@article{Virshup_2023,
	doi = {10.1038/s41587-023-01733-8},
	year = 2023,
	month = {apr},
	publisher = {Springer Science and Business Media {LLC}},
	author = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
	title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
	journal = {Nature Biotechnology}
}
@article{Yang_2022,
    title = {Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution},
    journal = {Cell},
    volume = {185},
    number = {11},
    pages = {1905-1923.e25},
    year = {2022},
    issn = {0092-8674},
    doi = {10.1016/j.cell.2022.04.015},
    author = {Dian Yang and Matthew G. Jones and Santiago Naranjo and William M. Rideout and Kyung Hoi (Joseph) Min and Raymond Ho and Wei Wu and Joseph M. Replogle and Jennifer L. Page and Jeffrey J. Quinn and Felix Horns and Xiaojie Qiu and Michael Z. Chen and William A. Freed-Pastor and Christopher S. McGinnis and David M. Patterson and Zev J. Gartner and Eric D. Chow and Trever G. Bivona and Michelle M. Chan and Nir Yosef and Tyler Jacks and Jonathan S. Weissman},
    keywords = {lineage tracing, tumor evolution, phylogenetics, single cell, fitness, plasticity, transcriptome heterogeneity, genetically engineered mouse model, lung cancer},
}

@article{Packer_2019,
	title = {A lineage-resolved molecular atlas of {C}. elegans embryogenesis at single-cell resolution},
	volume = {365},
	doi = {10.1126/science.aax1971},
	abstract = {Caenorhabditis elegans is an animal with few cells but a wide diversity of cell types. In this study, we characterize the molecular basis for their specification by profiling the transcriptomes of 86,024 single embryonic cells. We identify 502 terminal and preterminal cell types, mapping most single-cell transcriptomes to their exact position in C. elegans’ invariant lineage. Using these annotations, we find that (i) the correlation between a cell’s lineage and its transcriptome increases from middle to late gastrulation, then falls substantially as cells in the nervous system and pharynx adopt their terminal fates; (ii) multilineage priming contributes to the differentiation of sister cells at dozens of lineage branches; and (iii) most distinct lineages that produce the same anatomical cell type converge to a homogenous transcriptomic state.},
	number = {6459},
	urldate = {2025-06-24},
	journal = {Science},
	author = {Packer, Jonathan S. and Zhu, Qin and Huynh, Chau and Sivaramakrishnan, Priya and Preston, Elicia and Dueck, Hannah and Stefanik, Derek and Tan, Kai and Trapnell, Cole and Kim, Junhyong and Waterston, Robert H. and Murray, John I.},
	month = sep,
	year = {2019},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {eaax1971},
}

@misc{Koblan_2025,
	title = {High-resolution spatial mapping of cell state and lineage dynamics in vivo with {PEtracer}},
	copyright = {© 2025, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
	doi = {10.1101/2025.06.15.659774},
	abstract = {Charting the spatiotemporal dynamics of cell fate determination in development and disease is a long-standing objective in biology. Here we present the design, development, and extensive validation of PEtracer, a prime editing-based, evolving lineage tracing technology compatible with both single-cell sequencing and multimodal imaging methodologies to jointly profile cell state and lineage in dissociated cells or while preserving cellular context in tissues with high spatial resolution. Using PEtracer coupled with MERFISH spatial transcriptomic profiling in a syngeneic mouse model of tumor metastasis, we reconstruct the growth of individually-seeded tumors in vivo and uncover distinct modules of cell-intrinsic and cell-extrinsic factors that coordinate tumor growth. More generally, PEtracer enables systematic characterization of cell state and lineage relationships in intact tissues over biologically-relevant temporal and spatial scales.},
	language = {en},
	urldate = {2025-06-24},
	publisher = {bioRxiv},
	author = {Koblan, Luke W. and Yost, Kathryn E. and Zheng, Pu and Colgan, William N. and Jones, Matthew G. and Yang, Dian and Kumar, Arhan and Sandhu, Jaspreet and Schnell, Alexandra and Sun, Dawei and Ergen, Can and Saunders, Reuben A. and Zhuang, Xiaowei and Allen, William E. and Yosef, Nir and Weissman, Jonathan S.},
	month = jun,
	year = {2025},
}

@article{Richards_2013,
	title = {A quantitative model of normal \textit{{Caenorhabditis} elegans} embryogenesis and its disruption after stress},
	volume = {374},
	issn = {0012-1606},
	doi = {10.1016/j.ydbio.2012.11.034},
	abstract = {The invariant lineage of Caenorhabditis elegans has powerful potential for quantifying developmental variability in normal and stressed embryos. Previous studies of division timing by automated lineage tracing suggested that variability in cell cycle timing is low in younger embryos, but manual lineage tracing of specific lineages suggested that variability may increase for later divisions. We developed improved automated lineage tracing methods that allowroutine lineage tracing through the last round of embryonic cell divisions and we applied these methods to trace the lineage of 18 wild-type embryos. Cell cycle lengths, division axes and cell positions are remarkably consistent among these embryos at all stages, with only slight increase in variability later in development. The resulting quantitative 4-dimensional model of embryogenesis provides a powerful reference dataset to identify defects in mutants or in embryos that have experienced environmental perturbations. We also traced the lineages of embryos imaged at higher temperatures to quantify the decay in developmental robustness under temperature stress. Developmental variability increases modestly at 25°C compared with 22°C and dramatically at 26°C, and we identify homeotic transformations in a subset of embryos grown at 26°C. The deep lineage tracing methods provide a powerful tool for analysis of normal development, gene expression and mutants and we provide a graphical user interface to allow other researchers to explore the average behavior of arbitrary cells in a reference embryo.},
	number = {1},
	urldate = {2025-06-24},
	journal = {Developmental Biology},
	author = {Richards, Julia L. and Zacharias, Amanda L. and Walton, Travis and Burdick, Joshua T. and Murray, John Isaac},
	month = feb,
	year = {2013},
	keywords = {Cell lineage, Image analysis, Microscopy, Robustness, Stress},
	pages = {12--23},
}
