Bette Korber

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. ncbi request reprint Diversity considerations in HIV-1 vaccine selection
    Brian Gaschen
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Science 296:2354-60. 2002
  2. pmc Immunoinformatics comes of age
    Bette Korber
    Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 2:e71. 2006
  3. pmc Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections
    S Gnanakaran
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Pathog 7:e1002209. 2011
  4. pmc Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies
    S Gnanakaran
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 6:e1000955. 2010
  5. pmc Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing
    Will Fischer
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 5:e12303. 2010
  6. pmc Distinct evolutionary pressures underlie diversity in simian immunodeficiency virus and human immunodeficiency virus lineages
    Will Fischer
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    J Virol 86:13217-31. 2012
  7. pmc Definition of the viral targets of protective HIV-1-specific T cell responses
    Beatriz Mothe
    IrsiCaixa AIDS Research Institute HIVACAT, Badalona, Spain
    J Transl Med 9:208. 2011
  8. pmc A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
    Anne Kathrin Schultz
    Institute of Microbiology and Genetics, University of Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 7:265. 2006
  9. pmc Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
    Elena E Giorgi
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Bioinformatics 11:532. 2010
  10. doi request reprint The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility
    Bette Korber
    Los Alamos National Laboratory, Los Alamos, NM, USA
    Curr Opin HIV AIDS 4:408-17. 2009

Collaborators

Detail Information

Publications46

  1. ncbi request reprint Diversity considerations in HIV-1 vaccine selection
    Brian Gaschen
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Science 296:2354-60. 2002
    ..Consensus or ancestor sequences could be used in vaccine design to minimize the genetic differences between vaccine strains and contemporary isolates, effectively reducing the extent of diversity by half...
  2. pmc Immunoinformatics comes of age
    Bette Korber
    Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 2:e71. 2006
    ..The public health implications are vast, including designing vaccines, understanding autoimmune diseases, and defining the correlates of immune protection...
  3. pmc Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections
    S Gnanakaran
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Pathog 7:e1002209. 2011
    ....
  4. pmc Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies
    S Gnanakaran
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 6:e1000955. 2010
    ..Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1...
  5. pmc Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing
    Will 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...
  6. pmc Distinct evolutionary pressures underlie diversity in simian immunodeficiency virus and human immunodeficiency virus lineages
    Will Fischer
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    J Virol 86:13217-31. 2012
    ....
  7. pmc Definition of the viral targets of protective HIV-1-specific T cell responses
    Beatriz Mothe
    IrsiCaixa AIDS Research Institute HIVACAT, Badalona, Spain
    J Transl Med 9:208. 2011
    ..However, current HIV vaccine designs are largely based on viral sequence alignments only, not incorporating experimental data on T cell function and specificity...
  8. pmc A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
    Anne Kathrin Schultz
    Institute of Microbiology and Genetics, University of Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 7:265. 2006
    ..This approach is particularly useful for dealing with recombination events...
  9. pmc Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
    Elena E Giorgi
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Bioinformatics 11:532. 2010
    ..g., BEAST), which are instead based on the simulation of genealogies...
  10. doi request reprint The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility
    Bette Korber
    Los Alamos National Laboratory, Los Alamos, NM, USA
    Curr Opin HIV AIDS 4:408-17. 2009
    ..Strategies for rational vaccine design, to enhance coverage of HIV's natural diversity, are considered...
  11. ncbi request reprint AIDS Vaccine 2003. 18-21 September 2003, New York, NY, USA
    Bette Korber
    Los Alamos National Laboratory and the Sante Fe Institute, MS K710, T 10, Theoretical Division, NM 87545, USA
    IDrugs 6:1046-8. 2003
  12. ncbi request reprint Founder effects in the assessment of HIV polymorphisms and HLA allele associations
    Tanmoy Bhattacharya
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Science 315:1583-6. 2007
    ..This approach has practical implications for understanding the impact of host immunity on pathogen evolution and for defining relevant variants for inclusion in vaccine antigens...
  13. doi request reprint Web-based design and evaluation of T-cell vaccine candidates
    James Thurmond
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bioinformatics 24:1639-40. 2008
    ..To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial...
  14. ncbi request reprint Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin
    Ming Zhang
    Theoretical Biology Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
    Glycobiology 14:1229-46. 2004
    ..Human influenza A hemagglutinin H3 HA1 is accumulating sequons over time, but this trend is not evident in any other avian or human influenza A serotypes...
  15. pmc The role of recombination in the emergence of a complex and dynamic HIV epidemic
    Ming Zhang
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Retrovirology 7:25. 2010
    ....
  16. pmc A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein
    Anurag Sethi
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    PLoS Comput Biol 9:e1003046. 2013
    ....
  17. pmc A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
    Johanna Brodin
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Bioinformatics 14:255. 2013
    ....
  18. pmc Hepatitis C genotype 1 mosaic vaccines are immunogenic in mice and induce stronger T-cell responses than natural strains
    Karina Yusim
    Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    Clin Vaccine Immunol 20:302-5. 2013
    ..They elicited stronger T-cell responses to NS3-NS4a and E1-E2 proteins than did natural strains, as assessed with vaccine-matched peptides...
  19. doi request reprint Viral genome analysis and knowledge management
    Carla Kuiken
    Los Alamos National Laboratory, Theoretical Biology and Biophysics MS K710, Los Alamos, NM, USA
    Methods Mol Biol 939:253-61. 2013
    ..The database/analysis platforms described in this chapter can be accessed at http://hiv.lanl.gov http://hcv.lanl.gov http://hfv.lanl.gov...
  20. pmc Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage
    Paul W Fenimore
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 7:e44769. 2012
    ..We demonstrate in vivo immunogenicity and protection against a heterologous challenge in a mouse model. This design work delineates the likely requirements and limitations on broadly-protective filoviral CTL vaccines...
  21. pmc Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120
    S Gnanakaran
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Virol 81:4886-91. 2007
    ..Generally, shorter V4 loops are incompatible with a glycine occurring in the alpha2-helix in clade C, an intriguing association that could be exploited to inform Env immunogen design...
  22. doi request reprint Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity
    Karina Yusim
    Los Alamos National Laboratory, Theory Division, Los Alamos, NM 87545, USA
    J Gen Virol 91:1194-206. 2010
    ..More than 75% coverage of all HCV proteins was achieved with a three-antigen mosaic cocktail, suggesting that genotype-specific vaccines could also include the more variable proteins...
  23. pmc The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data
    Irina Maljkovic Berry
    Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Epidemics 1:230-9. 2009
    ..Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events...
  24. pmc HIV sequence databases
    Carla Kuiken
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    AIDS Rev 5:52-61. 2003
    ..The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail...
  25. ncbi request reprint The spread of HIV in Africa
    John Mokili
    Theoretical Biology T10, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    J Neurovirol 11:66-75. 2005
    ..Finally, we review the relationship of HIV lineages to related simian retroviruses and the evolutionary history and the origins of the HIV epidemic...
  26. ncbi request reprint Public health. A sound rationale needed for phase III HIV-1 vaccine trials
    Dennis R Burton
    Scripps Research Institute, La Jolla, California, USA
    Science 303:316. 2004
  27. ncbi request reprint Cross-reactive CD8+ T cell epitopes identified in US adolescent minorities
    Steffanie Sabbaj
    Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    J Acquir Immune Defic Syndr 33:426-38. 2003
    ..Frequent recognition of several of these CTL epitopes in persons of diverse racial backgrounds bodes well for the development of a broadly reactive HIV-1 vaccine...
  28. ncbi request reprint T cell responses in HIV type 1-infected adolescent minorities share similar epitope specificities with whites despite significant differences in HLA class I alleles
    Anju Bansal
    Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    AIDS Res Hum Retroviruses 19:1017-26. 2003
    ..Hence host genetic variation among different racial groups may have less impact on the utility of candidate HIV-1 vaccines than previously suspected...
  29. ncbi request reprint Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA
    Photini Kiepiela
    HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZuluNatal, 719 Umbilo Road, Durban 4015, South Africa
    Nature 432:769-75. 2004
    ..The dominant involvement of HLA-B in influencing HIV disease outcome is of specific relevance to the direction of HIV research and to vaccine design...
  30. pmc Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA
    Alasdair Leslie
    Peter Medawar Building, University of Oxford, Oxford OX13SY, UK
    J Exp Med 201:891-902. 2005
    ..These data help to explain how HIV is evolving at a population level. Understanding the direction of HIV evolution has important implications for vaccine development...
  31. ncbi request reprint Epitope escape mutation and decay of human immunodeficiency virus type 1-specific CTL responses
    Beth D Jamieson
    Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    J Immunol 171:5372-9. 2003
    ..Our data show surprisingly consistent decay of CTL responses after epitope escape mutation and provide insight into potential mechanisms for both immune failure and shifting CTL specificities...
  32. pmc jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
    Ming Zhang
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Gottingen, Germany
    Nucleic Acids Res 34:W463-5. 2006
    ..jpHMM is available online at http://jphmm.gobics.de/...
  33. pmc Genetic and functional analysis of full-length human immunodeficiency virus type 1 env genes derived from brain and blood of patients with AIDS
    Asa Ohagen
    Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    J Virol 77:12336-45. 2003
    ....
  34. ncbi request reprint Advantage of rare HLA supertype in HIV disease progression
    Elizabeth 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...
  35. pmc Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences
    Marcus Altfeld
    Partners AIDS Research Center and Infectious Disease Unit, Massachusetts General Hospital, and Division of AIDS, Harvard Medical School, Boston, Massachusetts, USA
    J Virol 77:7330-40. 2003
    ..They also demonstrate that CD8 T-cell responses to the variable HIV-1 proteins are more common than previously reported...
  36. ncbi request reprint Host genetic profiles predict virological and immunological control of HIV-1 infection in adolescents
    Jianming Tang
    Department of Medicine, University of Alabama at Birmingham, AL 39294 0022, USA
    AIDS 16:2275-84. 2002
    ..To evaluate the correlation between host genetic profiles and virological and immunological outcomes among HIV-1-seropositive participants from the Reaching for Excellence in Adolescent Care and Health (REACH) cohort...
  37. ncbi request reprint Mother-to-child transmission in the United States of subtypes D and A/G human immunodeficiency virus type 1
    Paul Krogstad
    Department of Pediatrics, University of California Los Angeles School of Medicine, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
    AIDS Res Hum Retroviruses 18:413-7. 2002
    ..Non-B subtypes should be considered in the management of HIV-1-infected pregnant women and children to optimize strategies to prevent and treat pediatric HIV-1 infection...
  38. ncbi request reprint HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity
    Mathias Lichterfeld
    Partners AIDS Research Center and Howard Hughes Medical Institute, Massachusetts General Hospital and Division of AIDS, Harvard Medical School, Boston, Massachusetts 02129, USA
    AIDS 18:1383-92. 2004
    ....
  39. pmc Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies
    James M Binley
    IMM2, Department of Immunology, The Scripps Research Institute, 10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
    J Virol 78:13232-52. 2004
    ..As well as the significance for vaccine design, our data have implications for passive-immunization studies in countries where clade C viruses are common, given that only MAbs b12 and 4E10 were effective against viruses from this clade...
  40. pmc Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels
    Bhavna Chohan
    Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, C3 168 Seattle, WA 98109 1024, USA
    J Virol 79:6528-31. 2005
    ..Thus, our study also suggests that the extent of glycosylation in the infecting virus could impact disease progression...
  41. pmc HLA-B63 presents HLA-B57/B58-restricted cytotoxic T-lymphocyte epitopes and is associated with low human immunodeficiency virus load
    Nicole Frahm
    Partners AIDS Research Center, Massachusetts General Hospital, No 5214, 149 13th Street, Charlestown, MA 02129, USA
    J Virol 79:10218-25. 2005
    ..The data support an important role of the presented epitope in mediating relative control of HIV replication and help to better define immune correlates of controlled HIV infection...
  42. pmc Structure of a V3-containing HIV-1 gp120 core
    Chih Chin Huang
    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
    Science 310:1025-8. 2005
    ..The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization...
  43. pmc Coping with viral diversity in HIV vaccine design: a response to Nickle et al
    Will Fischer
    PLoS Comput Biol 4:e15; author reply e25. 2008
  44. pmc Design and pre-clinical evaluation of a universal HIV-1 vaccine
    Sven L├ętourneau
    Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
    PLoS ONE 2:e984. 2007
    ..One of the big roadblocks in development of HIV-1/AIDS vaccines is the enormous diversity of HIV-1, which could limit the value of any HIV-1 vaccine candidate currently under test...
  45. pmc Role of maternal autologous neutralizing antibody in selective perinatal transmission of human immunodeficiency virus type 1 escape variants
    Ruth Dickover
    Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 LeConte Ave, Los Angeles, CA 90095, USA
    J Virol 80:6525-33. 2006
    ..These data indicate that maternal autologous neutralizing antibody can exert powerful protective and selective effects in perinatal HIV-1 transmission and therefore has important implications for vaccine development...
  46. ncbi request reprint A plea for justice for jailed medical workers
    Sunil K Ahuja
    Science 314:924-5. 2006