Channel:  Impact of Genomic Variation on Function (IGVF)

232 Articles

A systematic survey of distal element-gene regulatory interactions with Direct-Capture Targeted Perturb-seq
Ray, J., Jagoda, E., Sheth, M. U., Galante, J., Amgalan, D., Mattei, E., Gschwind, A. R., Munger, C. J., Huang, J., Munson, G., Murphy, M., Barry, T., Singh, V., Baskaran, A., Kang, H., Issner, R., Epstein, C. B., Najm, F. J., Katsevich, E., Gaskell, E., Steinmetz, L. M., Engreitz, J.
10.1101/2025.09.16.676677 — Posted: 2026-08-06
Determining gene specificity from multivariate single-cell RNA sequencing data
Swarna, N. P., Booeshaghi, A. S., Rebboah, E., Gordon, M. G., Kathail, P., Li, T., Alvarez, M., Ye, C. J., Wold, B. J., Mortazavi, A., Pachter, L.
10.1101/2025.11.21.689845 — Posted: 2026-07-30
SEEK-VEC: Augmenting topic modeling with spectral ensemble learning
Danning, R., Ke, Z. T., Ma, R., Lin, X.
10.64898/2025.12.12.693799 — Posted: 2026-07-21
ARSENAL: Learning Transferable Regulatory DNA Representations with Targeted Short-Context Language Models
Patel, A., Kundaje, A.
10.64898/2026.02.05.703637 — Posted: 2026-07-12
Regulatory network hubs guide dynamic human lineage specification
Takeuchi, C., Sivakumar, S., Sundarrajan, A., Wang, Y., Goetsch, S. C., Zhao, H., Wang, L., Nzima, M., Deng, M., Kulkarni, K. N., Xu, L., Wu, J., Posner, B. A., Chahrour, M. H., Kraus, W. L., Munshi, N. V., Hon, G. C.
10.64898/2025.12.15.694070 — Posted: 2026-06-15
Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation
Weber, R., Carilli, M., Rebboah, E., Filimban, G., Liang, H. Y., Trout, D., Duffield, M., Mahdipoor, P., Taghizadeh, E., Fattahi, N., Mojgani, N., Mojaverzargar, R., Swarna, N. P., Kawauchi, S., Williams, B. A., MacGregor, G., Wold, B., Pachter, L., Hallgrimsdottir, I. B., Mortazavi, A.
10.64898/2026.04.02.716195 — Posted: 2026-06-09
Comparing bulk and single-cell methodologies and models to profile gene expression, chromatin accessibility and regulatory links in endothelial cells treated with TNFα
Zevounou, J., Lo, K. S., McGinnis, C. S., Satpathy, A. T., Lettre, G.
10.64898/2026.03.13.711357 — Posted: 2026-05-27
NERINE reveals rare variant associations in gene networks across phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease
Nazeen, S., Wang, X., Morrow, A. R., Strom, R., Ethier, E., Ritter, D., Henderson, A. B. H., Afroz, J., Cassa, C. S., Stitziel, N. O., Gupta, R. M., Luk, K. C., Studer, L., Khurana, V., Sunyaev, S. R.
10.1101/2025.01.07.631688 — Posted: 2026-05-04
Decoding Chromatin Dynamics in Cardiac Organoids Reveals Genetic Drivers of Human Heart Development and Disease
Metzl-Raz, E., Zhao, R., Deshpande, S., Powell, J., Porter, E. G., Zouaghi, Y., Liu, B. B., Kim, S. H., Abdi, I., Evergreen, I., Agarwal, M., Sheth, M. U., Rico, J., Miyamoto, M., Sanchez, J. M., Engreitz, J. M., Kundaje, A., Greenleaf, W. J., Gifford, C. A.
10.1101/2025.10.15.680997 — Posted: 2026-04-23
The landscape of regional missense mutational intolerance quantified from 730,947 exomes
Wang, L., Chao, K. R., Panchal, R., Liao, C., Abderrazzaq, H., Ye, R., Schultz, P., Compitello, J., Grant, R. H., Kosmicki, J. A., Weisburd, B., Phu, W., Wilson, M. W., Laricchia, K. M., Goodrich, J. K., Goldstein, D., Goldstein, J. I., Vittal, C., Poterba, T., Baxter, S., Watts, N. A., Solomonson, M., gnomAD consortium, , Tiao, G., Rehm, H. L., Neale, B. M., Talkowski, M. E., MacArthur, D. G., O'Donnell-Luria, A., Karczewski, K. J., Radivojac, P., Daly, M. J., Samocha, K. E.
10.1101/2024.04.11.588920 — Posted: 2026-04-23

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