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

An encyclopedia of enhancer-gene regulatory interactions in the human genome
Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R. N., Xi, W., Tan, A. S., Jones, H., Ma, X. R., Yao, D., Nasser, J., Avsec, Z., James, B. T., Shamim, M. S., Durand, N. C., Rao, S. S. P., Mahajan, R., Doughty, B. R., Andreeva, K., Ulirsch, J. C., Fan, K., Perez, E. M., Nguyen, T. C., Kelley, D. R., Finucane, H. K., Moore, J. E., Weng, Z., Kellis, M., Bassik, M. C., Price, A. L., Beer, M. A., Guigo, R., Stamatoyannopoulos, J. A., Aiden, E. L., Greenleaf, W. J., Leslie, C. S., Steinmetz, L. M., Kundaje, A., Engreitz, J. M.
10.1101/2023.11.09.563812 — Posted: 2023-11-13
Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals
Oh, J. W., Beer, M. A.
10.1101/2023.10.06.561128 — Posted: 2023-10-06
Regulatory Transposable Elements in the Encyclopedia of DNA Elements
Du, A. Y., Chobirko, J. D., Zhuo, X., Feschotte, C., Wang, T.
10.1101/2023.09.05.556380 — Posted: 2023-09-06
Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons
Yang, X., Jones, I. R., Chen, P. B., Yang, H., Ren, X., Zheng, L., Li, B., Li, Y. E., Sun, Q., Wen, J., Beaman, C., Cui, X., Li, Y., Wang, W., Hu, M., Ren, B., Shen, Y.
10.1101/2023.08.30.555359 — Posted: 2023-08-30
Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth
Zhang, Y., Chen, K., Tang, S. C., Cai, Y., Nambu, A., See, Y. X., Fu, C., Raju, A., Lebeau, B., Ling, Z., Mutwil, M., Lakshmanan, M., Osato, M., Tergaonkar, V., Fullwood, M. J.
10.1101/2023.08.29.555291 — Posted: 2023-08-30
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
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

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