Channel: ENCODE

144 Articles

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The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Rozowsky, J., Drenkow, J., Yang, Y., Gursoy, G., Galeev, T., Borsari, B., Epstein, C., Xiong, K., Xu, J., Gao, J., Yu, K., Berthel, A., Chen, Z., Navarro, F., Liu, J., Sun, M., Wright, J., Chang, J., Cameron, C., Shoresh, N., Gaskell, E., Adrian, J., Aganezov, S., Balderrama-Gutierrez, G., Banskota, S., Corona, G., Chee, S., Chhetri, S., Martins, G., Danyko, C., Davis, C., Farid, D., Farrell, N., Gabdank, I., Gofin, Y., Gorkin, D., Gu, M., Hecht, V., Hitz, B., Issner, R., Kirsche, M., Kong, X., Lam, B., Li, S., Li, B., Li, T., Li, X., Lin, K., Luo, R., Mackiewicz, M., Moore, J., Mudge, J., Nel

10.1101/2021.04.26.441442 — Posted: 2022-11-22

Predicting A/B compartments from histone modifications using deep learning

Zheng, S., Thakkar, N., Harris, H. L., Zhang, M., Liu, S., Gerstein, M., Aiden, E. L., Rowley, J., Noble, W. S., Gursoy, G., Singh, R.

10.1101/2022.04.19.488754 — Posted: 2022-09-19

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

Schreiber, J. M., Boix, C. A., Lee, J. w., Li, H., Guan, Y., Chang, C.-C., Chang, J.-C., Hawkins-Hooker, A., Schoelkopf, B., Schweikert, G., Rojas Carulla, M., Canakoglu, A., Guzzo, F., Nanni, L., Masseroli, M., Carman, M. J., Pinoli, P., Hong, C., Yip, K. Y., Spence, J. P., Batra, S. S., Song, Y. S., Mahony, S., Zhang, Z., Tan, W., Shen, Y., Sun, Y., Shi, M., Adrian, J., Sandstrom, R. S., Farrell, N., Halow, J. M., Lee, K., Jiang, L., Yang, X., Epstein, C. B., Strattan, J. S., Snyder, M. P., Kellis, M., Noble, W. S., Kundaje, A. B.

10.1101/2022.07.30.502157 — Posted: 2022-08-02

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

Dey, K. K., Gazal, S. K., van de Geijn, B., Kim, S. S., Nasser, J., Engreitz, J. M., Price, A.

10.1101/2020.09.02.279059 — Posted: 2022-07-15

Uncovering Hidden Enhancers Through Unbiased In Vivo Testing

Mannion, B. J., Osterwalder, M., Tran, S., Plajzer-Frick, I., Novak, C. S., Afzal, V., Akiyama, J. A., Barton, S., Beckman, E., Garvin, T. H., Godfrey, P., Godoy, J., Hunter, R. D., Kato, M., Kosicki, M., Kronshage, A. H., Lee, E. A., Meky, E. M., Pham, Q. T., von Maydell, K., Zhu, Y., Lopez-Rios, J., Dickel, D. E., Visel, A., Pennacchio, L. A.

10.1101/2022.05.29.493901 — Posted: 2022-05-30

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

Schmidt, H., Zhang, M., Mourelatos, H., Sanchez-Rivera, F. J., Lowe, S. W., Ventura, A., Leslie, C. S., Pritykin, Y.

10.1101/2022.05.02.490368 — Posted: 2022-05-03

Evolution of transposable element-derived enhancer activity

Du, A. Y., Zhuo, X., Sundaram, V., Jensen, N. O., Chaudhari, H. G., Saccone, N. L., Cohen, B. A., Wang, T.

10.1101/2022.03.16.483999 — Posted: 2022-03-17

Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes and gene regulation

Choudhary, M. N., Quaid, K., Xing, X., Schmidt, H., Wang, T.

10.1101/2022.02.01.475239 — Posted: 2022-02-03

Chromatin interaction aware gene regulatory modeling with graph attention networks

Karbalayghareh, A., Sahin, M., Leslie, C. S.