi, John, Friend, Sherree, Tong, Wei, Orange, Jordan S, Paw, Barry H, Weiss, Mitchell J (August 2010) miR-451 protects against erythroid oxidant stress by repressing 14-3-3zeta. Genes and Development, 24 (15). pp. 1620-1633. ISSN 0890-9369

Z

Zeng, L., Choi, S. C., Danko, C. G., Siepel, A., Stanhope, M. J., Burne, R. A. (2013) Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One, 8 (3). e60465. ISSN 1932-6203

Zhu, X., Lin, C. R., Prefontaine, G. G., Tollkuhn, J., Rosenfeld, M. G. (June 2005) Genetic control of pituitary development and hypopituitarism. Curr Opin Genet Dev, 15 (3). pp. 332-40. ISSN 0959-437X (Print)0959-437X (Linking)

Zhu, Y., Pak, D., Qin, Y., McCormack, S. G., Kim, M. J., Baumgart, J. P., Velamoor, V., Auberson, Y. P., Osten, P., Van Aelst, L., Sheng, M., Zhu, J. J. (2005) Rap2-JNK removes synaptic AMPA receptors during depotentiation. Neuron, 46 (6). pp. 905-916. ISSN 08966273 (ISSN)

Zhu, Chuanmei, Liu, Lei, Crowell, Olivia, Zhao, Hui, Brutnell, Thomas P, Jackson, David, Kellogg, Elizabeth A (2021) The CLV3 Homolog in Setaria viridis Selectively Controls Inflorescence Meristem Size. Frontiers in Plant Science, 12. p. 636749. ISSN 1664-462X