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

Measuring the reproducibility and quality of Hi-C data
Yardımcı, G. G., Ozadam, H., Sauria, M. E. G., Ursu, O., Yan, K.-K., Yang, T., Chakraborty, A., Kaul, A., Lajoie, B. R., Song, F., Zhan, Y., Ay, F., Gerstein, M., Kundaje, A., Li, Q., Taylor, J., Yue, F., Dekker, J., Noble, W. S.
10.1101/188755 — Posted: 2018-02-05
Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture
Schreiber, J., Libbrecht, M., Bilmes, J., Noble, W.
10.1101/103614 — Posted: 2018-07-15
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
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
TopicNet: a framework for measuring transcriptional regulatory network change
Lou, S., Li, T., Kong, X., Zhang, J., Liu, J., Lee, D., Gerstein, M.
10.1101/862177 — Posted: 2020-01-23
DiNeR: a Differential Graphical Model for analysis of co-regulation Network Rewiring
Zhang, J., Liu, J., Lee, D., Lou, S., Chen, Z., Gursoy, G., Gerstein, M.
10.1101/2020.05.29.124164 — Posted: 2020-05-30
Epigenome-based Splicing Prediction using a Recurrent Neural Network
Lee, D., Zhang, J., Liu, J., Gerstein, M.
10.1101/2020.02.03.932251 — Posted: 2020-05-06
The changing mouse embryo transcriptome at whole tissue and single-cell resolution
Peng He, Brian A Williams, Diane Trout, Georgi K Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A Pennacchio, Diane E Dickel, Axel Visel, Bing Ren, Ross C Hardison, Yu Zhang, Barbara J Wold
10.1101/2020.06.14.150599 — Posted: 2020-07-12
Atlas and developmental dynamics of mouse DNase I hypersensitive sites
Breeze, C. E., Lazar, J., Mercer, T., Halow, J., Washington, I., Lee, K., Ibarrientos, S., Castillo, A., Neri, F., Haugen, E., Rynes, E., Reynolds, A., Bates, D., Diegel, M., Dunn, D., Kaul, R., Sandstrom, R., Meuleman, W., Bender, M. A., Groudine, M., Stamatoyannopoulos, J. A.
10.1101/2020.06.26.172718 — Posted: 2020-06-28
Loop competition and extrusion model predicts CTCF interaction specificity
Xi, W., Beer, M. A.
10.1101/2020.07.02.185389 — Posted: 2021-01-11

RSS  Channel RSS