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

Evaluating the informativeness of deep learning annotations for human complex diseases
Dey, K. K., van de Geijn, B. K., Kim, S. S., Hormozdiari, F., Kelley, D. R., Price, A.
10.1101/784439 — Posted: 2020-04-17
ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis
Granja, J. M., Corces, M. R., Pierce, S. E., Bagdatli, S. T., Choudhry, H., Chang, H., Greenleaf, W.
10.1101/2020.04.28.066498 — Posted: 2020-04-29
Allele-specific alternative splicing in human tissues
Amoah, K., Hsiao, Y.-H. E., Bahn, J. H., Sun, Y., Burghard, C., Tan, B. X., Yang, E.-W., Xiao, X.
10.1101/2020.05.04.077255 — Posted: 2020-05-05
HCR-FlowFISH: A flexible CRISPR screening method to identify cis-regulatory elements and their target genes
Reilly, S. K., Gosai, S. J., Guiterrez, A., Ulirsch, J. C., Kanai, M., Berenzy, D., Kales, S., Butler, G. B., Gladden-Young, A., Finucane, H. K., Sabeti, P. C., Tewhey, R.
10.1101/2020.05.11.078675 — Posted: 2020-05-12
STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions
Lee, D., Shi, M., Moran, J., Wall, M., Zhang, J., Liu, J., Fitzgerald, D., Kyono, Y., Ma, L., White, K. P., Gerstein, M. B.
10.1101/694869 — Posted: 2020-05-05
An integrative ENCODE resource for cancer genomics
Zhang, J., Lee, D., Dhiman, V., Jiang, P., Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., Gu, M., Li, S., Lou, S., Xu, J., Lochovsky, L., Ung, M., Ma, L., Yu, S., Cao, Q., Harmanci, A., Yan, K.-K., Sethi, A., Gursoy, G., Schoenberg, M. R., Rozowsky, J., Warrell, J., Emani, P., Yang, Y. T., Galeev, T., Kong, X., Liu, S., Li, X., Krishnan, J., Feng, Y., Rivera-Mulia, J. C., Adrian, J., Broach, J. R., Bolt, M., Moran, J., Fitzgerald, D., Dileep, V., Liu, T., Mei, S., Sasaki, T., Trevilla-Garcia, C., Wang, S., Wang, Y., Zang, C., Wang, D., Klein, R., Snyder, M., Gilbert, D.
10.1101/706424 — Posted: 2019-07-18
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples
Schreiber, J., Bilmes, J., Noble, W.
10.1101/533273 — Posted: 2019-01-29
Multi-scale deep tensor factorization learns a latent representation of the human epigenome
Schreiber, J., Durham, T. J., Bilmes, J., Noble, W. S.
10.1101/364976 — Posted: 2019-04-11
Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history
Sisu, C., Muir, P., Frankish, A., Fiddes, I., Diekhans, M., Thybert, D., Odom, D., Flicek, P., Keane, T., Hubbard, T., Harrow, J., Gerstein, M.
10.1101/386656 — Posted: 2018-08-07
Detecting sample swaps in diverse NGS data types using linkage disequilibrium
Javed, N. M., Farjoun, Y., Fennell, T. J., Epstein, C. B., Bernstein, B. E., Shoresh, N.
10.1101/2020.03.15.992750 — Posted: 2020-06-21

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