A maximum-likelihood approach for building cell-type trees by lifting

Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. Bernard

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Background: In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant role in cell differentiation. We previously introduce cell-type trees to represent the differentiation of cells into more specialized types, a representation that partakes of both ontogeny and phylogeny. Results: We propose a maximum-likelihood (ML) approach to build cell-type trees and show that this ML approach outperforms our earlier distance-based and parsimony-based approaches. We then study the reconstruction of ancestral cell types; since both ancestral and derived cell types can coexist in adult organisms, we propose a lifting algorithm to infer internal nodes. We present results on our lifting algorithm obtained both through simulations and on real datasets. Conclusions: We show that our ML-based approach outperforms previously proposed techniques such as distance-based and parsimony-based methods. We show our lifting-based approach works well on both simulated and real data.

Original languageEnglish (US)
Article number14
JournalBMC genomics
Volume17
Issue number1
DOIs
StatePublished - Jan 11 2016

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Cell Differentiation
Histone Code
Phylogeny
Epigenomics
Genome
Datasets

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Nair, N. U., Hunter, L., Shao, M., Grnarova, P., Lin, Y., Bucher, P., & Bernard, B. M. (2016). A maximum-likelihood approach for building cell-type trees by lifting. BMC genomics, 17(1), [14]. https://doi.org/10.1186/s12864-015-2297-3
Nair, Nishanth Ulhas ; Hunter, Laura ; Shao, Mingfu ; Grnarova, Paulina ; Lin, Yu ; Bucher, Philipp ; Bernard, Bernard M. / A maximum-likelihood approach for building cell-type trees by lifting. In: BMC genomics. 2016 ; Vol. 17, No. 1.
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Nair, NU, Hunter, L, Shao, M, Grnarova, P, Lin, Y, Bucher, P & Bernard, BM 2016, 'A maximum-likelihood approach for building cell-type trees by lifting', BMC genomics, vol. 17, no. 1, 14. https://doi.org/10.1186/s12864-015-2297-3

A maximum-likelihood approach for building cell-type trees by lifting. / Nair, Nishanth Ulhas; Hunter, Laura; Shao, Mingfu; Grnarova, Paulina; Lin, Yu; Bucher, Philipp; Bernard, Bernard M.

In: BMC genomics, Vol. 17, No. 1, 14, 11.01.2016.

Research output: Contribution to journalArticle

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AU - Shao, Mingfu

AU - Grnarova, Paulina

AU - Lin, Yu

AU - Bucher, Philipp

AU - Bernard, Bernard M.

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