Now showing items 1-6 of 6
Social and genetic networks of HIV-1 transmission in New York City
Background Sexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify, and offer testing to persons linked in these ...
Detecting individual sites subject to episodic diversifying selection
(Public Library of Science, 2012-07-02)
The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, ...
Modeling HIV-1 drug resistance as episodic directional selection
(PLOS Computational Biology, 2011-05)
The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in ...
Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution
Models of protein evolution currently come in two flavors: generalist and specialist. Generalist models (e.g. PAM, JTT, WAG) adopt a one-size-fits-all approach, where a single model is estimated from a number of different ...
On the validity of evolutionary models with site-specific parameters
Evolutionary models that make use of site-specific parameters have recently been criticized on the grounds that parameter estimates obtained under such models can be unreliable and lack theoretical guarantees of convergence. ...
Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models
(BioMed Central, 2013-12-02)
Background Identification of the epitopes targeted by antibodies that can neutralize diverse HIV-1 strains can provide important clues for the design of a preventative vaccine. Methods We ...