Channel:  ENCODE

142 Articles

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
Yang, T., Zhang, F., Yardimci, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F., Li, Q.
10.1101/101386 — Posted: 2017-08-04
Systematic mapping of chromatin state landscapes during mouse development
Gorkin, D., Barozzi, I., Zhang, Y., Lee, A. Y., Lee, B., Zhao, Y., Wildberg, A., Ding, B., Zhang, B., Wang, M., Strattan, J. S., Davidson, J. M., Qiu, Y., Afzal, V., Akiyama, J. A., Plajzer-Frick, I., Pickle, C. S., Kato, M., Garvin, T. H., Pham, Q. T., Harrington, A. N., Mannion, B. J., Lee, E. A., Fukuda-Yuzawa, Y., He, Y., Preissl, S., Chee, S., Williams, B. A., Trout, D., Amrhein, H., Yang, H., Cherry, J. M., Shen, Y., Ecker, J. R., Wang, W., Dickel, D. E., Visel, A., Pennacchio, L. A., Ren, B.
10.1101/166652 — Posted: 2017-08-03
Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus
He, Y., Hariharan, M., Gorkin, D. U., Dickel, D. E., Luo, C., Castanon, R. G., Nery, J. R., Lee, A. Y., Williams, B. A., Trout, D., Amrhein, H., Fang, R., Chen, H., Li, B., Visel, A., Pennacchio, L. A., Ren, B., Ecker, J. R.
10.1101/166744 — Posted: 2017-07-21
Segway 2.0: Gaussian mixture models and minibatch training
Chan, R. C. W., Libbrecht, M. W., Roberts, E. G., Noble, W. S., Hoffman, M. M.
10.1101/147470 — Posted: 2017-06-08
Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development
Phanstiel, D. H., Van Bortle, K., Spacek, D. V., Hess, G. T., Saad Shamim, M., Machol, I., Love, M. I., Lieberman Aiden, E., Bassik, M. C., Snyder, M. P.
10.1101/142026 — Posted: 2017-05-25
Cohesin Loss Eliminates All Loop Domains, Leading To Links Among Superenhancers And Downregulation Of Nearby Genes
Rao, S., Huang, S.-C., Glenn St. Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bochkov, I. D., Huang, X., Shamim, M. S., Omer, A. D., Bernstein, B. E., Casellas, R., Lander, E. S., Lieberman Aiden, E.
10.1101/139782 — Posted: 2017-05-18
PREDICTD: PaRallel Epigenomics Data Imputation With Cloud-based Tensor Decomposition
Durham, T. J., Libbrecht, M. W., Howbert, J. J., Bilmes, J., Noble, W. S.
10.1101/123927 — Posted: 2017-04-04
An Integrative Framework For Detecting Structural Variations In Cancer Genomes
Dixon, J., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardimci, G. G., Chakraborty, A., Bann, D. V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Mulia, J. C. R., Ozadam, H., Lajoie, B. R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D. T., Stamatoyannopoulos, J. A., Broach, J. R., Hardison, R., Ay, F., Noble, W. S., Dekker, J., Gilbert, D. M., Yue, F.
10.1101/119651 — Posted: 2017-03-28
LR-DNase: Predicting TF binding from DNase-seq data
van der Velde, A. G., Purcaro, M., Noble, W. S., Weng, Z.
10.1101/082594 — Posted: 2016-10-24
Choosing panels of genomics assays using submodular optimization
Kai Wei, Maxwell W Libbrecht, Jeffrey A Bilmes, William Noble
10.1101/036137 — Posted: 2016-05-27

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