Channel:  Impact of Genomic Variation on Function (IGVF)

232 Articles

Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions
Kotliar, D., Curtis, M., Agnew, R., Weinand, K., Nathan, A., Baglaenko, Y., Zhao, Y., Sabeti, P. C., Rao, D. A., Raychaudhuri, S.
10.1101/2024.05.03.592310 — Posted: 2024-05-05
Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions
Omelchenko, A. A., Siwek, J. C., Chhibbar, P., Arshad, S., Nazarali, I., Nazarali, K., Rosengart, A., Rahimikollu, J., Tilstra, J., Shlomchik, M. J., Koes, D. R., Joglekar, A. V., Das, J.
10.1101/2024.05.01.592062 — Posted: 2024-05-04
regionalpcs: improved discovery of DNA methylation associations with complex traits
Eulalio, T., Sun, M. W., Gevaert, O., Greicius, M. D., Montine, T. J., Nachun, D., Montgomery, S. B.
10.1101/2024.05.01.590171 — Posted: 2024-05-01
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
Chardon, F. M., McDiarmid, T. A., Page, N. F., Daza, R., Martin, B. K., Domcke, S., Regalado, S. G., Lalanne, J.-B., Calderon, D., Li, X., Starita, L. M., Sanders, S. J., Ahituv, N., Shendure, J.
10.1101/2023.03.28.534017 — Posted: 2024-04-30
Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity
Kosicki, M., Cintron, D. L., Page, N. F., Georgakopoulos-Soares, I., Akiyama, J. A., Plajzer-Frick, I., Novak, C. S., Kato, M., Hunter, R. D., von Maydell, K., Barton, S., Godfrey, P., Beckman, E., Sanders, S. J., Pennacchio, L. A., Ahituv, N.
10.1101/2024.04.22.590634 — Posted: 2024-04-23
Massively parallel jumping assay decodes Alu retrotransposition activity
Ahituv, N., Matharu, N., Zhao, J., Sohota, A., Deng, L., Hung, Y., Li, Z., Sims, J., Rattanasopha, S., Meyer, J., Carbone, L., Kircher, M.
10.1101/2024.04.16.589814 — Posted: 2024-04-19
The impact of package selection and versioning on single-cell RNA-seq analysis
Rich, J. M., Moses, L., Einarsson, P. H., Jackson, K., Luebbert, L., Booeshaghi, A. S., Antonsson, S., Sullivan, D. K., Bray, N., Melsted, P., Pachter, L.
10.1101/2024.04.04.588111 — Posted: 2024-04-11
Transcript-specific enrichment enables profiling rare cell states via scRNA-seq
Abay, T., Stickels, R. R., Takizawa, M. T., Nalbant, B. N., Hsieh, Y.-H., Hwang, S., Snopkowski, C., Yu, K. K. H., Abou-Mrad, Z., Tabar, V., Ludwig, L. S., Chaligne, R., Satpathy, A. T., Lareau, C. A.
10.1101/2024.03.27.587039 — Posted: 2024-03-27
Assessing NGS-based computational methods for predicting transcriptional regulators with query gene sets
Lu, Z., Xiao, X., Zheng, Q., Wang, X., Xu, L.
10.1101/2024.02.01.578316 — Posted: 2024-03-22
Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs
Raychaudhuri, S., Valencia, C., Nathan, A., Kang, J. B., Rumker, L., Lee, H.
10.1101/2024.02.20.581100 — Posted: 2024-02-22

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