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.

138 Articles

Isoform and pathway-specific post-transcriptional RNA processing in human cells
Bedi, K., Magnuson, B., Narayanan, I. V., McShane, A., Ashaka, M., Paulsen, M. T., Wilson, T. E., Ljungman, M.
10.1101/2024.06.12.598705 — Posted: 2024-06-12
Characterizing nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in the ENCODE4 deeply profiled cell lines
McShane, A., Venkata Narayanan, I., Paulsen, M. T., Ashaka, M., Blinkiewicz, H., Yang, N. T., Magnuson, B., Bedi, K., Wilson, T. E., Ljungman, M.
10.1101/2024.04.09.588612 — Posted: 2024-05-03
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
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
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
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

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