C Kuiken

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. ncbi request reprint Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus
    C Kuiken
    Los Alamos National Laboratory, NM 87545, USA
    Am J Epidemiol 152:814-22. 2000
  2. ncbi request reprint Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research
    Peter T Hraber
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM, USA
    Antivir Chem Chemother 18:113-23. 2007
  3. pmc A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame
    Thomas Kuntzen
    Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
    J Med Virol 80:1370-8. 2008
  4. 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
  5. pmc The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses
    Carla Kuiken
    Theoretical Biology and Biophysics, T 10, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Nucleic Acids Res 40:D587-92. 2012
  6. pmc Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes
    Peter T Hraber
    Theoretical Biology and Biophysics, T 10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545, USA
    Virol J 3:103. 2006
  7. 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
  8. doi request reprint Designing a low-cost drug resistance database for viral hepatitis
    Carla Kuiken
    HIV database project, Los Alamos National Laboratory, Los Alamos, NM, USA
    Antivir Ther 15:517-20. 2010
  9. pmc The hepatitis C sequence database in Los Alamos
    Carla Kuiken
    HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA
    Nucleic Acids Res 36:D512-6. 2008
  10. ncbi request reprint Hepatitis C databases, principles and utility to researchers
    Carla Kuiken
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Hepatology 43:1157-65. 2006

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus
    C Kuiken
    Los Alamos National Laboratory, NM 87545, USA
    Am J Epidemiol 152:814-22. 2000
    ..Although data are still scarce, the authors attempt to use these patterns in the reconstruction of the worldwide spread of the HIV epidemic...
  2. ncbi request reprint Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research
    Peter 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...
  3. pmc A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame
    Thomas Kuntzen
    Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
    J Med Virol 80:1370-8. 2008
    ..Reference sequences for accurate HCV genotyping are required for optimized treatment, and a better knowledge of the global viral sequence diversity is needed to guide vaccines or new drugs effective in the world wide epidemic...
  4. 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...
  5. pmc The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses
    Carla Kuiken
    Theoretical Biology and Biophysics, T 10, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Nucleic Acids Res 40:D587-92. 2012
    ..is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov...
  6. pmc Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes
    Peter 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...
  7. 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...
  8. doi request reprint Designing a low-cost drug resistance database for viral hepatitis
    Carla Kuiken
    HIV database project, Los Alamos National Laboratory, Los Alamos, NM, USA
    Antivir Ther 15:517-20. 2010
    ....
  9. pmc The hepatitis C sequence database in Los Alamos
    Carla 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...
  10. ncbi request reprint Hepatitis C databases, principles and utility to researchers
    Carla Kuiken
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Hepatology 43:1157-65. 2006
    ..In this paper, we briefly describe each of these databases and their associated websites and tools, and give some examples of their use in furthering HCV research...
  11. 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...
  12. ncbi request reprint Retrieval and on-the-fly alignment of sequence fragments from the HIV database
    B Gaschen
    HIV Database and Analysis Group T10, Los Alamos National Laboratory, Mail Stop K710, Los Alamos, NM 87545, USA
    Bioinformatics 17:415-8. 2001
    ..We set out to provide our users with a tool that will retrieve and create an initial alignment of the HIV sequences that are available for a given genomic region...
  13. ncbi request reprint The Los Alamos hepatitis C sequence database
    Carla Kuiken
    HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA
    Bioinformatics 21:379-84. 2005
    ..At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide...
  14. ncbi request reprint Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection
    Peter Hraber
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Hepatology 46:1713-21. 2007
    ....
  15. 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...
  16. pmc Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index
    Peter 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...
  17. ncbi request reprint Recent evolutionary history of human immunodeficiency virus type 1 subtype B--response
    Una R Smith
    J Mol Evol 56:643-4; author reply 645-7. 2003
    ..We review published evidence, which suggests that their estimate is too late...
  18. 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/...
  19. ncbi request reprint Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6
    Ling Lu
    Division of Gastroenterology Hepatology, Department of Medicine, University of Kansas Medical Center, 4035 Delp, MS 1023, Kansas City, KS 66160, USA
    J Gen Virol 87:629-34. 2006
    ..However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype...
  20. ncbi request reprint Construction of an infectious HIV type 1 molecular clone from an African patient with a subtype D/C Recombinant Virus
    Binshan Shi
    Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA
    AIDS Res Hum Retroviruses 20:1015-8. 2004
    ..This infectious HIV-1 subtype D/C recombinant molecular clone obtained from a Kenyan long-term survivor promises to be useful to study pathogenesis and vaccine design...
  21. ncbi request reprint A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes
    Carla Kuiken
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
    Hepatology 44:1355-61. 2006
  22. ncbi request reprint Recombination following superinfection by HIV-1
    Guowei Fang
    Wadsworth Center, NY State Department of Health, Albany, 12208, USA
    AIDS 18:153-9. 2004
    ..There is increasing recognition of recombinant HIV-1 strains globally, but it has been unclear whether recombination results from superinfection during untreated, chronic infection...
  23. ncbi request reprint Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patients
    Jennifer E Layden-Almer
    Department of Medicine, University of Illinois at Chicago, 60612, USA
    J Infect Dis 192:1078-87. 2005
    ..The results of this study, in conjunction with those of a previous study illustrating the impaired IFN effectiveness in African Americans, suggest a role for host-related factors...
  24. ncbi request reprint Long-term survivors in Nairobi: complete HIV-1 RNA sequences and immunogenetic associations
    Guowei Fang
    Wadsworth Center, NY State Department of Health, Albany, New York 12208, USA
    J Infect Dis 190:697-701. 2004
    ..0048). Studying the interaction among immunogenetics, immune responses, and viral sequences from all HIV-1 subtypes may increase our understanding of slow HIV-1 disease progression...
  25. ncbi request reprint Ancient co-speciation of simian foamy viruses and primates
    William M Switzer
    HIV and Retrovirology Branch, Division of HIV AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, MS G 19, Atlanta, Georgia 30333, USA
    Nature 434:376-80. 2005
    ..These results indicate that SFVs might have co-speciated with Old World primates for at least 30 million years, making them the oldest known vertebrate RNA viruses...
  26. ncbi request reprint Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    Hepatology 42:962-73. 2005
    ..In conclusion, these proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future...
  27. doi request reprint Transition from long-term nonprogression to HIV-1 disease associated with escape from cellular immune control
    Kimdar Sherefa Kemal
    Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
    J Acquir Immune Defic Syndr 48:119-26. 2008
    ..These data are relevant to vaccine design and identification of the correlates of protection from disease progression...
  28. pmc Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and Anthropoidea
    Kevin J Kunstman
    Department of Medicine, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
    J Virol 77:12310-8. 2003
    ..Our results suggest that the shared structure and function of primate CCR5 homologue proteins would not impede the movement of primate immunodeficiency viruses between species...
  29. 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...
  30. ncbi request reprint Antiviral drug-resistant HBV: standardization of nomenclature and assays and recommendations for management
    Anna S Lok
    Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109 0362, USA
    Hepatology 46:254-65. 2007
    ..Thus, there is a need to standardize nomenclature relating to hepatitis B antiviral resistance, and to define genotypic, phenotypic, and clinical resistance to NA therapy...
  31. ncbi request reprint Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants
    Will Fischer
    Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nat Med 13:100-6. 2007
    ..Mosaics provide diversity coverage comparable to that afforded by thousands of separate peptides, but, because the fragments of natural proteins are compressed into a small number of native-like proteins, they are tractable for vaccines...
  32. pmc Genomic analysis of HIV type 1 strains derived from a mother and child pair of long-term nonprogressors
    Milan Reinis
    Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
    AIDS Res Hum Retroviruses 23:309-15. 2007
    ..This study highlights the potential of full genome analysis in the investigation of pathogenesis and immune selection during HIV-1 evolution...