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.

141 Articles

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
A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation
Sethi, A., Gu, M., Gumusgoz, E., Chan, L., Yan, K.-K., Rozowsky, J. S., Barozzi, I., Afzal, V., Akiyama, J., Plajzer-Frick, I., Yan, C., Pickle, C., Kato, M., Garvin, T., Pham, Q., Harrington, A., Mannion, B., Lee, E., Fukuda-Yuzawa, Y., Visel, A., Dickle, D. E., Yip, K., Sutton, R., Pennacchio, L. A., Gerstein, M.
10.1101/385237 — Posted: 2018-08-05
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
Nir, G., Farabella, I., Perez Estrada, C., Ebeling, C. G., Beliveau, B. J., Sasaki, H. M., Lee, S. H., Nguyen, S. C., McCole, R. B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N. M. C., Nguyen, H. Q., Hannan, M. A., Russell, S., Durand, N. C., Rao, S. S. P., Kishi, J. Y., Soler-Vila, P., Di Pierro, M., Onuchic, J. N., Callahan, S., Schreiner, J., Stuckey, J., Yin, P., Lieberman Aiden, E., Marti-Renom, M. A., Wu, C.- t.
10.1101/374058 — Posted: 2018-07-28
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
Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT
Harvey, S., Xu, Y., Lin, X., Gao, X. D., Qiu, Y., Ahn, J., Xiao, X., Cheng, C.
10.1101/301267 — Posted: 2018-04-13
GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs
Ursu, O., Boley, N., Taranova, M., Wang, Y. X. R., Yardimci, G. G., Noble, W. S., Kundaje, A.
10.1101/181842 — Posted: 2018-03-08
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
Juicebox.js provides a cloud-based visualization system for Hi-C data
Robinson, J., Turner, D., Durand, N. C., Thorvaldsdottir, H., Mesirov, J. P., Aiden, E. L.
10.1101/205740 — Posted: 2017-10-19
De Novo Prediction of Human Chromosome Structures: Epigenetic Marking Patterns Encode Genome Architecture
Di Pierro, M., Cheng, R. R., Lieberman Aiden, E., Wolynes, P. G., Onuchic, J. N.
10.1101/173088 — Posted: 2017-08-07
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

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