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...
- Impact of pre-adapted HIV transmissionJonathan M Carlson
Microsoft Research, Redmond, Washington, USA
Nat Med 22:606-13. 2016..Accounting for these holes may be key for vaccine strategies seeking to elicit functional responses from viral variants, and to HIV cure strategies that require broad CTL responses to achieve successful eradication of HIV reservoirs. ..
- 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...
- HIV-1 adaptation to HLA: a window into virus-host immune interactionsJonathan M Carlson
Microsoft Research, Redmond, WA, USA
Trends Microbiol 23:212-24. 2015....
- 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...
- Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamicsMorgane Rolland
Department of Microbiology, University of Washington, Seattle, Washington, United States of America
PLoS ONE 5:. 2010....