Channel:  ENCODE

142 Articles

Genome-wide annotation of gene regulatory elements linked to cell fitness
ter Weele, M., Klann, T. S., Barrera, A., Ettyreddy, A. R., Liu, S., Rickels, R. A., Bryois, J., Jiang, S., Adkar, S. S., Iglesias, N., Sullivan, P. F., Reddy, T. E., Allen, A. S., Crawford, G. E., Gersbach, C.
10.1101/2021.03.08.434470 — Posted: 2025-07-20
An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation
Moore, J. E., Pratt, H. E., Fan, K., Phalke, N., Fisher, J., Elhajjajy, S. I., Andrews, G., Gao, M., Shedd, N., Fu, Y., Lacadie, M. C., Meza, J., Ganna, M., Choudhury, E., Swofford, R., Farrell, N. P., Pampari, A., Ramalingam, V., Reese, F., Borsari, B., Yu, X., Wattenberg, E. S., Ruiz-Romero, M., Razavi-Mohseni, M., Xu, J., Galeev, T., Beer, M. A., Guigo, R., Gerstein, M., Engreitz, J. M., Ljungman, M., Reddy, T. E., Snyder, M., Epstein, C. B., Gaskell, E., Bernstein, B. E., Dickel, D. E., Visel, A., Pennacchio, L. A., Mortazavi, A., Kundaje, A., Weng, Z.
10.1101/2024.12.26.629296 — Posted: 2024-12-26
Directionality of Transcriptional Regulatory Elements
Chen, Y., Shah, S. R., Leung, A., Paramo, M. I., Cochran, K., Kundaje, A., Clark, A. G., Lis, J. T., Yu, H.
10.1101/2024.12.01.621925 — Posted: 2024-12-02
Quantifying Functional Conservation of Human and Mouse Regulatory Elements via FUNCODE
Fang, W., Chen, C., Zhang, B., Wang, Y., Zhao, R., Zhou, W., Ji, H.
10.1101/2024.10.31.620766 — Posted: 2024-11-03
CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription
Ren, X., Zheng, L., Maliskova, L., Tam, T. W., Sun, Y., Liu, H., Lee, J., Takagi, M. A., Li, B., Ren, B., Wang, W., Shen, Y.
10.1101/2024.10.08.616922 — Posted: 2024-10-10
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

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