Channel:  ENCODE

143 Articles

A pitfall for machine learning methods aiming to predict across cell types
Schreiber, J., Singh, R., Bilmes, J., Noble, W. S.
10.1101/512434 — Posted: 2019-04-26
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
A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays
Klein, J. C., Agarwal, V., Inoue, F., Keith, A., Martin, B., Kircher, M., Ahituv, N., Shendure, J.
10.1101/576405 — Posted: 2019-03-13
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
Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Patwardhan, T. A., Nguyen, T. H., Kane, M., Doughty, B., Perez, E. M., Durand, N. C., Stamenova, E. K., Lieberman Aiden, E., Lander, E. S., Engreitz, J. M.
10.1101/529990 — Posted: 2019-01-26
The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state
Stamenova, E. K., Durand, N., Dudchenko, O., Shamim, M. S., Huang, S.-C., Jiang, Y., Bochkov, I. D., Rao, S. S. P., Lander, E. S., Gnirke, A., Aiden, E. L.
10.1101/481283 — Posted: 2018-11-29
Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair
Chen, W., McKenna, A., Schreiber, J., Yin, Y., Agarwal, V., Noble, W. S., Shendure, J.
10.1101/481069 — Posted: 2018-11-28
RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins
Zhang, J., Liu, J., Lee, D., Feng, J.-J., Lochovsky, L., Lou, S., Rutenberg-Schoenberg, M., Gerstein, M.
10.1101/474072 — Posted: 2018-11-19
Occupancy patterns of 208 DNA-associated proteins in a single human cell type
Partridge, E. C., Chhetri, S. B., Prokop, J. W., Ramaker, R. C., Jansen, C. S., Goh, S.-T., Mackiewicz, M., Newberry, K. M., Brandsmeier, L. A., Meadows, S. K., Messer, C. L., Hardigan, A. A., Dean, E. C., Jiang, S., Savic, D., Mortazavi, A., Wold, B. J., Myers, R. M., Mendenhall, E. M.
10.1101/464800 — Posted: 2018-11-07
Widespread RNA editing dysregulation in Autism Spectrum Disorders
Tran, S., Jun, H.-I., Bahn, J. H., Azghadi, A., Ramaswami, G., Van Nostrand, E. L., Nguyen, T. B., Hsiao, Y.-H. E., Lee, C., Pratt, G. A., Yeo, G. W., Geschwind, D. H., Xiao, X.
10.1101/446625 — Posted: 2018-10-17

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