References#
R.C. Griffiths and Simon Tavaré. The age of a mutation in a general coalescent tree. Communications in Statistics. Stochastic Models, 14(1-2):273–295, January 1998. Publisher: Taylor & Francis _eprint: https://doi.org/10.1080/15326349808807471. URL: https://doi.org/10.1080/15326349808807471 (visited on 2025-11-13), doi:10.1080/15326349808807471.
Luke W. Koblan, Kathryn E. Yost, Pu Zheng, William N. Colgan, Matthew G. Jones, Dian Yang, Arhan Kumar, Jaspreet Sandhu, Alexandra Schnell, Dawei Sun, Can Ergen, Reuben A. Saunders, Xiaowei Zhuang, William E. Allen, Nir Yosef, and Jonathan S. Weissman. High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer. June 2025. doi:10.1101/2025.06.15.659774.
Richard A Neher, Colin A Russell, and Boris I Shraiman. Predicting evolution from the shape of genealogical trees. eLife, 3:e03568, nov 2014. URL: https://doi.org/10.7554/eLife.03568, doi:10.7554/eLife.03568.
Jonathan S. Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, Robert H. Waterston, and John I. Murray. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science, 365(6459):eaax1971, September 2019. Publisher: American Association for the Advancement of Science. doi:10.1126/science.aax1971.
Julia L. Richards, Amanda L. Zacharias, Travis Walton, Joshua T. Burdick, and John Isaac Murray. A quantitative model of normal \textit Caenorhabditis elegans embryogenesis and its disruption after stress. Developmental Biology, 374(1):12–23, February 2013. doi:10.1016/j.ydbio.2012.11.034.
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. doi:10.1038/s41587-023-01733-8.
Dian Yang, Matthew G. Jones, Santiago Naranjo, William M. Rideout, Kyung Hoi (Joseph) Min, Raymond Ho, Wei Wu, Joseph M. Replogle, Jennifer L. Page, Jeffrey J. Quinn, Felix Horns, Xiaojie Qiu, Michael Z. Chen, William A. Freed-Pastor, Christopher S. McGinnis, David M. Patterson, Zev J. Gartner, Eric D. Chow, Trever G. Bivona, Michelle M. Chan, Nir Yosef, Tyler Jacks, and Jonathan S. Weissman. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell, 185(11):1905–1923.e25, 2022. doi:10.1016/j.cell.2022.04.015.