Journal Publications, 2013
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April
eLIFE
Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.
Sun S, Xiang Y, Akahata W, Holdaway H, Pal P, Zhang X, Diamond MS, Nabel GJ, Rossmann MG.
Elife. 2013;2:e00435. doi: 10.7554/eLife.00435. Epub 2013 Apr 2.
Journal of Infectious Diseases
The Phenotype of the Cryptococcus-Specific CD4+ Memory T-Cell Response Is Associated With Disease Severity and Outcome in HIV-Associated Cryptococcal Meningitis.
Jarvis JN, Casazza JP, Stone HH, Meintjes G, Lawn SD, Levitz SM, Harrison TS, Koup RA.
J Infect Dis. 2013 Apr 3. [Epub ahead of print]
Nature
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.
Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF.
Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3.
Public Library of Science One
DNA Vaccine Delivered by a Needle-Free Injection Device Improves Potency of Priming for Antibody and CD8+ T-Cell Responses after rAd5 Boost in a Randomized Clinical Trial.
Graham BS, Enama ME, Nason MC, Gordon IJ, Peel SA, Ledgerwood JE, Plummer SA, Mascola JR, Bailer RT, Roederer M, Koup RA, Nabel GJ; VRC 008 Study Team.
PLoS One. 2013;8(4):e59340. doi: 10.1371/journal.pone.0059340. Epub 2013 Apr 8.
Journal of Infectious Diseases
Therapeutic Vaccination Expands and Improves the Function of the HIV-Specific Memory T-Cell Repertoire.
Casazza JP, Bowman KA, Adzaku S, Smith EC, Enama ME, Bailer RT, Price DA, Gostick E, Gordon IJ, Ambrozak DR, Nason MC, Roederer M, Andrews CA, Maldarelli FM, Wiegand A, Kearney MF, Persaud D, Ziemniak C, Gottardo R, Ledgerwood JE, Graham BS, Koup RA; the VRC 101 Study Team.
J Infect Dis. 2013 Apr 11. [Epub ahead of print]
Journal of Virology
Suppressed Th17 Levels Correlate with Elevated PIAS3, SHP2, and SOCS3 Expression in CD4 T cells During Acute Simian Immunodeficiency Virus Infection.
Bixler SL, Sandler NG, Douek DC, Mattapallil JJ.
J Virol. 2013 Apr 17. [Epub ahead of print]
Vaccine
Strategic priorities for respiratory syncytial virus (RSV) vaccine development.
Anderson LJ, Dormitzer PR, Nokes DJ, Rappuoli R, Roca A, Graham BS.
Vaccine. 2013 Apr 18;31 Suppl 2:B209-15. doi: 10.1016/j.vaccine.2012.11.106.
Vaccine
The need and challenges for development of an Epstein-Barr virus vaccine.
Cohen JI, Mocarski ES, Raab-Traub N, Corey L, Nabel GJ.
Vaccine. 2013 Apr 18;31 Suppl 2:B194-6. doi: 10.1016/j.vaccine.2012.09.041.
Vaccine
Report of the Cent Gardes HIV Vaccine Conference: The B-cell response to HIV Part 2: Non-neutralizing antibodies: Fondation Mérieux Conference Center, Veyrier du Lac, France 5-7 November 2012.
Girard MP, Picot V, Longuet C, Nabel GJ.
Vaccine. 2013 Apr 18. doi:pii: S0264-410X(13)00258-2. 10.1016/j.vaccine.2013.02.067. [Epub ahead of print]
Vaccine
Accelerating the development of a safe and effective HIV vaccine: HIV vaccine case study for the Decade of Vaccines.
Koff WC, Russell ND, Walport M, Feinberg MB, Shiver JW, Karim SA, Walker BD, McGlynn MG, Nweneka CV, Nabel GJ.
Vaccine. 2013 Apr 18;31 Suppl 2:B204-8. doi: 10.1016/j.vaccine.2012.10.115.
Journal of Virology
The Lack of Maturation of Ebola Virus-Infected Dendritic Cells Results from the Cooperative Effect of at Least Two Viral Domains.
Lubaki NM, Ilinykh P, Pietzsch C, Tigabu B, Freiberg AN, Koup RA, Bukreyev A.
J Virol. 2013 Apr 24. [Epub ahead of print]
Science
Structure of RSV Fusion Glycoprotein Trimer Bound to a Prefusion-Specific Neutralizing Antibody.
McLellan JS, Chen M, Leung S, Graepel KW, Du X, Yang Y, Zhou T, Baxa U, Yasuda E, Beaumont T, Kumar A, Modjarrad K, Zheng Z, Zhao M, Xia N, Kwong PD, Graham BS.
Science. 2013 Apr 25. [Epub ahead of print]
March
Journal of Acquired Immune Deficiency Syndromes
Neither microbial translocation nor TLR responsiveness are likely explanations for pre-existing immune activation in women who subsequently acquired HIV in CAPRISA004.
Naranbhai V, Samsunder N, Sandler NG, Roque A, Karim QA, Ndung'u T, Carr WH, Altfeld M, Douek DC, Abdool Karim SS; and The CAPRISA004 Trial Team.
J Acquir Immune Defic Syndr. 2013 Mar 11. [Epub ahead of print]
Journal of Infectious Diseases
Therapeutic Vaccination Expands and Improves the Function of the HIV-specific Memory T Cell Repertoire.
Casazza JP, Bowman K, Adzaku S, Smith EC, Enama ME, Bailer RT, Price DA, Gostick E, Gordon I, Ambrozak DR, Nason M, Roederer M, Andrews CA, Maldarelli FM, Wiegand A, Kearney MF, Persaud D, Ziemniak C, Gottardo R, Ledgerwood JE, Graham BS, Koup RA; The VRC 101 Study Team.
J Infect Dis. 2013 Mar 12. [Epub ahead of print]
Journal of Immunological Methods
Highly multiplexed quantitation of gene expression on single cells.
Dominguez MH, Chattopadhyay PK, Ma S, Lamoreaux L, McDavid A, Finak G, Gottardo R, Koup RA, Roederer M.
J Immunol Methods. 2013 Mar 13. doi:pii: S0022-1759(13)00090-2. 10.1016/j.jim.2013.03.002. [Epub ahead of print]
Vaccine
Report of the Cent Gardes HIV Vaccine Conference the B-cell Response to HIV. Part 1: Broadly Neutralizing Antibodies Fondation Mérieux Conference Center, Veyrier du Lac, France, 5-7 November 2012.
Girard MP, Picot V, Longuet C, Nabel GJ.
Vaccine. 2013 Mar 13. doi:pii: S0264-410X(13)00259-4. 10.1016/j.vaccine.2013.02.068. [Epub ahead of print]
Journal of Infectious Diseases
The Phenotype of the Cryptococcus-specific CD4 Memory T-cell Response is Associated with Disease Severity and Outcome in HIV-associated Cryptococcal Meningitis.
Jarvis JN, Casazza JP, Stone H, Meintjes G, Lawn SD, Levitz SM, Harrison TS, Koup RA.
J Infect Dis. 2013 Mar 14. [Epub ahead of print]
Journal of Immunology
Polyinosinic-Polycytidylic Acid Is the Most Effective TLR Adjuvant for SIV Gag Protein-Induced T Cell Responses In Nonhuman Primates.
Park H, Adamson L, Ha T, Mullen K, Hagen SI, Nogueron A, Sylwester AW, Axthelm MK, Legasse A, Piatak M Jr, Lifson JD, McElrath JM, Picker LJ, Seder RA.
J Immunol. 2013 Mar 15. [Epub ahead of print]
The Lancet Infectious Diseases
AS03-adjuvanted influenza vaccine in elderly people.
Ledgerwood JE.
Lancet Infect Dis. 2013 Mar 18. doi:pii: S1473-3099(13)70038-0. 10.1016/S1473-3099(13)70038-0. [Epub ahead of print] No abstract available.
Immunity
A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8(+) T Cells.
Ladell K, Hashimoto M, Iglesias MC, Wilmann PG, McLaren JE, Gras S, Chikata T, Kuse N, Fastenackels S, Gostick E, Bridgeman JS, Venturi V, Arkoub ZA, Agut H, van Bockel DJ, Almeida JR, Douek DC, Meyer L, Venet A, Takiguchi M, Rossjohn J, Price DA, Appay V.
Immunity. 2013 Mar 21;38(3):425-36. doi: 10.1016/j.immuni.2012.11.021.
Proceedings of the National Academy of Science USA
Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains.
Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, Parks R, Eudailey J, Lloyd KE, Blinn J, Alam SM, Haynes BF, Simek M, Burton DR, Koff WC; NISC Comparative Sequencing Program, Mullikin JC, Mascola JR, Shapiro L, Kwong PD.
Proc Natl Acad Sci U S A. 2013 Mar 27. [Epub ahead of print]
Cell
Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization.
Klein F, Diskin R, Scheid JF, Gaebler C, Mouquet H, Georgiev IS, Pancera M, Zhou T, Incesu RB, Fu BZ, Gnanapragasam PN, Oliveira TY, Seaman MS, Kwong PD, Bjorkman PJ, Nussenzweig MC.
Cell. 2013 Mar 28;153(1):126-38. doi: 10.1016/j.cell.2013.03.018.
February
Journal of Virology
Loss of a tyrosine-dependent trafficking motif in the simian immunodeficiency virus envelope cytoplasmic tail spares mucosal CD4 cells but does not prevent disease progression.
Breed MW, Jordan AP, Aye PP, Lichtveld CF, Midkiff CC, Schiro FR, Haggarty BS, Sugimoto C, Alvarez X, Sandler NG, Douek DC, Kuroda MJ, Pahar B, Piatak M Jr, Lifson JD, Keele BF, Hoxie JA, Lackner AA.
J Virol. 2013 Feb;87(3):1528-43. doi: 10.1128/JVI.01928-12. Epub 2012 Nov 14.
Cytometry A
Quantifying spillover spreading for comparing instrument performance and aiding in multicolor panel design.
Nguyen R, Perfetto S, Mahnke YD, Chattopadhyay P, Roederer M.
Cytometry A. 2013 Mar;83(3):306-15. doi: 10.1002/cyto.a.22251. Epub 2013 Feb 6.
Journal of Immunology
Comparative Analysis of the Magnitude, Quality, Phenotype, and Protective Capacity of Simian Immunodeficiency Virus Gag-Specific CD8+ T Cells following Human-, Simian-, and Chimpanzee-Derived Recombinant Adenoviral Vector Immunization.
Quinn KM, Da Costa A, Yamamoto A, Berry D, Lindsay RW, Darrah PA, Wang L, Cheng C, Kong WP, Gall JG, Nicosia A, Folgori A, Colloca S, Cortese R, Gostick E, Price DA, Gomez CE, Esteban M, Wyatt LS, Moss B, Morgan C, Roederer M, Bailer RT, Nabel GJ, Koup RA, Seder RA.
J Immunol. 2013 Feb 6. [Epub ahead of print]
New England Journal of Medicine
Designing tomorrow's vaccines.
Nabel GJ.
N Engl J Med. 2013 Feb 7;368(6):551-60. doi: 10.1056/NEJMra1204186. Review. No abstract available.
Public Library of Science One
N332-Directed Broadly Neutralizing Antibodies Use Diverse Modes of HIV-1 Recognition: Inferences from Heavy-Light Chain Complementation of Function.
Pancera M, Yang Y, Louder MK, Gorman J, Lu G, McLellan JS, Stuckey J, Zhu J, Burton DR, Koff WC, Mascola JR, Kwong PD.
PLoS One. 2013;8(2):e55701. doi: 10.1371/journal.pone.0055701. Epub 2013 Feb 19.
January
Journal of Clinical Investigation
Superior T memory stem cell persistence supports long-lived T cell memory.
Lugli E, Dominguez MH, Gattinoni L, Chattopadhyay PK, Bolton DL, Song K, Klatt NR, Brenchley JM, Vaccari M, Gostick E, Price DA, Waldmann TA, Restifo NP, Franchini G, Roederer M.
J Clin Invest. 2013 Jan 2. doi:pii: 66327. 10.1172/JCI66327. [Epub ahead of print]
Virology
Impact of viral attachment factor expression on antibody-mediated neutralization of flaviviruses.
Obara CJ, Dowd KA, Ledgerwood JE, Pierson TC.
Virology. 2013 Jan 9. doi:pii: S0042-6822(12)00589-2. 10.1016/j.virol.2012.11.016. [Epub ahead of print]
Immunity
Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2.
Liao HX, Bonsignori M, Alam SM, McLellan JS, Tomaras GD, Moody MA, Kozink DM, Hwang KK, Chen X, Tsao CY, Liu P, Lu X, Parks RJ, Montefiori DC, Ferrari G, Pollara J, Rao M, Peachman KK, Santra S, Letvin NL, Karasavvas N, Yang ZY, Dai K, Pancera M, Gorman J, Wiehe K, Nicely NI, Rerks-Ngarm S, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Sinangil F, Kim JH, Michael NL, Kepler TB, Kwong PD, Mascola JR, Nabel GJ, Pinter A, Zolla-Pazner S, Haynes BF.
Immunity. 2013 Jan 24;38(1):176-86. doi: 10.1016/j.immuni.2012.11.011. Epub 2013 Jan 11.
AIDS
Dendritic cell recruitment in response to skin antigen tests in HIV-1 infected individuals correlates with the level of T cell infiltration.
Liang F, Bond E, Sandgren KJ, Smed-Sörensen A, Rangaka MX, Lange C, Koup RA, McComsey GA, Lederman MM, Wilkinson RJ, Andersson J, Loré K.
AIDS. 2013 Jan 16. [Epub ahead of print]
Public Library of Science One
Analysis of V2 Antibody Responses Induced in Vaccinees in the ALVAC/AIDSVAX HIV-1 Vaccine Efficacy Trial.
Zolla-Pazner S, Decamp AC, Cardozo T, Karasavvas N, Gottardo R, Williams C, Morris DE, Tomaras G, Rao M, Billings E, Berman P, Shen X, Andrews C, O'Connell RJ, Ngauy V, Nitayaphan S, de Souza M, Korber B, Koup R, Bailer RT, Mascola JR, Pinter A, Montefiori D, Haynes BF, Robb ML, Rerks-Ngarm S, Michael NL, Gilbert PB, Kim JH.
PLoS One. 2013;8(1):e53629. doi: 10.1371/journal.pone.0053629. Epub 2013 Jan 17.
Bioinformatics
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.
McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, Roederer M, Gottardo R.
Bioinformatics. 2013 Jan 21. [Epub ahead of print]
Archives of Virology
Virus nomenclature below the species level: a standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae.
Kuhn JH, Bao Y, Bavari S, Becker S, Bradfute S, Brister JR, Bukreyev AA, Caì Y, Chandran K, Davey RA, Dolnik O, Dye JM, Enterlein S, Gonzalez JP, Formenty P, Freiberg AN, Hensley LE, Honko AN, Ignatyev GM, Jahrling PB, Johnson KM, Klenk HD, Kobinger G, Lackemeyer MG, Leroy EM, Lever MS, Lofts LL, Mühlberger E, Netesov SV, Olinger GG, Palacios G, Patterson JL, Paweska JT, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST.
Arch Virol. 2013 Jan 29. [Epub ahead of print]