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.

140 Articles

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
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

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