Channel:  ENCODE

142 Articles

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.
10.1101/2021.03.31.437978 — Posted: 2021-12-10
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Yang, R., Das, A., Gao, V. R., Karbalayghareh, A., Noble, W. S., Bilmes, J. A., Leslie, C. S.
10.1101/2021.12.02.470663 — Posted: 2021-12-03
Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics
Jagadeesh, K. A., Dey, K. K., Montoro, D. T., Mohan, R., Gazal, S., Engreitz, J. M., Xavier, R. J., Price, A. L., Regev, A.
10.1101/2021.03.19.436212 — Posted: 2021-11-23
Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells
Chen, W., Choi, J., Nathans, J. F., Agarwal, V., Martin, B., Nichols, E., Leith, A., Lee, C., Shendure, J.
10.1101/2021.11.05.467434 — Posted: 2021-11-05

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