Items where Subject is "cis-regulatory elements"

Paper

Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., Kent, W. J., Haussler, D. (May 2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441 (7089). pp. 87-90. ISSN 0028-0836

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

Benoit, Matthias (January 2022) Hot 'n cold: Applying the cis-regulatory code to predict heat and cold stress response in maize. The Plant cell, 34 (1). pp. 497-498. ISSN 1532-298X

Capellini, T. D., Dunn, M. P., Passamaneck, Y. J., Selleri, L., Di Gregorio, A. (November 2008) Conservation of notochord gene expression across chordates: insights from the Leprecan gene family. Genesis, 46 (11). pp. 683-96. ISSN 1526-954x

Castel, S. E., Cervera, A., Mohammadi, P., Aguet, F., Reverter, F., Wolman, A., Guigo, R., Iossifov, I., Vasileva, A., Lappalainen, T. (August 2018) Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat Genet, 50 (9). pp. 1327-1334. ISSN 1061-4036

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

Dukler, Noah, Huang, Yi-Fei, Siepel, Adam (September 2019) Phylogenetic modeling of regulatory element turnover based on epigenomic data. BioRxiv. (Unpublished)

Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., Sanyal, A., Shoresh, N., Simon, J. M., Song, L., Trinklein, N. D., Altshuler, R. C., Birney, E., Brown, J. B., Cheng, C., Djebali, S., Dong, X. J., Ernst, J., Furey, T. S., Gerstein, M., Giardine, B., Greven, M., Hardison, R. C., Harris, R. S., Herrero, J., Hoffman, M. M., Iyer, S., Kellis, M., Kheradpour, P., Lassmann, T., Li, Q. H., Lin, X., Marinov, G. K., Merkel, A., Mortazavi, A., Parker, S. C. J., Reddy, T. E., Rozowsky, J., Schlesinger, F., Thurman, R. E., Wang, J., Ward, L. D., Whitfield, T. W., Wilder, S. P., Wu, W., Xi, H. L. S., Yip, K. Y., Zhuang, J. L., Bernstein, B. E., Green, E. D., Gunter, C., Snyder, M., Pazin, M. J., Lowdon, R. F., Dillon, L. A. L., Adams, L. B., Kelly, C. J., Zhang, J., Wexler, J. R., Good, P. J., Feingold, E. A., Crawford, G. E., Dekker, J., Elnitski, L., Farnham, P. J., Giddings, M. C., Gingeras, T. R., Guigo, R., Hubbard, T. J., Kent, W. J., Lieb, J. D., Margulies, E. H., Myers, R. M., Stamatoyannopoulos, J. A., Tenenbaum, S. A., Weng, Z. P., White, K. P., Wold, B., Yu, Y., Wrobel, J., Risk, B. A., Gunawardena, H. P., Kuiper, H. C., Maier, C. W., Xie, L., Chen, X., Mikkelsen, T. S., Gillespie, S. (September 2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414). pp. 57-74. ISSN 0028-0836

Dunn, M. P., Di Gregorio, A. (April 2009) The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord. Dev Biol, 328 (2). pp. 561-74. ISSN 0012-1606

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

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)

Gao, Yuan, He, Xue-Yan, Wu, Xiaoli S, Huang, Yu-Han, Toneyan, Shushan, Ha, Taehoon, Ipsaro, Jonathan J, Koo, Peter K, Joshua-Tor, Leemor, Bailey, Kelly M, Egeblad, Mikala, Vakoc, Christopher R (January 2023) ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation. Nature Cell Biology. ISSN 1465-7392 (Public Dataset)

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

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

Lanctot, Amy, Hendelman, Anat, Udilovich, Peter, Robitaille, Gina M, Lippman, Zachary (November 2024) Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness. bioRxiv. ISSN 2692-8205 (Submitted)

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

Sadowski, C. L., Henry, R. W., Lobo, S. M., Hernandez, N. (February 1994) Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE. Genes & Development, 7 (8). pp. 1535-1548. ISSN 0890-9369

Siepel, A., Arbiza, L. (December 2014) Cis-regulatory elements and human evolution. Curr Opin Genet Dev, 29c. pp. 81-89. ISSN 0959-437x

Wang, J., Smith, P. J., Krainer, A. R., Zhang, M. Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res, 33 (16). pp. 5053-62. ISSN 1362-4962 (Electronic)

Wang, X. W., Gu, J., Zhang, M. Q., Li, Y. D. (January 2008) Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics, 24 (2). pp. 165-171. ISSN 1367-4803

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

Wei, Y., Gokhale, R. H., Sonnenschein, A., Montgomery, K. M., Ingersoll, A., Arnosti, D. N. (October 2016) Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator. Development, 143 (19). pp. 3591-3603. ISSN 0950-1991

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)

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

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

Thesis

Tang, Ziqi (April 2024) Exploring the Representational Power of Genomic Deep Learning Models. PhD thesis, Cold Spring Harbor Laboratory.