Channel:  Impact of Genomic Variation on Function (IGVF)

232 Articles

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Clonal memory of colitis accumulates and promotes tumor growth
Nagaraja, S., Ojeda-Miron, L., Zhang, R., Oreskovic, E., Hu, Y., Zeve, D., Sharma, K., Hyman, R. R., Zhang, Q., Castillo, A., Breault, D. T., Yilmaz, O. H., Buenrostro, J. D.
10.1101/2025.02.13.638099 — Posted: 2025-02-17
Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq
Zhang, H., Li, X., Song, D., Yukselen, O., Nanda, S., Kucukural, A., Li, J. J., Garber, M., Walhout, A. J. M.
10.1101/2025.02.02.636107 — Posted: 2025-02-03
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
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
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
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

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