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Updated: Apr 11, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

LAML-Pro: Joint Maximum Likelihood Inference of Cell Genotypes and Cell Lineage Trees.

Gillian Chu¹, Henri Schmidt¹, Benjamin J Raphael¹

¹Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.

Biorxiv : the Preprint Server for Biology

|April 10, 2026

Summary

This summary is machine-generated.

This study introduces LAML-Pro, a new computational method for cell lineage tracing. LAML-Pro accurately reconstructs cell family trees by correcting errors in genetic data, improving upon existing lineage tracing techniques.

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Area of Science:

Computational Biology
Genomics
Cell Biology

Background:

Dynamic lineage tracing uses genome editing to create heritable mutations for reconstructing cell lineages.
Current methods separate genotype identification from lineage tree inference, leading to inaccuracies due to genotyping errors (≈25-50% in imaging).

Purpose of the Study:

To develop a computational method that jointly infers cell genotypes and lineage trees, improving accuracy in cell lineage reconstruction.
To address the challenge of genotype errors in dynamic lineage tracing data.

Main Methods:

Introduced LAML-Pro (Lineage Analysis via Maximum Likelihood with PRobabilistic Observations), a novel algorithm based on the Probabilistic Mixed-type Missing Observation (PMMO) model.
The PMMO model accounts for both genome editing and genotype observation processes.
Leveraged model sparsity for efficient lineage tree construction from thousands of cells.

Main Results:

LAML-Pro corrects genotype errors and infers more accurate cell lineage trees compared to existing methods.
Reduced genotype errors by 5-fold in imaging-based lineage tracing data.
Produced more spatially coherent lineage trees.

Conclusions:

LAML-Pro offers a significant advancement in cell lineage tracing by integrating genotype inference and tree reconstruction.
The method improves the accuracy and reliability of lineage trees derived from dynamic lineage tracing experiments.
LAML-Pro is available for broader research use.