Dewar, Sean and Grasegger, Georg and Kubjas, Kaie and Mohammadi, Fatemeh and Nixon, Anthony (2025) Single-cell 3D genome reconstruction in the haploid setting using rigidity theory. Journal of Mathematical Biology, 90 (4): 45. ISSN 0303-6812
Full text not available from this repository.Abstract
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this problem, and use techniques from graph rigidity theory to determine identifiability. Biologically, our models come from Hi-C data, microscopy data, and combinations thereof. Mathematically, we use unit ball and sphere packing models, as well as models consisting of distance and inequality constraints. In each setting, we describe and/or derive new results on realisability and uniqueness. We then propose a 3D reconstruction method based on semidefinite programming and apply it to synthetic and real data sets using our models.