Cas9-Enabled single cell lineage tracing tree reconstruction

Cassiopeia is a software suite for processing CRISPR/Cas9-based lineage tracing sequencing data into phylogenies. The software contains three modules for (a) preprocessing sequencing reads into “character matrices”; (b) reconstructing phylogenies from these character matrices; and (c) providing analysis tools for deriving insights from these phylogenies. The core methodology is described in our publication entitled “Inference of Single-Cell Phylogenies from Lineage Tracing Data”.

You can view and install the tool from GitHub.

Relevant publications

Theoretical Guarantees for Phylogeny Inference from Single-Cell Lineage Tracing
R. Wang*, RY. Zhang*, A. Khodaverdian*, Nir Yosef
Proc Natl Acad Sci , 2023
Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution
D. Yang*, MG. Jones*, S. Naranjo, WM. Rideout III, KH. Min, R. Ho, W. Wu, RM. Replogle, JL. Page, JJ. Quinn, F. Horns, X. Qiu, MZ. Chen, WA. Freed-Pastor, CS. McGinnis, DM. Patterson, ZJ. Gartner, ED. Chow, TG. Bivona, MM. Chan, N. Yosef†, T. Jacks†, JS. Weissman†
Cell , 2022
Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision
MG. Jones*, Y. Rosen*, N. Yosef
Cell Reports Methods , 2022
Content Sharing link
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts.
JJ. Quinn*, MG. Jones*, RA. Okimoto, S. Nanjo, MM. Chan, N. Yosef†, TG. Bivona†, JS. Weissman†
Science , 2021
bioRxiv preprint
Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees.
W. Gong*, AA Granados*, J Hu*, MG. Jones*, O. Raz*, I. Salvador-Martinez*, H. Zhang*,…, N. Yosef, J. Shendure, M. Telford, E. Shapiro, MB. Elowitz, P. Meyer
Cell Systems , 2021
Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data.
K. Ouardini, R. Lopez, MG. Jones, S. Prillo, R. Zhang, MI. Jordan, N. Yosef
ICML 2021 Workshop on Computational Biology , 2021
bioRxiv preprint
Inference of Single-Cell Phylogenies from Lineage Tracing Data.
MG. Jones*, A. Khodaverdian*, JJ. Quinn*, MM. Chan, JA. Hussmann, R. Wang, C. Xu, JS. Weissman†, N. Yosef†
Genome Biology , 2020
Molecular recording of mammalian embryogenesis.
MM. Chan, ZD. Smith, S. Grosswendt, H. Kretzmer, TM. Norman, B. Adamson, M. Jost, JJ. Quinn, D. Yang, MG. Jones, A. Khodaverdian, N. Yosef, A. Meissner, JS. Weissman
Nature , 2019