Channel:  Impact of Genomic Variation on Function (IGVF)

bioRxiv posts many COVID19-related papers. A reminder: they have not been formally peer-reviewed and should not guide health-related behavior or be reported in the press as conclusive.

107 Articles

Reconstructing Spatial Transcriptomics at the Single-cell Resolution with BayesDeep
Jiang, X., Dong, L., Wang, S., Wen, Z., Chen, M., Xu, L., Xiao, G., Li, Q.
10.1101/2023.12.07.570715 — Posted: 2023-12-08
Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries
Weile, J., Ferra, G., Boyle, G., Pendyala, S., Amorosi, C., Yeh, C.-L., Cote, A. G., Kishore, N., Tabet, D., van Loggerenberg, W., Rayhan, A., Fowler, D. M., Dunham, M. J., Roth, F. P.
10.1101/2023.02.22.529427 — Posted: 2023-12-07
Decoding Heterogenous Single-cell Perturbation Responses
Song, B., Liu, D., Dai, W., McMyn, N., Wang, Q., Yang, D., Krejci, A., Vasilyev, A., Untermoser, N., Loregger, A., Song, D., Williams, B., Rosen, B., Cheng, X., Chao, L., Kale, H. T., Zhang, H., Diao, Y., Bürckstümmer, T., Siliciano, J. M., Li, J. J., Siliciano, R., Huangfu, D., Li, W.
10.1101/2023.10.30.564796 — Posted: 2023-11-29
MPRAbase: A Massively Parallel Reporter Assay Database
Zhao, J., Baltoumas, F. A., Konnaris, M. A., Mouratidis, I., Liu, Z., Sims, J., Agarwal, V., Pavlopoulos, G. A., Georgakopoulos-Soares, I., Ahituv, N.
10.1101/2023.11.19.567742 — Posted: 2023-11-22
Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes
Wang, Y., Armendariz, D. A., Wang, L., Zhao, H., Xie, S., Hon, G. C.
10.1101/2023.11.20.567880 — Posted: 2023-11-20
Identifying genetic variants that influence the abundance of cell states in single-cell data
Rumker, L., Sakaue, S., Reshef, Y., Kang, J. B., Yazar, S., Alquicira-Hernandez, J., Valencia, C., Lagattuta, K. A., Mah-Som, A., Nathan, A., Powell, J. E., Loh, P.-R., Raychaudhuri, S.
10.1101/2023.11.13.566919 — Posted: 2023-11-15
An encyclopedia of enhancer-gene regulatory interactions in the human genome
Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R. N., Xi, W., Tan, A. S., Jones, H., Ma, X. R., Yao, D., Nasser, J., Avsec, Z., James, B. T., Shamim, M. S., Durand, N. C., Rao, S. S. P., Mahajan, R., Doughty, B. R., Andreeva, K., Ulirsch, J. C., Fan, K., Perez, E. M., Nguyen, T. C., Kelley, D. R., Finucane, H. K., Moore, J. E., Weng, Z., Kellis, M., Bassik, M. C., Price, A. L., Beer, M. A., Guigo, R., Stamatoyannopoulos, J. A., Aiden, E. L., Greenleaf, W. J., Leslie, C. S., Steinmetz, L. M., Kundaje, A., Engreitz, J. M.
10.1101/2023.11.09.563812 — Posted: 2023-11-13
A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Li, X., Chen, H., Selvaraj, M. S., Van Buren, E., Zhou, H., Wang, Y., Sun, R., McCaw, Z. R., Yu, Z., Arnett, D. K., Bis, J. C., Blangero, J., Boerwinkle, E., Bowden, D. W., Brody, J. A., Cade, B. E., Carson, A. P., Carlson, J. C., Chami, N., Chen, Y.-D. I., Curran, J. E., de Vries, P. S., Fornage, M., Franceschini, N., Freedman, B. I., Gu, C., Heard-Costa, N. L., He, J., Hou, L., Hung, Y.-J., Irvin, M. R., Kaplan, R. C., Kardia, S. L. R., Kelly, T., Konigsberg, I., Kooperberg, C., Kral, B. G., Li, C., Loos, R. J. F., Mahaney, M. C., Martin, L. W., Mathias, R. A., Minster, R. L., Mitchell, B. D
10.1101/2023.10.30.564764 — Posted: 2023-11-02
Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency
Nair, S., Ameen, M., Sundaram, L., Pampari, A., Schreiber, J., Balsubramani, A., Wang, Y. X., Burns, D., Blau, H. M., Karakikes, I., Wang, K. C., Kundaje, A.
10.1101/2023.10.04.560808 — Posted: 2023-10-21
Assigning credit where it's due: An information content score to capture the clinical value of Multiplexed Assays of Variant Effect
Ranola, J. M., Horton, C., Pesaran, T., Fayer, S., Starita, L. M., Shirts, B. H.
10.1101/2023.10.20.562794 — Posted: 2023-10-20

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