Research Topics
Species | C KuikenSummaryAffiliation: Los Alamos National Laboratory Country: USA Publications
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Detail Information
Publications
Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virusC 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...- 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 set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frameThomas 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...
Viral genome analysis and knowledge managementCarla 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...- The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat virusesCarla 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... - 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... - A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomesAnne 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... - Designing a low-cost drug resistance database for viral hepatitisCarla Kuiken
HIV database project, Los Alamos National Laboratory, Los Alamos, NM, USA
Antivir Ther 15:517-20. 2010.... - 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... - Hepatitis C databases, principles and utility to researchersCarla 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... - HIV sequence databasesCarla 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... - Retrieval and on-the-fly alignment of sequence fragments from the HIV databaseB Gaschen
HIV Database and Analysis Group T10, Los Alamos National Laboratory, Mail Stop K710, Los Alamos, NM 87545, USA
Bioinformatics 17:415-8. 2001..Retrieving and aligning the almost 560 gp120 sequences (approximately>1500 nt) stored in the database is at least 1500 times faster than a similar Clustal alignment... - The Los Alamos hepatitis C sequence databaseCarla Kuiken
HCV database, Los Alamos National Laboratory, Los Alamos, NM, USA
Bioinformatics 21:379-84. 2005..Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. AVAILABILITY: The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org... - 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.... - Web-based design and evaluation of T-cell vaccine candidatesJames 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. AVAILABILITY: http://hiv.lanl.gov/content/sequence/MOSAIC/... - 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... - Recent evolutionary history of human immunodeficiency virus type 1 subtype B--responseUna 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... - jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1Ming Zhang
, Abteilung Bioinformatik, Goldschmidtstrasse 1, , Germany
Nucleic Acids Res 34:W463-5. 2006..jpHMM is available online at http://jphmm.gobics.de/... - Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6Ling 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... - Construction of an infectious HIV type 1 molecular clone from an African patient with a subtype D/C Recombinant VirusBinshan 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... - A comprehensive system for consistent numbering of HCV sequences, proteins and epitopesCarla Kuiken
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
Hepatology 44:1355-61. 2006 - Recombination following superinfection by HIV-1Guowei Fang
Wadsworth Center, NY State Department of Health, Albany, 12208, USA
AIDS 18:153-9. 2004..Recombination resulting from superinfection with diverse strains may pose problems for eliciting broad immune responses necessary for an effective vaccine... - Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patientsJennifer 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... - Long-term survivors in Nairobi: complete HIV-1 RNA sequences and immunogenetic associationsGuowei 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... - Ancient co-speciation of simian foamy viruses and primatesWilliam 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... - Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypesPeter 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... - Transition from long-term nonprogression to HIV-1 disease associated with escape from cellular immune controlKimdar 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... - Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and AnthropoideaKevin 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... - Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutininMing 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... - Antiviral drug-resistant HBV: standardization of nomenclature and assays and recommendations for managementAnna 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... - Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variantsWill 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... - Genomic analysis of HIV type 1 strains derived from a mother and child pair of long-term nonprogressorsMilan 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...