Channel:  ENCODE

bioRxiv posts many COVID19-related papers. A reminder: they have not been formally peer-reviewed and should not guide health-related behavior or be reported in the press as conclusive.

136 Articles

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
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
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
Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
Tayyebi, Z., Pine, A. R., Leslie, C. S.
10.1101/2022.05.02.490310 — Posted: 2023-08-08
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
Three linked opposing regulatory variants under selection associate with IVD
Brown, E. A., Kales, S., Boyle, M. J., Vitti, J., Kotliar, D., Schaffner, S. F., Tewhey, R. S., Sabeti, P. C.
10.1101/2022.12.22.521605 — Posted: 2022-12-22
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
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types
Agarwal, V., Inoue, F., Schubach, M., Martin, B., Dash, P., Zhang, Z., Sohota, A., Noble, W., Yardimci, G., Kircher, M., Shendure, J., Ahituv, N.
10.1101/2023.03.05.531189 — Posted: 2023-03-06
Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function
McCutcheon, S., Swartz, A., Brown, M., Barrera, A., McRoberts Amador, C., Siklenka, K., Humayun, L., Isaacs, J., Reddy, T. E., Nair, S., Antonia, S., Gersbach, C. A.
10.1101/2023.05.01.538906 — Posted: 2023-05-01
Multi-center integrated analysis of non-coding CRISPR screens
Yao, D., Tycko, J., Oh, W., Bounds, L. R., Gosai, S. J., Lataniotis, L., Mackay-Smith, A., Doughty, B. R., Gabdank, I., Schmidt, H., Youngworth, I., Andreeva, K., Ren, X., Barrera, A., Luo, Y., Siklenka, K., Yardimci, G. G., The ENCODE4 Consortium, , Tewhey, R., Kundaje, A., Greenleaf, W. J., Sabeti, P. C., Leslie, C., Pritykin, Y., Moore, J. E., Beer, M. A., Gersbach, C., Reddy, T. E., Shen, Y., Engreitz, J. M., Bassik, M. C., Reilly, S. K.
10.1101/2022.12.21.520137 — Posted: 2022-12-22

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