Discussion of “Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-seq Data”

References

• Cusanovich, D. A., Hill, A. J., Aghamirzaie, D., Daza, R. M., Pliner, H. A., Berletch, J. B., Filippova, G. N., Huang, X., Christiansen, L., DeWitt, W. S., Lee, C., Regalado, S. G., Read, D. F., Steemers, F. J., Disteche, C. M., Trapnell, C., and Shendure, J. (2018), “A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility,” Cell, 174, 1309–1324.e18.
   PubMed Web of Science ®Google Scholar
• Lawrence, H., and Phipps, A. (1985), “Comparing Partitions,” Journal of Classification, 2, 193–218.
   Web of Science ®Google Scholar
• Lin, K. Z., Lei, J., and Roeder, K. (2021), “Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-seq Data,” Journal of the American Statistical Association 116, 457–470.
   PubMedGoogle Scholar
• McInnes, L., Healy, J., and Melville, J. (2018), “UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction,” arXiv no. 1802.03426.
   Google Scholar
• Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., Clevers, H., Deplancke, B., Dunham, I., Eberwine, J., Eils, R., Enard, W., Farmer, A., Fugger, L., Göttgens, B., Hacohen, N., Haniffa, M., Hemberg, M., Kim, S., Klenerman, P., Kriegstein, A., Lein, E., Linnarsson, S., Lundberg, E., Lundeberg, J., Majumder, P., Marioni, J. C., Merad, M., Mhlanga, M., Nawijn, M., Netea, M., Nolan, G., Pe’er, D., Phillipakis, A., Ponting, C. P., Quake, S., Reik, W., Rozenblatt-Rosen, O., Sanes, J., Satija, R., Schumacher, T. N., Shalek, A., Shapiro, E., Sharma, P., Shin, J. W., Stegle, O., Stratton, M., Stubbington, M. J. T., Theis, F. J., Uhlen, M., van Oudenaarden, A., Wagner, A., Watt, F., Weissman, J., Wold, B., Xavier, R., Yosef, N., and Human Cell Atlas Meeting Participants (2017), “The Human Cell Atlas,” eLife, 6, e27041. DOI: https://doi.org/10.7554/eLife.27041.
   PubMed Web of Science ®Google Scholar
• Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., 3rd, Hao, Y., Stoeckius, M., Smibert, P., and Satija, R. (2019), “Comprehensive Integration of Single-Cell Data,” Cell, 177, 1888–1902.e21.
   PubMed Web of Science ®Google Scholar
• Su, Y., Chen, D., Yuan, D., Lausted, C., Choi, J., Dai, C. L., Voillet, V., Duvvuri, V. R., Scherler, K., Troisch, P., Baloni, P., Qin, G., Smith, B., Kornilov, S. A., Rostomily, C., Xu, A., Li, J., Dong, S., Rothchild, A., Zhou, J., Murray, K., Edmark, R., Hong, S., Heath, J. E., Earls, J., Zhang, R., Xie, J., Li, S., Roper, R., Jones, L., Zhou, Y., Rowen, L., Liu, R., Mackay, S., O’Mahony, D. S., Dale, C. R., Wallick, J. A., Algren, H. A., Zager, M. A., Unit, I.-S. C. B., Wei, W., Price, N. D., Huang, S., Subramanian, N., Wang, K., Magis, A. T., Hadlock, J. J., Hood, L., Aderem, A., Bluestone, J. A., Lanier, L. L., Greenberg, P. D., Gottardo, R., Davis, M. M., Goldman, J. D., and Heath, J. R. (2020), “Multi-Omics Resolves a Sharp Disease-State Shift Between Mild and Moderate Covid-19,” Cell, 183, 1479–1495.e20.
   PubMed Web of Science ®Google Scholar
• van der Maaten, L., and Hinton, G. (2008), “Visualizing Data Using t-SNE,” Journal of Machine Learning Research, 9, 2579–2605.
   Web of Science ®Google Scholar
• Zheng, G. X. Y., Terry, J. M., Belgrader, P., Ryvkin, P., Bent, Z. W., Wilson, R., Ziraldo, S. B., Wheeler, T. D., McDermott, G. P., Zhu, J., Gregory, M. T., Shuga, J., Montesclaros, L., Underwood, J. G., Masquelier, D. A., Nishimura, S. Y., Schnall-Levin, M., Wyatt, P. W., Hindson, C. M., Bharadwaj, R., Wong, A., Ness, K. D., Beppu, L. W., Deeg, H. J., McFarland, C., Loeb, K. R., Valente, W. J., Ericson, N. G., Stevens, E. A., Radich, J. P., Mikkelsen, T. S., Hindson, B. J., and Bielas, J. H. (2017), “Massively Parallel Digital Transcriptional Profiling of Single Cells,” Nature Communications, 8, 14049. DOI: https://doi.org/10.1038/ncomms14049.
   PubMed Web of Science ®Google Scholar