Channel:  Impact of Genomic Variation on Function (IGVF)

232 Articles

Multiplex, multimodal mapping of variant effects in secreted proteins
Popp, N. A., Powell, R. L., Wheelock, M. K., Holmes, K. J., Zapp, B. D., Sheldon, K. M., Fletcher, S. N., Wu, X., Fayer, S., Rubin, A. F., Lannert, K. W., Chang, A. T., Sheehan, J. P., Johnsen, J. M., Fowler, D. M.
10.1101/2024.04.01.587474 — Posted: 2025-01-29
Long-read sequencing transcriptome quantification with lr-kallisto
Loving, R. K., Sullivan, D. K., Booeshaghi, A. S., Reese, F., Rebboah, E., Sakr, J., Rezaie, N., Liang, H. Y., Filimban, G., Kawauchi, S., Oakes, C., Trout, D., Williams, B. A., MacGregor, G., Wold, B., Mortazavi, A., Pachter, L.
10.1101/2024.07.19.604364 — Posted: 2025-01-29
Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq
Ota, M., Spence, J. P., Zeng, T., Dann, E., Marson, A., Pritchard, J. K.
10.1101/2025.01.22.634424 — Posted: 2025-01-24
Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells
Sivakumar, S., Wang, Y., Goetsch, S. C., Pandit, V., Wang, L., Zhao, H., Sundarrajan, A., Armendariz, D. A., Takeuchi, C., Nzima, M., Chen, W.-C., Dederich, A. E., El Hayek, L., Gao, T., Ghazawi, R., Gogate, A., Kaur, K., Kim, H. B., McCoy, M., Niederstrasser, H., Oura, S., Pinzon-Arteaga, C. A., Sanghvi, M., Schmitz, D. A., Yu, L., Zhang, Y., Zhou, Q., Kraus, W. L., Xu, L., Wu, J., Posner, B. A., Chahrour, M. H., Hon, G. C., Munshi, N. V.
10.1101/2025.01.21.633969 — Posted: 2025-01-23
Wnt signaling drives stromal inflammation in inflammatory arthritis
Mueller, A. A., Zou, A. E., Marsh, L.-J., Kemble, S., Nayar, S., Watts, G. F. M., Murphy, C. L., Taylor, E., Major, T., Gardner, D., Buckley, C. D., Wei, K., Raychaudhuri, S., Korsunsky, I., Filer, A., Croft, A. P., Brenner, M. B.
10.1101/2025.01.06.631510 — Posted: 2025-01-08
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: 2025-01-08
Specificity, length, and luck: How genes are prioritized by rare and common variant association studies
Spence, J. P., Mostafavi, H., Ota, M., Milind, N., Gjorgjieva, T., Smith, C. J., Simons, Y. B., Sella, G., Pritchard, J. K.
10.1101/2024.12.12.628073 — Posted: 2024-12-16
Directionality of Transcriptional Regulatory Elements
Chen, Y., Shah, S. R., Leung, A., Paramo, M. I., Cochran, K., Kundaje, A., Clark, A. G., Lis, J. T., Yu, H.
10.1101/2024.12.01.621925 — Posted: 2024-12-02
Mapping enhancer-gene regulatory interactions from single-cell data
Sheth, M. U., Qiu, W.-L., Ma, X. R., Gschwind, A. R., Jagoda, E., Tan, A. S., Einarsson, H., Gorissen, B. L., Dubocanin, D., McGinnis, C. S., Amgalan, D., Satpathy, A. T., Jones, T. R., Steinmetz, L. M., Kundaje, A., Ustun, B., Engreitz, J. M., Andersson, R.
10.1101/2024.11.23.624931 — Posted: 2024-11-24
Dissecting the cis-regulatory syntax of transcription initiation with deep learning
Cochran, K., Yin, M., Mantripragada, A., Schreiber, J., Marinov, G. K., Shah, S. R., Yu, H., Lis, J. T., Kundaje, A.
10.1101/2024.05.28.596138 — Posted: 2024-11-21

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