Title |
A maximum-likelihood approach for building cell-type trees by lifting
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Published in |
BMC Genomics, January 2016
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DOI | 10.1186/s12864-015-2297-3 |
Pubmed ID | |
Authors |
Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret |
Abstract |
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. 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. 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. |
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United States | 1 | 25% |
Germany | 1 | 25% |
France | 1 | 25% |
Unknown | 1 | 25% |
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Scientists | 2 | 50% |
Members of the public | 2 | 50% |
Mendeley readers
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Brazil | 1 | 6% |
Unknown | 15 | 88% |
Demographic breakdown
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Student > Ph. D. Student | 7 | 41% |
Student > Bachelor | 2 | 12% |
Researcher | 2 | 12% |
Professor | 1 | 6% |
Student > Master | 1 | 6% |
Other | 1 | 6% |
Unknown | 3 | 18% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 4 | 24% |
Computer Science | 1 | 6% |
Physics and Astronomy | 1 | 6% |
Neuroscience | 1 | 6% |
Other | 0 | 0% |
Unknown | 4 | 24% |