Channel: Impact of Genomic Variation on Function (IGVF)

120 Articles

An encyclopedia of enhancer-gene regulatory interactions in the human genome

Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R. N., Xi, W., Tan, A. S., Jones, H., Ma, X. R., Yao, D., Nasser, J., Avsec, Z., James, B. T., Shamim, M. S., Durand, N. C., Rao, S. S. P., Mahajan, R., Doughty, B. R., Andreeva, K., Ulirsch, J. C., Fan, K., Perez, E. M., Nguyen, T. C., Kelley, D. R., Finucane, H. K., Moore, J. E., Weng, Z., Kellis, M., Bassik, M. C., Price, A. L., Beer, M. A., Guigo, R., Stamatoyannopoulos, J. A., Aiden, E. L., Greenleaf, W. J., Leslie, C. S., Steinmetz, L. M., Kundaje, A., Engreitz, J. M.

10.1101/2023.11.09.563812 — Posted: 2023-11-13

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Li, X., Chen, H., Selvaraj, M. S., Van Buren, E., Zhou, H., Wang, Y., Sun, R., McCaw, Z. R., Yu, Z., Arnett, D. K., Bis, J. C., Blangero, J., Boerwinkle, E., Bowden, D. W., Brody, J. A., Cade, B. E., Carson, A. P., Carlson, J. C., Chami, N., Chen, Y.-D. I., Curran, J. E., de Vries, P. S., Fornage, M., Franceschini, N., Freedman, B. I., Gu, C., Heard-Costa, N. L., He, J., Hou, L., Hung, Y.-J., Irvin, M. R., Kaplan, R. C., Kardia, S. L. R., Kelly, T., Konigsberg, I., Kooperberg, C., Kral, B. G., Li, C., Loos, R. J. F., Mahaney, M. C., Martin, L. W., Mathias, R. A., Minster, R. L., Mitchell, B. D

10.1101/2023.10.30.564764 — Posted: 2023-11-02

Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency

Nair, S., Ameen, M., Sundaram, L., Pampari, A., Schreiber, J., Balsubramani, A., Wang, Y. X., Burns, D., Blau, H. M., Karakikes, I., Wang, K. C., Kundaje, A.

10.1101/2023.10.04.560808 — Posted: 2023-10-21

Assigning credit where it's due: An information content score to capture the clinical value of Multiplexed Assays of Variant Effect

Ranola, J. M., Horton, C., Pesaran, T., Fayer, S., Starita, L. M., Shirts, B. H.

10.1101/2023.10.20.562794 — Posted: 2023-10-20

Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia

Nuno, K., Azizi, A., Koehnke, T., Lareau, C., Ediriwickrema, A., Corces, M. R., Satpathy, A. T., Majeti, R.

10.1101/2023.10.10.561642 — Posted: 2023-10-10

Leveraging a machine learning derived surrogate phenotype to improve power for genome-wide association studies of partially missing phenotypes in population biobanks

McCaw, Z. R., Gao, J. R., Lin, X., Gronsbell, J.

10.1101/2022.12.12.520180 — Posted: 2023-10-05

5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells

Wei, A., Zhang, H., Qiu, Q., Fabyanic, E. B., Hu, P., Wu, H.