References

References#

[FCS+21]

Antonio De Falco, Francesca Caruso, Xiao-Dong Su, Antonio Iavarone, and Michele Ceccarelli. A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data. bioRxiv, November 2021. URL: https://doi.org/10.1101/2021.11.20.469390, doi:10.1101/2021.11.20.469390.

[MMR+20]

Ashley Maynard, Caroline E. McCoach, Julia K. Rotow, Lincoln Harris, Franziska Haderk, D. Lucas Kerr, Elizabeth A. Yu, Erin L. Schenk, Weilun Tan, Alexander Zee, Michelle Tan, Philippe Gui, Tasha Lea, Wei Wu, Anatoly Urisman, Kirk Jones, Rene Sit, Pallav K. Kolli, Eric Seeley, Yaron Gesthalter, Daniel D. Le, Kevin A. Yamauchi, David M. Naeger, Sourav Bandyopadhyay, Khyati Shah, Lauren Cech, Nicholas J. Thomas, Anshal Gupta, Mayra Gonzalez, Hien Do, Lisa Tan, Bianca Bacaltos, Rafael Gomez-Sjoberg, Matthew Gubens, Thierry Jahan, Johannes R. Kratz, David Jablons, Norma Neff, Robert C. Doebele, Jonathan Weissman, Collin M. Blakely, Spyros Darmanis, and Trever G. Bivona. Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing. Cell, 182(5):1232–1251.e22, September 2020. URL: https://doi.org/10.1016/j.cell.2020.07.017, doi:10.1016/j.cell.2020.07.017.

[RSY+21]

Gao R., Bai S., Henderson YC, Lin Y., Schalck A., Yan Y., Kumar T., Hu M., Sei E., Davis A., Wang F., Shaitelman SF, Wang JR, Chen K., Moulder S., Lai SY, and Navin NE. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nature Biotechnology, 39:599–608, January 2021. URL: https://doi.org/10.1038/s41587-020-00795-2, doi:10.1038/s41587-020-00795-2.

[TVH+16]

I. Tirosh, A. S. Venteicher, C. Hebert, L. E. Escalante, A. P. Patel, K. Yizhak, J. M. Fisher, C. Rodman, C. Mount, M. G. Filbin, C. Neftel, N. Desai, J. Nyman, B. Izar, C. C. Luo, J. M. Francis, A. A. Patel, M. L. Onozato, N. Riggi, K. J. Livak, D. Gennert, R. Satija, B. V. Nahed, W. T. Curry, R. L. Martuza, R. Mylvaganam, A. J. Iafrate, M. P. Frosch, T. R. Golub, M. N. Rivera, G. Getz, O. Rozenblatt-Rosen, D. P. Cahill, M. Monje, B. E. Bernstein, D. N. Louis, A. Regev, and M. L. Suvà. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature, 539(7628):309–313, 11 2016.

[VBH+23]

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis and. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, apr 2023. URL: https://doi.org/10.1038%2Fs41587-023-01733-8, doi:10.1038/s41587-023-01733-8.

[WFH+21]

Fengying Wu, Jue Fan, Yayi He, Anwen Xiong, Jia Yu, Yixin Li, Yan Zhang, Wencheng Zhao, Fei Zhou, Wei Li, Jie Zhang, Xiaosheng Zhang, Meng Qiao, Guanghui Gao, Shanhao Chen, Xiaoxia Chen, Xuefei Li, Likun Hou, Chunyan Wu, Chunxia Su, Shengxiang Ren, Margarete Odenthal, Reinhard Buettner, Nan Fang, and Caicun Zhou. Single-cell profiling of tumor heterogeneity and the microenvironment in advanced non-small cell lung cancer. Nature Communications, May 2021. URL: https://doi.org/10.1038/s41467-021-22801-0, doi:10.1038/s41467-021-22801-0.