Channel:  Impact of Genomic Variation on Function (IGVF)

120 Articles

Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells
Pulecio, J., Tayyebi, Z., Liu, D., Wong, W., Luo, R., Damodaran, J. R., Kaplan, S., Cho, H., Yan, J., Murphy, D. J., Rickert, R., Shukla, A., Zhong, A., Gonzalez, F., Yang, D., Li, W., Zhou, T., Apostolou, E., Leslie, C., Huangfu, D.
10.1101/2023.06.14.544990 — Posted: 2023-06-14
Studying stochastic systems biology of the cell with single-cell genomics data
Gorin, G., Vastola, J. J., Pachter, L.
10.1101/2023.05.17.541250 — Posted: 2023-05-29
Characterizing glucokinase variant mechanisms using a multiplexed abundance assay
Gersing, S., Schulze, T. K., Cagiada, M., Stein, A., Roth, F. P., Lindorff-Larsen, K., Hartmann-Petersen, R.
10.1101/2023.05.24.542036 — Posted: 2023-05-24
SLC12A9 is a lysosome-detoxifying ammonium - chloride co-transporter
Levin-Konigsberg, R., Mitra, K., Nigam, A., Spees, K., Hivare, P., Liu, K., Kundaje, A., Krishnan, Y., Bassik, M.
10.1101/2023.05.22.541801 — Posted: 2023-05-22
A mutation rate model at the basepair resolution identifies the mutagenic effect of Polymerase III transcription
Seplyarskiy, V., Lee, D. J., Koch, E. M., Lichtman, J. S., Luan, H. H., Sunyaev, S. R.
10.1101/2022.08.20.504670 — Posted: 2023-05-17
De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding
Alexandari, A. M., Horton, C. A., Shrikumar, A., Shah, N., Li, E., Weilert, M., Pufall, M. A., Zeitlinger, J., Fordyce, P. M., Kundaje, A.
10.1101/2023.05.11.540401 — Posted: 2023-05-11
Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data
Carilli, M. T., Gorin, G., Choi, Y., Chari, T., Pachter, L.
10.1101/2023.01.13.523995 — Posted: 2023-05-02
Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function
McCutcheon, S., Swartz, A., Brown, M., Barrera, A., McRoberts Amador, C., Siklenka, K., Humayun, L., Isaacs, J., Reddy, T. E., Nair, S., Antonia, S., Gersbach, C. A.
10.1101/2023.05.01.538906 — Posted: 2023-05-01
Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness
Lareau, C. A., Yin, Y., Gutierrez, J. C., Dhindsa, R. S., Gribling-Burrer, A.-S., Hsieh, Y.-H., Nitsch, L., Buquicchio, F. A., Abay, T., Zielinski, S., Stickels, R. R., Ulirsch, J. C., Yan, P., Wang, F., Miao, Z., Sandor, K., Daniel, B., Liu, V., Wang, Q., Hu, F., Smith, K. R., Deevi, S. V. V., Maschmeyer, P., Petrovski, S., Smyth, R. P., Greenleaf, W. J., Kundaje, A., Munschauer, M., Ludwig, L. S., Satpathy, A. T.
10.1101/2023.04.23.537997 — Posted: 2023-04-23
Assessing the multimodal tradeoff
Booeshaghi, A. S., Gao, F., Pachter, L.
10.1101/2021.12.08.471788 — Posted: 2023-04-18

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