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Karina Yusim

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Karina Yusim; Erica Borducchi; Rebecca Dilan; William Fischer; Elena Giorgi; Bette Korber; Joseph Marcotrigiano; Kelly Stanley; James Theiler; Dan H Barouch
Hepatitis C genotype 1 mosaic vaccines are immunogenic in mice and induce stronger T-cell responses than natural strains.
Chris Ford; Michael Chase; Shihai Feng; Mary Greene; Thomas R Ioerger; Bette Korber; Karina Yusim; Sarah Fortune
Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing.
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.

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All Publications

2013: Karina Yusim; Erica Borducchi; Rebecca Dilan; William Fischer; Elena Giorgi; Bette Korber; Joseph Marcotrigiano; Kelly Stanley; James Theiler; Dan H Barouch
Hepatitis C genotype 1 mosaic vaccines are immunogenic in mice and induce stronger T-cell responses than natural strains.
Clinical and vaccine immunology : CVI 2013;20(2):302-5.
2012: Chris Ford; Michael Chase; Shihai Feng; Mary Greene; Thomas R Ioerger; Bette Korber; Karina Yusim; Sarah Fortune
Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing.
Tuberculosis (Edinburgh, Scotland) 2012;92(3):194-201.
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.
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: Paul A Goepfert; Wendy Lumm; Paul Farmer; Philippa Matthews; Andrew Prendergast; Jonathan M Carlson; Cynthia A Derdeyn; Jianming Tang; Richard A Kaslow; Anju Bansal; Karina Yusim; David Heckerman; Joseph Mulenga; Susan Allen; Philip J R Goulder; Eric Hunter
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients.
The Journal of experimental medicine 2008;205(5):1009-17.
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: Anju Bansal; Ling Yue; Joan Conway; Karina Yusim; Jianming "James" Tang; John C Kappes; Richard A Kaslow; Craig M Wilson; Paul A Goepfert
Immunological control of chronic HIV-1 infection: HLA-mediated immune function and viral evolution in adolescents.
AIDS (London, England) 2007;21(18):2387-97.
2007: Nicole Frahm; Daniel E Kaufmann; Karina Yusim; Mark Muldoon; Can Kesmir; Caitlyn H Linde; Will Fischer; Todd M Allen; Bin Li; Ben H McMahon; Kellie L Faircloth; Hannah S Hewitt; Elizabeth W Mackey; Toshiyuki Miura; Ashok Khatri; Steven Wolinsky; Andrew McMichael; Robert Funkhouser; Bruce D Walker; Christian Brander; Bette T Korber
Increased sequence diversity coverage improves detection of HIV-specific T cell responses.
Journal of immunology (Baltimore, Md. : 1950) 2007;179(10):6638-50.
2007: Nicole Frahm; Karina Yusim; Todd J Suscovich; Sharon Adams; John Sidney; Peter T Hraber; Hannah S Hewitt; Caitlyn H Linde; Daniel G Kavanagh; Tonia Woodberry; Leah M Henry; Kellie Faircloth; Jennifer Listgarten; Carl Kadie; Nebojsa Jojic; Kaori Sango; Nancy V Brown; Eunice Pae; M Tauheed Zaman; Florian Bihl; Ashok Khatri; Mina John; Simon Mallal; Francesco M Marincola; Bruce D Walker; Alessandro Sette; David Heckerman; Bette T Korber; Christian Brander
Extensive HLA class I allele promiscuity among viral CTL epitopes.
European journal of immunology 2007;37(9):2419-33.
2007: Tanmoy Bhattacharya; Marcus Daniels; David Heckerman; Brian Foley; Nicole Frahm; Carl Kadie; Jonathan Carlson; Karina Yusim; Ben McMahon; Brian Gaschen; Simon Mallal; James I Mullins; David C Nickle; Joshua Herbeck; Christine M Rousseau; Gerald Learn; Toshiyuki Miura; Christian Brander; Bruce Walker; Bette Korber
Founder effects in the assessment of HIV polymorphisms and HLA allele associations.
Science (New York, N.Y.) 2007;315(5818):1583-6.
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: Ruth Dickover; Eileen Garratty; Karina Yusim; Catherine Miller; Bette Korber; Yvonne Bryson
Role of maternal autologous neutralizing antibody in selective perinatal transmission of human immunodeficiency virus type 1 escape variants.
Journal of virology 2006;80(13):6525-33.
2006: Bette Korber; Montiago LaBute; Karina Yusim
Immunoinformatics comes of age.
PLoS computational biology 2006;2(6):e71.
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: Florian Bihl; Nicole Frahm; Loriana Di Giammarino; John Sidney; Mina John; Karina Yusim; Tonia Woodberry; Kaori Sango; Hannah S Hewitt; Leah Henry; Caitlyn H Linde; John V Chisholm; Tauheed M Zaman; Eunice Pae; Simon Mallal; Bruce D Walker; Alessandro Sette; Bette T Korber; David Heckerman; Christian Brander
Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses.
Journal of immunology (Baltimore, Md. : 1950) 2006;176(7):4094-101.
2005: Alasdair Leslie; Daniel Kavanagh; Isobella Honeyborne; Katja Pfafferott; Charles Edwards; Tilly Pillay; Louise Hilton; Christina Thobakgale; Danni Ramduth; Rika Draenert; Sylvie Le Gall; Graz Luzzi; Anne Edwards; Christian Brander; Andrew K Sewell; Sarah Moore; James Mullins; Corey Moore; Simon Mallal; Nina Bhardwaj; Karina Yusim; Rodney Phillips; Paul Klenerman; Bette Korber; Photini Kiepiela; Bruce Walker; Philip J R Goulder
Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA.
The Journal of experimental medicine 2005;201(6):891-902.
2005: Anju Bansal; Ethan Gough; Steffanie Sabbaj; Doug Ritter; Karina Yusim; Greg Sfakianos; Grace M Aldrovandi; Richard A Kaslow; Craig M Wilson; Mark MULLIGAN; J. Michael Kilby; Paul A Goepfert
CD8 T-cell responses in early HIV-1 infection are skewed towards high entropy peptides.
AIDS (London, England) 2005;19(3):241-50.
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: Nicole Frahm; Bette T Korber; C M Adams; James Szinger; Rika Draenert; Marylyn M Addo; Margaret E Feeney; Karina Yusim; Kaori Sango; Nancy V Brown; D SenGupta; A Piechocka-Trocha; T Simonis; Francesco M Marincola; Alysse Wurcel; David R Stone; Christopher J Russell; P Adolf; Daniel Cohen; Timothy Roach; A StJohn; Ashok Khatri; K Davis; James Mullins; Philip J R Goulder; Bruce D Walker; Christian Brander
Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities.
Journal of virology 2004;78(5):2187-200.
2003: Xiaofeng Fan; Dorothy M Lang; Yanjuan Xu; Andre C Lyra; Karina Yusim; James E Everhart; Bette T Korber; Alan S Perelson; Adrian M Di Bisceglie
Liver transplantation with hepatitis C virus-infected graft: interaction between donor and recipient viral strains.
Hepatology (Baltimore, Md.) 2003;38(1):25-33.
2002: Andre C Lyra; Xiaofeng Fan; Dorothy M Lang; Karina Yusim; Sanjay Ramrakhiani; Elizabeth M Brunt; Bette Korber; Alan S Perelson; Adrian M Di Bisceglie
Evolution of hepatitis C viral quasispecies after liver transplantation.
Gastroenterology 2002;123(5):1485-93.
2002: Michael R Betts; Karina Yusim; Richard A Koup
Optimal antigens for HIV vaccines based on CD8+ T response, protein length, and sequence variability.
DNA and cell biology 2002;21(9):665-70.
2002: Karina Yusim; Can Kesmir; Brian Gaschen; Marylyn M Addo; Marcus Altfeld; Søren Brunak; Alexandre Chigaev; Vincent Detours; Bette T Korber
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation.
Journal of virology 2002;76(17):8757-68.
2002: Brian Gaschen; Jesse Taylor; Karina Yusim; Brian Foley; Feng Gao; Dorothy Lang; Vladimir Novitsky; Barton Haynes; Beatrice H Hahn; Tanmoy Bhattacharya; Bette Korber
Diversity considerations in HIV-1 vaccine selection.
Science (New York, N.Y.) 2002;296(5577):2354-60.
2001: Karina Yusim; Hanna Parnas; Lee Segel
One-vesicle hypothesis for neurotransmitter release: a possible molecular mechanism.
Bulletin of mathematical biology 2001;63(6):1025-40.
2001: Karina Yusim; M Peeters; O G Pybus; Tanmoy Bhattacharya; E Delaporte; C Mulanga; Mark Muldoon; James Theiler; Bette Korber
Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2001;356(1410):855-66.
2001: Karina Yusim; Shlomo Nir; N Lahav
A model for proto-tRNA loading.
Journal of theoretical biology 2001;208(1):109-16.
2001: Bette Korber; Brian Gaschen; Karina Yusim; R Thakallapally; Can Kesmir; Vincent Detours
Evolutionary and immunological implications of contemporary HIV-1 variation.
British medical bulletin 2001;58():19-42.
2000: Karina Yusim; Hanna Parnas; Lee Segel
Theory for the feedback inhibition of fast release of neurotransmitter.
Bulletin of mathematical biology 2000;62(4):717-57.
1999: Karina Yusim; Hanna Parnas; Lee Segel
Theory of fast neurotransmitter release control based on voltage-dependent interaction between autoreceptors and proteins of the exocytotic machinery.
Bulletin of mathematical biology 1999;61(4):701-25.