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.

141 Articles

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
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
The ENCODE Uniform Analysis Pipelines
Hitz, B. C., Lee, J.-W., Jolanki, O., Kagda, M. S., Graham, K., Sud, P., Gabdank, I., Strattan, J. S., Sloan, C. A., Dreszer, T., Rowe, L. D., Podduturi, N. R., Malladi, V. S., Chan, E. T., Davidson, J. M., Ho, M., Miyasato, S., Simison, M., Tanaka, F., Luo, Y., Whaling, I., Lin, K., Jou, J., Hong, E. L., Lee, B. T., Sandstrom, R., Rynes, E., Nelson, J., Nishida, A., Ingersoll, A., Buckley, M., Frerker, M., Kim, D. S., Boley, N., Trout, D., Dobin, A., Rahmanian, S., Wyman, D., Balderrama-Gutierrez, G., Reese, F., Durand, N. C., Dudchenko, O., Weisz, D., Rao, S. S. P., Blackburn, A., Gkountarou
10.1101/2023.04.04.535623 — Posted: 2023-04-06
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
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
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
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

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