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Carla Kuiken

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Carla Kuiken; Chienchi Lo; Hyejin Yoon; Werner Abfalterer; Brian Gaschen; Bette Korber
Viral genome analysis and knowledge management.
Paul W Fenimore; William M Fischer; Brian T Foley; Mary Kate Hart; Bette Korber; Majidat A Muhammad; Michael Parker; James R Thurmond; Hyejin Yoon; Karina Yusim; Russell R Bakken; John Michael Dye; Carla Kuiken
Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage.
Karina Yusim; William Fischer; Hyejin Yoon; James Thurmond; Paul W Fenimore; Georg Lauer; Bette Korber; Carla Kuiken
Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.

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All Publications

2013: Carla Kuiken; Chienchi Lo; Hyejin Yoon; Werner Abfalterer; Brian Gaschen; Bette Korber
Viral genome analysis and knowledge management.
Methods in molecular biology (Clifton, N.J.) 2013;939():253-61.
2012: Paul W Fenimore; William M Fischer; Brian T Foley; Mary Kate Hart; Bette Korber; Majidat A Muhammad; Michael Parker; James R Thurmond; Hyejin Yoon; Karina Yusim; Russell R Bakken; John Michael Dye; Carla Kuiken
Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage.
PloS one 2012;7(10):e44769.
2010: Karina Yusim; William Fischer; Hyejin Yoon; James Thurmond; Paul W Fenimore; Georg Lauer; Bette Korber; Carla Kuiken
Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.
The Journal of general virology 2010;91(Pt 5):1194-206.
2010: Carla Kuiken
Designing a low-cost drug resistance database for viral hepatitis.
Antiviral therapy 2010;15(3 Pt B):517-20.
2009: Carla Kuiken; Peter Simmonds
Nomenclature and numbering of the hepatitis C virus.
Methods in molecular biology (Clifton, N.J.) 2009;510():33-53.
2008: James Thurmond; Hyejin Yoon; Carla Kuiken; Karina Yusim; Simon Perkins; James Theiler; Tanmoy Bhattacharya; Bette Korber; Will Fischer
Web-based design and evaluation of T-cell vaccine candidates.
Bioinformatics (Oxford, England) 2008;24(14):1639-40.
2008: Kimdar S. Kemal; Tara Beattie; Tao Dong; Barbara Weiser; Rupert Kaul; Carla Kuiken; Julian Sutton; Dorothy Lang; Hongbing Yang; Yan Chun Peng; Ronald Collman; Sean Philpott; Sarah Rowland-Jones; Harold Burger
Transition from long-term nonprogression to HIV-1 disease associated with escape from cellular immune control.
Journal of acquired immune deficiency syndromes (1999) 2008;48(2):119-26.
2008: Carla Kuiken; Peter T Hraber; James Thurmond; Karina Yusim
The hepatitis C sequence database in Los Alamos.
Nucleic acids research 2008;36(Database issue):D512-6.
2007: Peter T Hraber; Carla Kuiken; Karina Yusim
Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection.
Hepatology (Baltimore, Md.) 2007;46(6):1713-21.
2007: Milan Reinis; Barbara Weiser; Carla Kuiken; Tao Dong; Dorothy Lang; Sharon Nachman; Yonghong Zhang; Sarah Rowland-Jones; Harold Burger
Genomic analysis of HIV type 1 strains derived from a mother and child pair of long-term nonprogressors.
AIDS research and human retroviruses 2007;23(2):309-15.
2007: Peter T Hraber; Robert W Leach; Lee P Reilly; James Thurmond; Karina Yusim; Carla Kuiken
Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research.
Antiviral chemistry & chemotherapy 2007;18(3):113-23.
2007: Will Fischer; Simon Perkins; James Theiler; Tanmoy Bhattacharya; Karina Yusim; Robert Funkhouser; Carla Kuiken; Barton Haynes; Norman L Letvin; Bruce D Walker; Beatrice H Hahn; Bette T Korber
Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants.
Nature medicine 2007;13(1):100-6.
2006: Carla Kuiken; Christophe Combet; Jens Bukh; Tadasu Shin-i; Gilbert Deleage; Masashi Mizokami; Russell Richardson; Erwin Sablon; Karina Yusim; Jean-Michel Pawlotsky; Peter Simmonds
A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes.
Hepatology (Baltimore, Md.) 2006;44(5):1355-61.
2006: Ming Zhang; Anne-Kathrin Schultz; Charles Calef; Carla Kuiken; Thomas Leitner; Bette Korber; Burkhard Morgenstern; Mario Stanke
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.
Nucleic acids research 2006;34(Web Server issue):W463-5.
2006: Carla Kuiken; Masashi Mizokami; Gilbert Deleage; Karina Yusim; François Penin; Tadasu Shin-i; Céline Charavay; Ning Tao; Daniel Crisan; Delphine Grando; Anita Dalwani; Christophe Geourjon; Ashish Agrawal; Christophe Combet
Hepatitis C databases, principles and utility to researchers.
Hepatology (Baltimore, Md.) 2006;43(5):1157-65.
2006: Peter T Hraber; Will Fischer; William J Bruno; Thomas Leitner; Carla Kuiken
Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes.
Virology journal 2006;3():103.
2006: Anne-Kathrin Schultz; Ming Zhang; Thomas Leitner; Carla Kuiken; Bette Korber; Burkhard Morgenstern; Mario Stanke
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.
BMC bioinformatics 2006;7():265.
2005: Peter Simmonds; Jens Bukh; Christophe Combet; Gilbert Deléage; Nobuyuki Enomoto; Stephen Feinstone; Phillippe Halfon; Geneviève Inchauspé; Carla Kuiken; Geert Maertens; Masashi Mizokami; Donald G Murphy; Hiroaki Okamoto; Jean-Michel Pawlotsky; François Penin; Erwin Sablon; Tadasu Shin-i; Lieven Stuyver; Heinz-Jürgen Thiel; Sergei Viazov; Amy J Weiner; Anders Widell
Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes.
Hepatology (Baltimore, Md.) 2005;42(4):962-73.
2005: Jennifer E Layden; Carla Kuiken; Ruy M Ribeiro; Kevin Kunstman; Alan S Perelson; Thomas J Layden; Steven Wolinsky
Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patients.
The Journal of infectious diseases 2005;192(6):1078-87.
2005: William Switzer; Marco Salemi; Vedapuri Shanmugam; Feng Gao; Mian-Er Cong; Carla Kuiken; Vinod Bhullar; Brigitte E Beer; Dominique Vallet; Annie Gautier-Hion; Zena Tooze; Francios VILLINGER; Edward C Holmes; Walid Heneine
Ancient co-speciation of simian foamy viruses and primates.
Nature 2005;434(7031):376-80.
2005: Carla Kuiken; Karina Yusim; Laura Boykin; Russell Richardson
The Los Alamos hepatitis C sequence database.
Bioinformatics (Oxford, England) 2005;21(3):379-84.
2005: Karina Yusim; Russell Richardson; Ning Tao; Anita Dalwani; Ashish Agrawal; James Szinger; Robert Funkhouser; Bette Korber; Carla Kuiken
Los alamos hepatitis C immunology database.
Applied bioinformatics 2005;4(4):217-25.
2004: Ming Zhang; Brian Gaschen; Wendy Blay Puryear; Brian Foley; Nancy Haigwood; Carla Kuiken; Bette Korber
Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin.
Glycobiology 2004;14(12):1229-46.
2004: Binshan Shi; Sean Philpott; Barbara Weiser; Carla Kuiken; Cheryl Brunner; Guowei Fang; Keith R Fowke; Francis A Plummer; Sarah Rowland-Jones; Job Bwayo; Aggrey O Anzala; Joshua Kimani; Rupert Kaul; Harold Burger
Construction of an infectious HIV type 1 molecular clone from an African patient with a subtype D/C Recombinant Virus.
AIDS research and human retroviruses 2004;20(9):1015-8.
2004: Guowei Fang; Carla Kuiken; Barbara Weiser; Sarah Rowland-Jones; Francis A Plummer; Chih-Hsiung Chen; Rupert Kaul; Aggrey O Anzala; Job Bwayo; Joshua Kimani; Sean Philpott; Christina Kitchen; Janet S Sinsheimer; Brian Gaschen; Dorothy Lang; Binshan Shi; Kimdar S. Kemal; Tim Rostron; Cheryl Brunner; Simon Beddows; Quentin Sattenau; Ellen Paxinos; Julius Oyugi; Harold Burger
Long-term survivors in Nairobi: complete HIV-1 RNA sequences and immunogenetic associations.
The Journal of infectious diseases 2004;190(4):697-701.
2004: Guowei Fang; Barbara Weiser; Carla Kuiken; Sean Philpott; Sarah Rowland-Jones; Francis A Plummer; Joshua Kimani; Binshan Shi; Rupert Kaul; Job Bwayo; Omu Anzala; Harold Burger
Recombination following superinfection by HIV-1.
AIDS (London, England) 2004;18(2):153-9.
2003: Kevin Kunstman; Bridget Puffer; Bette T Korber; Carla Kuiken; Una R Smith; Jennifer Kunstman; Jennifer Stanton; Michael B Agy; Riri Shibata; Anne D Yoder; Satish Pillai; Robert W Doms; Preston Marx; Steven Wolinsky
Structure and function of CC-chemokine receptor 5 homologues derived from representative primate species and subspecies of the taxonomic suborders Prosimii and Anthropoidea.
Journal of virology 2003;77(22):12310-8.
2003: Una R Smith; Carla Kuiken; Bette T Korber
Recent evolutionary history of human immunodeficiency virus type 1 subtype B--response.
Journal of molecular evolution 2003;56(5):643-4; author reply 645-7.
2003: Carla Kuiken; Bette Korber; Robert W Shafer
HIV sequence databases.
AIDS reviews 2003;5(1):52-61.
2001: Brigitte E Beer; Brian Foley; Carla Kuiken; Zena Tooze; Robert M Goeken; Charles R Brown; J Hu; M St Claire; Bette T Korber; Vanessa M Hirsch
Characterization of novel simian immunodeficiency viruses from red-capped mangabeys from Nigeria (SIVrcmNG409 and -NG411).
Journal of virology 2001;75(24):12014-27.
2001: Brian Gaschen; Carla Kuiken; Bette Korber; Brian Foley
Retrieval and on-the-fly alignment of sequence fragments from the HIV database.
Bioinformatics (Oxford, England) 2001;17(5):415-8.
2000: Carla Kuiken; R Thakallapalli; A Esklid; A de Ronde
Genetic analysis reveals epidemiologic patterns in the spread of human immunodeficiency virus.
American journal of epidemiology 2000;152(9):814-22.
2000: David L Robertson; J P Anderson; J A Bradac; Jean K Carr; Brian Foley; Robert Funkhouser; F Gao; Beatrice H Hahn; Marcia L Kalish; Carla Kuiken; Gerald Learn; Thomas Leitner; F McCutchan; Saladin Osmanov; M Peeters; Danuta Pieniazek; M Salminen; Paul M Sharp; Steven Wolinsky; Bette Korber
HIV-1 nomenclature proposal.
Science (New York, N.Y.) 2000;288(5463):55-6.