Affiliation: Los Alamos National Laboratory
- Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV VariantsPeter Hraber
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Viruses 7:5443-75. 2015....
- HIV-1 subtype C superinfected individuals mount low autologous neutralizing antibody responses prior to intrasubtype superinfectionDebby Basu
Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA, USA
Retrovirology 9:76. 2012..We hypothesized that this reflected a blunted NAb response, which may have made these individuals more susceptible to superinfection...
- Timing and source of subtype-C HIV-1 superinfection in the newly infected partner of Zambian couples with disparate virusesColleen S Kraft
Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
Retrovirology 9:22. 2012..We have, therefore, investigated the incidence and viral origin of superinfection in these couples...
- Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching indexPeter Hraber
Theoretical Biology and Biophysics, T 10 MS K710, LANL, Los Alamos, NM 87545, USA
J Gen Virol 89:2098-107. 2008..In synthetic recombinants, regions without breakpoints are recognized accurately; regions with breakpoints do not represent any known subtype uniquely. Web-based services for viral subtype classification with the BI are available online...
- Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infectionPeter Hraber
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Hepatology 46:1713-21. 2007..05 x 10(-6)) than as low-resolution genotypes (P = 1.99 x 10(-3)). No significant associations between zygosity and HCV infection were found for other HLA loci...
- Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypesPeter T Hraber
Theoretical Biology and Biophysics, T 10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545, USA
Virol J 3:103. 2006..This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions...
- The hepatitis C sequence database in Los AlamosCarla Kuiken
HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA
Nucleic Acids Res 36:D512-6. 2008..The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org...
- Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral researchPeter T Hraber
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
Antivir Chem Chemother 18:113-23. 2007..This paper describes the types of data and the services that these databases offer, the tools they provide, and their configuration and use. Examples of applications to clonal analysis for drug-resistance mutations are shown...
- A multiple-alignment based primer design algorithm for genetically highly variable DNA targetsJohanna Brodin
Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
BMC Bioinformatics 14:255. 2013....
- Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodiesPeter Hraber
Los Alamos National Laboratory, Los Alamos, New Mexico, USA
J Virol 88:12623-43. 2014..These findings highlight important considerations for the design and testing of candidate HIV-1 vaccines that aim to elicit effective nAbs...
- Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencingWill Fischer
Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
PLoS ONE 5:e12303. 2010..Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape...
- Advantage of rare HLA supertype in HIV disease progressionElizabeth Trachtenberg
Children s Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way Oakland, California 94609, USA
Nat Med 9:928-35. 2003..The correlation of the frequency of the HLA supertypes with viral load suggests that HIV adapts to the most frequent alleles in the population, providing a selective advantage for those individuals who express rare alleles...