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A phylogenetic codon substitution model for antibody lineages

Abstract:

Phylogenetic methods have shown promise in understanding the development ofbroadly neutralizing antibody lineages (bNAbs). However, the mutational process that generates these lineages – somatic hypermutation (SHM) – is biased by hotspot motifs, which violates important assumptions in most phylogenetic substitution models. Here, we develop a modified GY94-type substitution model that partially accounts for this context-dependency while preserving independence of sites during calculation. This...

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Publication status:
Published
Peer review status:
Peer reviewed

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Publisher copy:
10.1534/genetics.116.196303

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Institution:
University of Oxford
Oxford college:
Linacre College
Role:
Author
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Institution:
University of Oxford
Division:
MPLS
Department:
Doctoral Training Centre - MPLS
Role:
Author
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Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
Human Genetics Wt Centre
Role:
Author
More from this funder
Funding agency for:
Hoehn, K
Publisher:
Genetics Society of America Publisher's website
Journal:
Genetics Journal website
Volume:
206
Issue:
1
Pages:
417-427
Publication date:
2017-05-05
Acceptance date:
2017-03-10
DOI:
EISSN:
1943-2631
ISSN:
0016-6731
Pubs id:
pubs:685577
UUID:
uuid:36f6c533-ea16-422d-8b9c-4a77ec298f97
Local pid:
pubs:685577
Deposit date:
2017-03-14

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