• Detecting individual sites subject to episodic diversifying selection 

      Murrell, Ben; Wertheim, Joel O.; Moola, Sasha; Weighill, Thomas; Scheffler, Konrad; Pond, Sergei L. Kosakovsky (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 

      Murrell, Ben; De Oliveira, Tulio; Seebregts, Chris; Pond, Sergei L. Kosakovsky; Scheffler, Konrad (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 

      Murrell, Ben; Weighill, Thomas; Buys, Jan; Ketteringham, Robert; Moola, Sasha; Benade, Gerdus; du Buisson, Lise; Kaliski, Daniel; Hands, Tristan; Scheffler, Konrad (PLOS, 2011-12-22)
      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 

      Scheffler, Konrad; Murrell, Ben; Pond, Sergei L. Kosakovsky (PLoS, 2014-04-10)
      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. ...
    • Social and genetic networks of HIV-1 transmission in New York City 

      Wertheim, Joel O.; Kosakovsky Pond, Sergei L.; Forgione, Lisa A.; Mehta, Sanjay R.; Murrell, Ben; Shah, Sharmila; Smith, Davey M.; Scheffler, Konrad; Torian, Lucia V. (PLoS, 2017-01-09)
      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 ...