Frequent toggling between alternative amino acids is driven by selection in HIV-1.

by Wayne Delport, Konrad Scheffler, Cathal Seoighe
Published 2008-12-01

On the validity of evolutionary models with site-specific parameters.

by Konrad Scheffler, Ben Murrell, Sergei L Kosakovsky Pond
Published 2014-01-01

Correcting the bias of empirical frequency parameter estimators in codon models.

by Sergei Kosakovsky Pond, Wayne Delport, Spencer V Muse, Konrad Scheffler
Published 2010-07-01

Benchmarking multi-rate codon models.

by Wayne Delport, Konrad Scheffler, Mike B Gravenor, Spencer V Muse, Sergei Kosakovsky Pond
Published 2010-07-01

Detecting individual sites subject to episodic diversifying selection.

by Ben Murrell, Joel O Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, Sergei L Kosakovsky Pond
Published 2012-01-01

CodonTest: modeling amino acid substitution preferences in coding sequences.

by Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B Gravenor, Spencer V Muse, Sergei L Kosakovsky Pond
Published 2010-08-01

Seminal Shedding of CMV and HIV Transmission among Men Who Have Sex with Men

by Sara Gianella, Konrad Scheffler, Sanjay R. Mehta, Susan J. Little, Lorri Freitas, Sheldon R. Morris, Davey M. Smith
Published 2015-07-01

Modeling HIV-1 drug resistance as episodic directional selection.

by Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L Kosakovsky Pond, Konrad Scheffler, Southern African Treatment and Resistance Network-SATuRN Consortium
Published 2012-01-01

Non-negative matrix factorization for learning alignment-specific models of protein evolution.

by Ben Murrell, Thomas Weighill, Jan Buys, Robert Ketteringham, Sasha Moola, Gerdus Benade, Lise du Buisson, Daniel Kaliski, Tristan Hands, Konrad Scheffler
Published 2011-01-01

Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR.

by Michelli Faria de Oliveira, Sara Gianella, Scott Letendre, Konrad Scheffler, Sergei L Kosakovsky Pond, Davey M Smith, Matt Strain, Ronald J Ellis
Published 2015-01-01

IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.

by N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith, Sergei L Kosakovsky Pond
Published 2014-09-01

Social and Genetic Networks of HIV-1 Transmission in New York City.

by Joel O Wertheim, Sergei L Kosakovsky Pond, Lisa A Forgione, Sanjay R Mehta, Ben Murrell, Sharmila Shah, Davey M Smith, Konrad Scheffler, Lucia V Torian
Published 2017-01-01

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.

by Paul T Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J Gartland, Allan C deCamp, Craig A Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Gustavo H Kijak, Meera Bose, RV144 Sequencing Team, Miguel A Arroyo, Robert J O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L Robb, Tatsiana Kirys, Ivelin S Georgiev, Peter D Kwong, Konrad Scheffler, Sergei L Kosakovsky Pond, Jonathan M Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim, Peter B Gilbert
Published 2015-02-01