Jonathan M Carlson
Affiliation: Microsoft Research
- HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneckJonathan M Carlson
Microsoft Research, Redmond, WA 98052, USA
Science 345:1254031. 2014..Thus, preventative or therapeutic approaches that even marginally reduce viral fitness may lower the overall transmission rates and offer long-term benefits even upon successful transmission. ..
- Widespread impact of HLA restriction on immune control and escape pathways of HIV-1Jonathan M Carlson
Microsoft Research, eScience Group, Los Angeles, California, USA
J Virol 86:5230-43. 2012..Given the clinical correlates of immune escape, such heterogeneity suggests that certain epitopes will lead to discordant outcomes if applied universally in a vaccine...
- Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 GagJonathan M Carlson
eScience Group, Microsoft Research, Redmond, Washington, United States of America
PLoS Comput Biol 4:e1000225. 2008..Phylogenetic dependency networks represent a major step toward systematically expanding our understanding of CTL escape to diverse populations and whole viral genes...
- Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative studySantiago Avila-Ríos
Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
Retrovirology 6:72. 2009..However, it is not known whether characteristic HLA frequency distributions in different populations have resulted in additional unique footprints...
- Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replicationJustine Sunshine
Department of Global Health, University of Washington, Seattle, Washington, USA
J Virol 88:1354-65. 2014..Additionally, sequence coverage serves as a valuable measure by which to evaluate the protective potential of future vaccination strategies. ..
- Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1Jonathan M Carlson
Microsoft Research, Los Angeles, California, USA
J Virol 86:13202-16. 2012..Thus, the factors defining protective cellular immune responses may be more complex than simply targeting conserved viral regions. The results provide new information to guide vaccine design and immunogenicity studies...
- HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspectiveJonathan M Carlson
Microsoft Research, Redmond, WA, USA
Microbes Infect 10:455-61. 2008..Here we summarize recent advances in our understanding of the consequences of CTL escape on HIV evolution at the population level and discuss its implications for HIV vaccine design...
- PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary treesBongshin Lee
Microsoft Research, One Microsoft Way, Redmond, WA 98052, USA
Bioinformatics 25:2611-2. 2009..In this note, we introduce PhyloDet (short for PhyloDetective), an evolutionary tree visualization tool that enables biologists to visualize multiple traits mapped to the tree...