Channel:  Impact of Genomic Variation on Function (IGVF)

120 Articles

scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution
Hingerl, J. C., Martens, L. D., Karollus, A., Manz, T., Buenrostro, J. D., Theis, F. J., Gagneur, J.
10.1101/2024.09.19.613754 — Posted: 2025-03-13
Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of RNA sensor MDA5 in atherosclerosis
Weldy, C. S., Li, Q., Monteiro, J. P., Guo, H., Galls, D., Gu, W., Cheng, P. P., Ramste, M., Li, D. Y., Palmisano, B. T., Sharma, D., Worssam, M. D., Zhao, Q., Bhate, A., Kundu, R., Nguyen, T., Li, J. B., Quertermous, T.
10.1101/2024.07.08.602569 — Posted: 2024-10-31
BIT: Bayesian Identification of Transcriptional Regulators from Epigenomics-Based Query Region Sets
Lu, Z., Xu, L., Wang, X.
10.1101/2024.06.02.597061 — Posted: 2024-10-08
Optimizing and benchmarking polygenic risk scores with GWAS summary statistics
Zhao, Z., Gruenloh, T., Yan, M., Wu, Y., Sun, Z., Miao, J., Wu, Y., Song, J., Lu, Q.
10.1101/2022.10.26.513833 — Posted: 2024-09-25
A cell and transcriptome atlas of the human arterial vasculature
Zhao, Q., Pedroza, A., Sharma, D., Gu, W., Dalal, A., Weldy, C., Jackson, W., Li, D. Y., Ryan, Y., Nguyen, T., Shad, R., Palmisano, B. T., Monteiro, J. P., Worssam, M., Berezwitz, A., Iyer, M., Shi, H., Kundu, R., Limbu, L., Kim, J. B., Kundaje, A., Fischbein, M., Wirka, R., Quertermous, T., Cheng, P.
10.1101/2024.09.10.612293 — Posted: 2024-09-10
CRISPR-CLEAR: Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing
Becerra, B., Wittibschlager, S., Patel, Z. M., Kutschat, A., Delano, J., Karjalainen, A., Wu, T., Starrs, M., Jankowiak, M., Bauer, D., Seruggia, D., Pinello, L.
10.1101/2024.09.09.612085 — Posted: 2024-09-09
Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER
Liu, S., Hamilton, M. C., Cowart, T. N., Barrera, A., Bounds, L. R., Nelson, A. C., Doty, R. W., Allen, A. S., Crawford, G. E., Majoros, W. H., Gersbach, C. A.
10.1101/2024.09.04.611293 — Posted: 2024-09-04
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Rosen, B. P., Li, Q. V., Cho, H. S., Liu, D., Yang, D., Graff, S., Yan, J., Luo, R., Verma, N., Damodaran, J. R., Kale, H. T., Kaplan, S. J., Beer, M. A., Sidoli, S., Huangfu, D.
10.1101/2023.05.03.539283 — Posted: 2024-09-01
BayeSMART: Bayesian Clustering of Multi-sample Spatially Resolved Transcriptomics Data
Guo, Y., Zhu, B., Tang, C., Rong, R., Ma, Y., Xiao, G., Xu, L., Li, Q.
10.1101/2024.08.30.610571 — Posted: 2024-09-01
Cohesin-mediated 3D contacts tune enhancer-promoter regulation
Guckelberger, P., Doughty, B. R., Munson, G., Rao, S. S. P., Tan, Y., Cai, X. S., Fulco, C. P., Nasser, J., Mualim, K. S., Bergman, D. T., Ray, J., Jagoda, E., Munger, C. J., Gschwind, A. R., Sheth, M. U., Tan, A. S., Pulido, S. G., Mitra, N., Weisz, D., Shamim, M. S., Durand, N. C., Mahajan, R., Khan, R., Steinmetz, L. M., Kanemaki, M. T., Lander, E. S., Meissner, A., Aiden, E. L., Engreitz, J. M.
10.1101/2024.07.12.603288 — Posted: 2024-07-22

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