Channel:  Impact of Genomic Variation on Function (IGVF)

232 Articles

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Pampari, A., Shcherbina, A., Kvon, E. Z., Kosicki, M., Nair, S., Kundu, S., Kathiria, A. S., Risca, V. I., Kuningas, K., Alasoo, K., Greenleaf, W., Pennacchio, L., Kundaje, A.
10.1101/2024.12.25.630221 — Posted: 2026-09-23
Multi-scale gene regulatory networks for resolving transcription factor and autoimmune variant impacts on human B cell fate dynamics
Pease, N. A., Fan, J., Keshari, S., Stratton, J., Gierlack, S. B., Sachan, A., Heidari Rarani, Z., Swaminathan, T., McGinnis, C. S., Zhang, W., Bisht, D., Chakraborty, T., Gerges, P., Manakkat Vijay, G., Lau, L., Macedo, C., Metes, D., Won, H., Satpathy, A. T., Jain, A. K., Sahni, N., Das, J., Singh, H.
10.1101/2025.04.23.649973 — Posted: 2026-09-22
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

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