Channel:  Impact of Genomic Variation on Function (IGVF)

120 Articles

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Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming
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: 2025-11-11
Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data
Gorin, G., Chari, T., Carilli, M., Vastola, J. J., Pachter, L.
10.1101/2022.06.11.495771 — Posted: 2025-11-06
A cell and transcriptome atlas of 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: 2025-08-04
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: 2025-07-16
Smooth muscle expression of RNA editing enzyme ADAR1 controls activation of RNA sensor MDA5 in atherosclerosis
Weldy, C. S., Li, Q., Monteiro, J. P., Peters, T. S., 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., Mokry, M., Miller, C. L., van der Laan, S. W., Li, J. B., Quertermous, T.
10.1101/2024.07.08.602569 — Posted: 2025-06-25
The epigenomic landscape of single vascular cells reflects developmental origin and identifies disease risk loci
Weldy, C. S., Kundu, S., Monteiro, J. P., Gu, W., Pedroza, A. J., Dalal, A. R., Worssam, M. D., Li, D. Y., Palmisano, B. T., Zhao, Q., Sharma, D., Nguyen, T., Kundu, R. K., Fischbein, M. P., Engreitz, J., Kundaje, A. B., Cheng, P. P., Quertermous, T.
10.1101/2022.05.18.492517 — Posted: 2025-05-06
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
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

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