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Items: 44

1.

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design.

Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B.

Cell Host Microbe. 2019 Aug 14;26(2):296. doi: 10.1016/j.chom.2019.07.016. No abstract available.

2.

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design.

Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B.

Cell Host Microbe. 2019 Jan 9;25(1):59-72.e8. doi: 10.1016/j.chom.2018.12.001. Erratum in: Cell Host Microbe. 2019 Aug 14;26(2):296.

3.

Infant transmitted/founder HIV-1 viruses from peripartum transmission are neutralization resistant to paired maternal plasma.

Kumar A, Smith CEP, Giorgi EE, Eudailey J, Martinez DR, Yusim K, Douglas AO, Stamper L, McGuire E, LaBranche CC, Montefiori DC, Fouda GG, Gao F, Permar SR.

PLoS Pathog. 2018 Apr 19;14(4):e1006944. doi: 10.1371/journal.ppat.1006944. eCollection 2018 Apr.

4.

Epigraph: A Vaccine Design Tool Applied to an HIV Therapeutic Vaccine and a Pan-Filovirus Vaccine.

Theiler J, Yoon H, Yusim K, Picker LJ, Fruh K, Korber B.

Sci Rep. 2016 Oct 5;6:33987. doi: 10.1038/srep33987.

5.

Integrated sequence and immunology filovirus database at Los Alamos.

Yusim K, Yoon H, Foley B, Feng S, Macke J, Dimitrijevic M, Abfalterer W, Szinger J, Fischer W, Kuiken C, Korber B.

Database (Oxford). 2016 Apr 21;2016. pii: baw047. doi: 10.1093/database/baw047. Print 2016.

6.

CATNAP: a tool to compile, analyze and tally neutralizing antibody panels.

Yoon H, Macke J, West AP Jr, Foley B, Bjorkman PJ, Korber B, Yusim K.

Nucleic Acids Res. 2015 Jul 1;43(W1):W213-9. doi: 10.1093/nar/gkv404. Epub 2015 Jun 4.

7.

A multivalent clade C HIV-1 Env trimer cocktail elicits a higher magnitude of neutralizing antibodies than any individual component.

Bricault CA, Kovacs JM, Nkolola JP, Yusim K, Giorgi EE, Shields JL, Perry J, Lavine CL, Cheung A, Ellingson-Strouss K, Rademeyer C, Gray GE, Williamson C, Stamatatos L, Seaman MS, Korber BT, Chen B, Barouch DH.

J Virol. 2015 Mar;89(5):2507-19. doi: 10.1128/JVI.03331-14. Epub 2014 Dec 24.

8.

Alternative effector-function profiling identifies broad HIV-specific T-cell responses in highly HIV-exposed individuals who remain uninfected.

Ruiz-Riol M, Llano A, Ibarrondo J, Zamarreño J, Yusim K, Bach V, Mothe B, Perez-Alvarez S, Fernandez MA, Requena G, Meulbroek M, Pujol F, Leon A, Cobarsi P, Korber BT, Clotet B, Ganoza C, Sanchez J, Coll J, Brander C.

J Infect Dis. 2015 Mar 15;211(6):936-46. doi: 10.1093/infdis/jiu534. Epub 2014 Sep 23.

9.

Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the β' subunit of RNA polymerase.

Song T, Park Y, Shamputa IC, Seo S, Lee SY, Jeon HS, Choi H, Lee M, Glynne RJ, Barnes SW, Walker JR, Batalov S, Yusim K, Feng S, Tung CS, Theiler J, Via LE, Boshoff HI, Murakami KS, Korber B, Barry CE 3rd, Cho SN.

Mol Microbiol. 2014 Mar;91(6):1106-19. doi: 10.1111/mmi.12520. Epub 2014 Feb 26.

10.

Hepatitis C genotype 1 mosaic vaccines are immunogenic in mice and induce stronger T-cell responses than natural strains.

Yusim K, Dilan R, Borducchi E, Stanley K, Giorgi E, Fischer W, Theiler J, Marcotrigiano J, Korber B, Barouch DH.

Clin Vaccine Immunol. 2013 Feb;20(2):302-5. doi: 10.1128/CVI.00605-12. Epub 2012 Dec 5.

11.

Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage.

Fenimore PW, Muhammad MA, Fischer WM, Foley BT, Bakken RR, Thurmond JR, Yusim K, Yoon H, Parker M, Hart MK, Dye JM, Korber B, Kuiken C.

PLoS One. 2012;7(10):e44769. doi: 10.1371/journal.pone.0044769. Epub 2012 Oct 3.

12.

Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing.

Ford C, Yusim K, Ioerger T, Feng S, Chase M, Greene M, Korber B, Fortune S.

Tuberculosis (Edinb). 2012 May;92(3):194-201. doi: 10.1016/j.tube.2011.11.003. Epub 2012 Jan 3.

13.

Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.

Yusim K, Fischer W, Yoon H, Thurmond J, Fenimore PW, Lauer G, Korber B, Kuiken C.

J Gen Virol. 2010 May;91(Pt 5):1194-206. doi: 10.1099/vir.0.017491-0. Epub 2010 Jan 6.

PMID:
20053820
14.

Web-based design and evaluation of T-cell vaccine candidates.

Thurmond J, Yoon H, Kuiken C, Yusim K, Perkins S, Theiler J, Bhattacharya T, Korber B, Fischer W.

Bioinformatics. 2008 Jul 15;24(14):1639-40. doi: 10.1093/bioinformatics/btn251. Epub 2008 May 29.

PMID:
18515277
15.

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients.

Goepfert PA, Lumm W, Farmer P, Matthews P, Prendergast A, Carlson JM, Derdeyn CA, Tang J, Kaslow RA, Bansal A, Yusim K, Heckerman D, Mulenga J, Allen S, Goulder PJ, Hunter E.

J Exp Med. 2008 May 12;205(5):1009-17. doi: 10.1084/jem.20072457. Epub 2008 Apr 21.

16.

Immunological control of chronic HIV-1 infection: HLA-mediated immune function and viral evolution in adolescents.

Bansal A, Yue L, Conway J, Yusim K, Tang J, Kappes J, Kaslow RA, Wilson CM, Goepfert PA.

AIDS. 2007 Nov 30;21(18):2387-97.

17.

The hepatitis C sequence database in Los Alamos.

Kuiken C, Hraber P, Thurmond J, Yusim K.

Nucleic Acids Res. 2008 Jan;36(Database issue):D512-6. Epub 2007 Nov 19.

18.

Increased sequence diversity coverage improves detection of HIV-specific T cell responses.

Frahm N, Kaufmann DE, Yusim K, Muldoon M, Kesmir C, Linde CH, Fischer W, Allen TM, Li B, McMahon BH, Faircloth KL, Hewitt HS, Mackey EW, Miura T, Khatri A, Wolinsky S, McMichael A, Funkhouser RK, Walker BD, Brander C, Korber BT.

J Immunol. 2007 Nov 15;179(10):6638-50.

19.

Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection.

Hraber P, Kuiken C, Yusim K.

Hepatology. 2007 Dec;46(6):1713-21.

PMID:
17935228
21.

Extensive HLA class I allele promiscuity among viral CTL epitopes.

Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, Hraber P, Hewitt HS, Linde CH, Kavanagh DG, Woodberry T, Henry LM, Faircloth K, Listgarten J, Kadie C, Jojic N, Sango K, Brown NV, Pae E, Zaman MT, Bihl F, Khatri A, John M, Mallal S, Marincola FM, Walker BD, Sette A, Heckerman D, Korber BT, Brander C.

Eur J Immunol. 2007 Sep;37(9):2419-33.

22.

Los Alamos hepatitis C virus sequence and human immunology databases: an expanding resource for antiviral research.

Hraber PT, Leach RW, Reilly LP, Thurmond J, Yusim K, Kuiken C; Los Alamos HIV database team.

Antivir Chem Chemother. 2007;18(3):113-23. Erratum in: Antivir Chem Chemother. 2007;18(4):243.

PMID:
17626595
23.

Founder effects in the assessment of HIV polymorphisms and HLA allele associations.

Bhattacharya T, Daniels M, Heckerman D, Foley B, Frahm N, Kadie C, Carlson J, Yusim K, McMahon B, Gaschen B, Mallal S, Mullins JI, Nickle DC, Herbeck J, Rousseau C, Learn GH, Miura T, Brander C, Walker B, Korber B.

Science. 2007 Mar 16;315(5818):1583-6.

24.

Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants.

Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, Hahn BH, Korber BT.

Nat Med. 2007 Jan;13(1):100-6. Epub 2006 Dec 24.

PMID:
17187074
25.

A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes.

Kuiken C, Combet C, Bukh J, Shin-I T, Deleage G, Mizokami M, Richardson R, Sablon E, Yusim K, Pawlotsky JM, Simmonds P; Los Alamos HIV Database Group.

Hepatology. 2006 Nov;44(5):1355-61. No abstract available.

PMID:
17058236
26.

Immunoinformatics comes of age.

Korber B, LaBute M, Yusim K.

PLoS Comput Biol. 2006 Jun 30;2(6):e71. Review.

27.
28.

Hepatitis C databases, principles and utility to researchers.

Kuiken C, Mizokami M, Deleage G, Yusim K, Penin F, Shin-I T, Charavay C, Tao N, Crisan D, Grando D, Dalwani A, Geourjon C, Agrawal A, Combet C.

Hepatology. 2006 May;43(5):1157-65.

PMID:
16628639
29.

Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses.

Bihl F, Frahm N, Di Giammarino L, Sidney J, John M, Yusim K, Woodberry T, Sango K, Hewitt HS, Henry L, Linde CH, Chisholm JV 3rd, Zaman TM, Pae E, Mallal S, Walker BD, Sette A, Korber BT, Heckerman D, Brander C.

J Immunol. 2006 Apr 1;176(7):4094-101.

30.

Los alamos hepatitis C immunology database.

Yusim K, Richardson R, Tao N, Dalwani A, Agrawal A, Szinger J, Funkhouser R, Korber B, Kuiken C.

Appl Bioinformatics. 2005;4(4):217-25.

PMID:
16309340
31.

Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA.

Leslie A, Kavanagh D, Honeyborne I, Pfafferott K, Edwards C, Pillay T, Hilton L, Thobakgale C, Ramduth D, Draenert R, Le Gall S, Luzzi G, Edwards A, Brander C, Sewell AK, Moore S, Mullins J, Moore C, Mallal S, Bhardwaj N, Yusim K, Phillips R, Klenerman P, Korber B, Kiepiela P, Walker B, Goulder P.

J Exp Med. 2005 Mar 21;201(6):891-902.

32.

CD8 T-cell responses in early HIV-1 infection are skewed towards high entropy peptides.

Bansal A, Gough E, Sabbaj S, Ritter D, Yusim K, Sfakianos G, Aldrovandi G, Kaslow RA, Wilson CM, Mulligan MJ, Kilby JM, Goepfert PA.

AIDS. 2005 Feb 18;19(3):241-50.

PMID:
15718834
33.

The Los Alamos hepatitis C sequence database.

Kuiken C, Yusim K, Boykin L, Richardson R.

Bioinformatics. 2005 Feb 1;21(3):379-84. Epub 2004 Sep 17.

PMID:
15377502
34.

Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities.

Frahm N, Korber BT, Adams CM, Szinger JJ, Draenert R, Addo MM, Feeney ME, Yusim K, Sango K, Brown NV, SenGupta D, Piechocka-Trocha A, Simonis T, Marincola FM, Wurcel AG, Stone DR, Russell CJ, Adolf P, Cohen D, Roach T, StJohn A, Khatri A, Davis K, Mullins J, Goulder PJ, Walker BD, Brander C.

J Virol. 2004 Mar;78(5):2187-200.

35.

Liver transplantation with hepatitis C virus-infected graft: interaction between donor and recipient viral strains.

Fan X, Lang DM, Xu Y, Lyra AC, Yusim K, Everhart JE, Korber BT, Perelson AS, Di Bisceglie AM.

Hepatology. 2003 Jul;38(1):25-33.

PMID:
12829983
36.

Evolution of hepatitis C viral quasispecies after liver transplantation.

Lyra AC, Fan X, Lang DM, Yusim K, Ramrakhiani S, Brunt EM, Korber B, Perelson AS, Di Bisceglie AM.

Gastroenterology. 2002 Nov;123(5):1485-93.

PMID:
12404223
37.

Optimal antigens for HIV vaccines based on CD8+ T response, protein length, and sequence variability.

Betts MR, Yusim K, Koup RA.

DNA Cell Biol. 2002 Sep;21(9):665-70.

PMID:
12396609
38.

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.

Yusim K, Kesmir C, Gaschen B, Addo MM, Altfeld M, Brunak S, Chigaev A, Detours V, Korber BT.

J Virol. 2002 Sep;76(17):8757-68.

39.

Diversity considerations in HIV-1 vaccine selection.

Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B, Hahn BH, Bhattacharya T, Korber B.

Science. 2002 Jun 28;296(5577):2354-60. Review.

PMID:
12089434
40.

One-vesicle hypothesis for neurotransmitter release: a possible molecular mechanism.

Yusim K, Parnas H, Segel LA.

Bull Math Biol. 2001 Nov;63(6):1025-40.

PMID:
11732174
41.

Evolutionary and immunological implications of contemporary HIV-1 variation.

Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V.

Br Med Bull. 2001;58:19-42. Review.

PMID:
11714622
42.

Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution.

Yusim K, Peeters M, Pybus OG, Bhattacharya T, Delaporte E, Mulanga C, Muldoon M, Theiler J, Korber B.

Philos Trans R Soc Lond B Biol Sci. 2001 Jun 29;356(1410):855-66. Review.

43.

A model for proto-tRNA loading.

Yusim K, Nir S, Lahav N.

J Theor Biol. 2001 Jan 7;208(1):109-16.

PMID:
11162056
44.

Theory for the feedback inhibition of fast release of neurotransmitter.

Yusim K, Parnas H, Segel LA.

Bull Math Biol. 2000 Jul;62(4):717-57.

PMID:
10938630

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