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Biorxiv : the Preprint Server for Biology|November 26, 2025
SCOUT: Ornstein-Uhlenbeck modelling of gene expression evolution on single-cell lineage treesHannah Stuart, Aaron McKennaBiorxiv : the Preprint Server for Biology|March 17, 2025
Hierarchical Lineage Tracing Reveals Diverse Pathways of AML Treatment ResistanceRachel Saxe, Hannah Stuart, Abigail Marshall, et al.Nature Communications|June 30, 2026
Hierarchical lineage tracing reveals diverse pathways of cytarabine resistanceRachel Saxe, Hannah Stuart, Abigail C Marshall, et al.Cancer Research|August 18, 2025
Generations in Flux: Tracking the Birth of Cellular Heterogeneity in CancerAaron McKennaBMC Biology|July 7, 2018
FlashFry: a fast and flexible tool for large-scale CRISPR target designAaron McKenna, Jay ShendureBiorxiv : the Preprint Server for Biology|April 8, 2024
Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infectionLeena Abdullah, Francesco E Emiliani, Chinmay M Vaidya, et al.Development (Cambridge, England)|June 29, 2019
Recording development with single cell dynamic lineage tracingAaron McKenna, James A GagnonACS Synthetic Biology|June 13, 2022
Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore SequencingFrancesco E Emiliani, Ian Hsu, Aaron McKennaImmunity|February 28, 2025
The endogenous antigen-specific CD8<sup>+</sup> T cell repertoire is composed of unbiased and biased clonotypes with differential fate commitmentsLeena Abdullah, Francesco E Emiliani, Chinmay M Vaidya, et al.Biorxiv : the Preprint Server for Biology|April 27, 2026
PALINCODE: Recording cell lineage with ternary palindromic CRISPR bitsMaryam Fathi, Aidan Cook, Bagheri Meisam, et al.Pageof 8