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Vaccine Research Center Journal Publications, 2008

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Gating-ML: XML-based gating descriptions in flow cytometry.
Spidlen J, Leif RC, Moore W, Roederer M; International Society for the Advancement of Cytometry Data Standards Task Force, Brinkman RR.
Cytometry A. 2008 Dec;73A(12):1151-7.

Journal of Infectious Diseases
Early depletion of Mycobacterium tuberculosis-specific T helper 1 cell responses after HIV-1 infection.
Geldmacher C, Schuetz A, Ngwenyama N, Casazza JP, Sanga E, Saathoff E, Boehme C, Geis S, Maboko L, Singh M, Minja F, Meyerhans A, Koup RA, Hoelscher M.
J Infect Dis. 2008 Dec 1;198(11):1590-8.

Journal of Immunology
TCR beta-chain sharing in human CD8+ T cell responses to cytomegalovirus and EBV.
Venturi V, Chin HY, Asher TE, Ladell K, Scheinberg P, Bornstein E, van Bockel D, Kelleher AD, Douek DC, Price DA, Davenport MP.
J Immunol. 2008 Dec 1;181(11):7853-62.

Nucleic Acids Research
The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA.
Keating CP, Hill MK, Hawkes DJ, Smyth RP, Isel C, Le SY, Palmenberg AC, Marshall JA, Marquet R, Nabel GJ, Mak J.
Nucleic Acids Res. 2008 Dec 23.

Journal of Virology
Expanded Breadth of the T-cell Response to Mosaic HIV-1 Envelope DNA Vaccination.
Kong WP, Wu L, Wallstrom TC, Fischer W, Yang ZY, Ko SY, Letvin N, Haynes BF, Hahn B, Korber B, Nabel GJ.
J Virol. 2008 Dec 24.

Journal of Virology
Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C.
Binley JM, Lybarger EA, Crooks ET, Seaman MS, Gray E, Davis KL, Decker JM, Wycuff D, Harris L, Hawkins N, Wood B, Nathe C, Richman D, Tomaras GD, Bibollet-Ruche F, Robinson JE, Morris L, Shaw GM, Montefiori DC, Mascola JR.
J Virol. 2008 Dec;82(23):11651-68.

Journal of Immunology
Cutting edge: Experimentally induced immune activation in natural hosts of simian immunodeficiency virus induces significant increases in viral replication and CD4+ T cell depletion.
Pandrea I, Gaufin T, Brenchley JM, Gautam R, Monjure C, Gautam A, Coleman C, Lackner AA, Ribeiro RM, Douek DC, Apetrei C.
J Immunol. 2008 Nov 15;181(10):6687-91.

Journal of Virology
HIV-1 Env-trimer immunization of macaques and impact of priming with viral vector or stabilized core protein.
Mörner A, Douagi I, Forsell MN, Sundling C, Dosenovic P, O'dell S, Dey B, Kwong PD, Voss G, Thorstensson R, Mascola JR, Wyatt RT, Karlsson Hedestam GB.
J Virol. 2008 Nov 12.

Journal of Virology
Analysis of the Neutralization Specificities in Polyclonal Sera Derived from Human Immunodeficiency Virus Type-1 Infected Individuals.
Li Y, Svehla K, Louder MK, Wycuff D, Phogat S, Tang M, Migueles SA, Wu X, Phogat A, Shaw GM, Connors M, Hoxie J, Mascola JR, Wyatt R.
J Virol. 2008 Nov 12.

Small-molecule CD4 mimics interact with a highly conserved pocket on HIV-1 gp120.
Madani N, Schön A;Princiotto AM, Lalonde JM, Courter JR, Soeta T, Ng D, Wang L, Brower ET, Xiang SH, Do Kwon Y, Huang CC, Wyatt R, Kwong PD, Freire E, Smith AB 3rd, Sodroski J.
Structure. 2008 Nov 12;16(11):1689-701.

High avidity myeloid leukemia-associated antigen-specific CD8+ T cells preferentially reside in the bone marrow.
Melenhorst JJ, Scheinberg P, Chattopadhyay PK, Gostick E, Ladell K, Roederer M, Hensel NF, Douek DC, Barrett AJ, Price DA.
Blood. 2008 Nov 7.

Journal of Virology
Enhanced induction of intestinal cellular immunity by oral priming with enteric adenovirus 41 vectors.
Ko SY, Cheng C, Kong WP, Wang L, Kanekiyo M, Einfeld D, King CR, Gall JG, Nabel GJ.
J Virol. 2008 Nov 5.

Cytometry A
Measuring antigen-specific immune responses, 2008 update.
Gratama JW, Kern F, Manca F, Roederer M.
Cytometry A. 2008 Nov;73(11):971-4.

Cytometry A
Techniques to improve the direct ex vivo detection of low frequency antigen-specific CD8+ T cells with peptide-major histocompatibility complex class I tetramers.
Chattopadhyay PK, Melenhorst JJ, Ladell K, Gostick E, Scheinberg P, Barrett AJ, Wooldridge L, Roederer M, Sewell AK, Price DA.
Cytometry A. 2008 Nov;73(11):1001-9.

Cytometry A
Phenotype and function of human T lymphocyte subsets: consensus and issues.
Appay V, van Lier RA, Sallusto F, Roederer M.
Cytometry A. 2008 Nov;73(11):975-83.

Cytometry A
Optimizing peptide matrices for identifying T-cell antigens.
Precopio ML, Butterfield TR, Casazza JP, Little SJ, Richman DD, Koup RA, Roederer M.
Cytometry A. 2008 Nov;73(11):1071-8.

Journal of Virology
Antiretroviral therapy prior to acute viral replication preserves CD4 T cells in the periphery but not in rectal mucosa during acute simian immunodeficiency virus infection.
Kader M, Hassan WM, Eberly M, Piatak M, Lifson JD, Roederer M, Mattapallil JJ.
J Virol. 2008 Nov;82(22):11467-71.

Journal of American Association of Lab Animal Sciences
Efficacy and safety of five injectable anesthetic regimens for chronic blood collection from the anterior vena cava of Guinea pigs.
Dang V, Bao S, Ault A, Murray C, McFarlane-Mills J, Chiedi C, Dillon M, Todd JP, Detolla L, Rao S.
J Am Assoc Lab Anim Sci. 2008 Nov;47(6):56-60.


Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections.
Brenchley JM, Paiardini M, Knox KS, Asher AI, Cervasi B, Asher TE, Scheinberg P, Price DA, Hage CA, Kholi LM, Khoruts A, Frank I, Else J, Schacker T, Silvestri G, Douek DC.
Blood. 2008 Oct 1;112(7):2826-35.

Journal of Molecular Biology
Combinatorial optimization of a CD4-mimetic miniprotein and cocrystal structures with HIV-1 gp120 envelope glycoprotein.
Stricher F, Huang CC, Descours A, Duquesnoy S, Combes O, Decker JM, Kwon YD, Lusso P, Shaw GM, Vita C, Kwong PD, Martin L.
J Mol Biol. 2008 Oct 3;382(2):510-24.

PLOS Pathogens
B cell recognition of the conserved HIV-1 co-receptor binding site is altered by endogenous primate CD4.
Forsell MN, Dey B, Mörner A, Svehla K, O'dell S, Högerkorp CM, Voss G, Thorstensson R, Shaw GM, Mascola JR, Karlsson Hedestam GB, Wyatt RT.
PLoS Pathog. 2008 Oct 3;4(10):e1000171.

Bioorganic and Medicinal Chemistry
Tyrosine-sulfate isosteres of CCR5 N-terminus as tools for studying HIV-1 entry.
Lam SN, Acharya P, Wyatt R, Kwong PD, Bewley CA.
Bioorg Med Chem. 2008 Oct 5.

Anti-HIV-1 response elicited in rabbits by anti-idiotype monoclonal antibodies mimicking the CD4-binding site.
Burioni R, Mancini N, De Marco D, Clementi N, Perotti M, Nitti G, Sassi M, Canducci F, Shvela K, Bagnarelli P, Mascola JR, Clementi M.
PLoS ONE. 2008 Oct 16;3(10):e3423.

Journal of Virology
Frequency and Phenotype of HIV Envelope-specific B Cells From Patients With Broadly Cross-Neutralizing Antibodies.
Doria-Rose NA, Klein RM, Manion MM, O'Dell S, Phogat A, Chakrabarti B, Hallahan CW, Migueles SA, Wrammert J, Ahmed R, Nason M, Wyatt RT, Mascola JR, Connors M.
J Virol. 2008 Oct 15.

Journal of Immunology
T cell responses to whole SARS coronavirus in humans.
Li CK, Wu H, Yan H, Ma S, Wang L, Zhang M, Tang X, Temperton NJ, Weiss RA, Brenchley JM, Douek DC, Mongkolsapaya J, Tran BH, Lin CL, Screaton GR, Hou JL, McMichael AJ, Xu XN.
J Immunol. 2008 Oct 15;181(8):5490-500.

Annual Review of Medicine
Emerging Concepts in the Immunopathogenesis of AIDS.
Douek DC, Roederer M, Koup RA.
Annu Rev Med. 2008 Oct 23.


Cytometry A.
Optimizing peptide matrices for identifying T-cell antigens.
Precopio ML, Butterfield TR, Casazza JP, Little SJ, Richman DD, Koup RA, Roederer M.
Cytometry A. 2008 Sep 9.

Generation of functionally active HIV-1 specific CD8(+) CTL in intestinal mucosa following mucosal, systemic or mixed prime-boost immunization.
Belyakov IM, Ahlers JD, Nabel GJ, Moss B, Berzofsky JA.
Virology. 2008 Sep 13.

Soluble CD4 broadens neutralization of V3-directed monoclonal antibodies and guinea pig vaccine sera against HIV-1 subtype B and C reference viruses.
Wu X, Sambor A, Nason MC, Yang ZY, Wu L, Zolla-Pazner S, Nabel GJ, Mascola JR.
Virology. 2008 Sep 17.

Journal of Immunological Methods
Detection of low avidity CD8(+) T cell populations with coreceptor-enhanced peptide-major histocompatibility complex class I tetramers.
Melenhorst JJ, Scheinberg P, Chattopadhyay PK, Lissina A, Gostick E, Cole DK, Wooldridge L, van den Berg HA, Bornstein E, Hensel NF, Douek DC, Roederer M, Sewell AK, Barrett AJ, Price DA.
J Immunol Methods. 2008 Sep 30;338(1-2):31-9.

Journal of Immunology
Potent simian immunodeficiency virus-specific cellular immune responses in the breast milk of simian immunodeficiency virus-infected, lactating rhesus monkeys.
Permar SR, Kang HH, Carville A, Mansfield KG, Gelman RS, Rao SS, Whitney JB, Letvin NL.
J Immunol. 2008 Sep 1;181(5):3643-50.


Journal of Immunology
Venturi V, Chin HY, Price DA, Douek DC, Davenport MP.
The role of production frequency in the sharing of simian immunodeficiency virus-specific CD8+ TCRs between macaques.
J Immunol. 2008 Aug 15;181(4):2597-609.

Journal of Infectious Disease
Estes J, Baker JV, Brenchley JM, Khoruts A, Barthold JL, Bantle A, Reilly CS, Beilman GJ, George ME, Douek DC, Haase AT, Schacker TW.
Collagen deposition limits immune reconstitution in the gut.
J Infect Dis. 2008 Aug 15;198(4):456-64.


Journal of Molecular Biology
Combinatorial Optimization of a CD4-Mimetic Miniprotein and Cocrystal Structures with HIV-1 gp120 Envelope Glycoprotein.
Stricher F, Huang CC, Descours A, Duquesnoy S, Combes O, Decker JM, Do Kwon Y, Lusso P, Shaw GM, Vita C, Kwong PD, Martin L.
J Mol Biol. 2008 Jul 1.

Proceedings of the national Academy of Sciences
A centralized gene-based HIV-1 vaccine elicits broad cross-clade cellular immune responses in rhesus monkeys.
Santra S, Korber BT, Muldoon M, Barouch DH, Nabel GJ, Gao F, Hahn BH, Haynes BF, Letvin NL.


Nature - Medicine
CD8+ T cell efficacy in vaccination and disease.
Appay V, Douek DC, Price DA.
Nat Med. 2008 Jun;14(6):623-8.

Journal of Leukocyte Biology
Pulmonary eosinophilia requires interleukin-5, eotaxin-1, and CD4+ T cells in mice immunized with respiratory syncytial virus G glycoprotein.
Johnson TR, Rothenberg ME, Graham BS.
J Leukoc Biol. 2008 Jun 2. [Epub ahead of print]

Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza in Chickens and Mice.
Rao SS, Kong WP, Wei CJ, Yang ZY, Nason M, Styles D, DeTolla LJ, Sorrell EM, Song H, Wan H, Ramirez-Nieto GC, Perez D, Nabel GJ.
PLoS One. 2008 Jun; 3(6): e2432.


Public Library of Sciences - Pathogens
Maturation of West Nile virus modulates sensitivity to antibody-mediated neutralization.
Nelson S, Jost CA, Xu Q, Ess J, Martin JE, Oliphant T, Whitehead SS, Durbin AP, Graham BS, Diamond MS, Pierson TC.
PLoS Pathog. 2008 May 9;4(5):e1000060.

Journal of Virology
Cross-Reactive Human Immunodeficiency Virus Type 1- Neutralizing Human Monoclonal Antibody which Recognizes A Novel Conformational Epitope on gp41 and Lacks Reactivity against Self Antigens.
Zhang MY, Vu BK, Choudhary A, Lu H, Humbert M, Ong H, Alam M, Ruprecht RM, Quinnan G, Jiang S, Montefiori DC, Mascola JR, Broder CC, Haynes BF, Dimitrov DS.
J Virol. 2008 May 14. [Epub ahead of print]

Cell Host Microbe
HIV-1 assembly: viral glycoproteins segregate quantally to lipid rafts that associate individually with HIV-1 capsids and virions.
Leung K, Kim JO, Ganesh L, Kabat J, Schwartz O, Nabel GJ.
Cell Host Microbe. 2008 May 15;3(5):285-92.

Journal of Immunology
Contribution of TCR-beta locus and HLA to the shape of the mature human Vbeta repertoire.
Melenhorst JJ, Lay MD, Price DA, Adams SD, Zeilah J, Sosa E, Hensel NF, Follmann D, Douek DC, Davenport MP, Barrett AJ.
J Immunol. 2008 May 15;180(10):6484-9.

Journal of Virology
Limited maintenance of vaccine-induced SIV-specific CD8 T cell receptor clonotypes after virus challenge.
Smith MZ, Asher TE, Venturi V, Davenport MP, Douek DC, Price DA, Kent SJ.
J Virol. 2008 May 28. [Epub ahead of print]


Journal of Virology
Virological outcome after structured interruption of antiretroviral therapy for human immunodeficiency virus infection is associated with the functional profile of virus-specific CD8+ T cells.
Daucher M, Price DA, Brenchley JM, Lamoreaux L, Metcalf JA, Rehm C, Nies-Kraske E, Urban E, Yoder C, Rock D, Gumkowski J, Betts MR, Dybul MR, Douek DC.
J Virol. 2008 Apr;82(8):4102-14. Epub 2008 Jan 30.

Journal of Immunology
Immune activation driven by ctla-4 blockade augments viral replication at mucosal sites in simian immunodeficiency virus infection.
Cecchinato V, Tryniszewska E, Ma ZM, Vaccari M, Boasso A, Tsai WP, Petrovas C, Fuchs D, Heraud JM, Venzon D, Shearer GM, Koup RA, Lowy I, Miller CJ, Franchini G.
J Immunol. 2008 Apr 15;180(8):5439-47.

Journal of Immunology
CD127 and CD25 Expression Defines CD4+ T Cell Subsets That Are Differentially Depleted during HIV Infection.
Dunham RM, Cervasi B, Brenchley JM, Albrecht H, Weintrob A, Sumpter B, Engram J, Gordon S, Klatt NR, Frank I, Sodora DL, Douek DC, Paiardini M, Silvestri G.
J Immunol. 2008 Apr 15;180(8):5582-92.

Journal of Virology
Comparative Efficacy of Neutralizing Antibodies Elicited by Recombinant Hemagglutinin Proteins from Avian H5N1 Influenza Virus.
Wei CJ, Xu L, Kong WP, Shi W, Canis K, Stevens J, Yang ZY, Dell A, Haslam SM, Wilson IA, Nabel GJ.
J Virol. 2008 Apr 16.

Journal of Virology
A Filovirus-unique Region of Ebola Virus Nucleoprotein Confers Aberrant Migration and Mediates Its Incorporation into Virions.
Shi W, Huang Y, Sutton-Smith M, Tissot B, Panico M, Morris HR, Dell A, Haslam SM, Boyington J, Graham BS, Yang ZY, Nabel GJ.
J Virol. 2008 Apr 16.

Current Opinion in HIV/AIDS
Mucosa and vaccine-induced immune protection in nonhuman primates.
Joseph J. Mattapallil and Mario Roederer
Current Opinion in HIV/AIDS 3(3):387-392.
*Currently no link


Cytometry Part A, Journal of International Society for Analytical Cytometry
How many events is enough? Are you positive?
Roederer M.
Cytometry A.M. 2008 Feb 28.

Nature Review - Immunology
T-cell quality in memory and protection: implications for vaccine design.
Seder RA, Darrah PA, Roederer M.
Nat Rev Immunol. 2008 Apr;8(4):247-58. Epub 2008 Mar 7.

Cytometry Part A, Journal of International Society for Analytical Cytometry
Nine color flow cytometry for accurate measurement of T cell subsets and cytokine responses. Part I: Panel design by an empiric approach.
McLaughlin BE, Baumgarth N, Bigos M, Roederer M, De Rosa SC, Altman JD, Nixon DF, Ottinger J, Oxford C, Evans TG, Asmuth DM.
Cytometry A. 2008 Mar 27.

Cytometry Part A, Journal of International Society for Analytical Cytometry
Nine-color flow cytometry for accurate measurement of T cell subsets and cytokine responses. Part II: Panel performance across different instrument platforms.
McLaughlin BE, Baumgarth N, Bigos M, Roederer M, De Rosa SC, Altman JD, Nixon DF, Ottinger J, Oxford C, Evans TG, Asmuth DM.
Cytometry A. 2008 Mar 27.

Nature Review - Immunology
The molecular basis for public T-cell responses?
Venturi V, Price DA, Douek DC, Davenport MP.
Nat Rev Immunol. 2008 Mar;8(3):231-8. Review.

Impaired T(H)17 cell differentiation in subjects with autosomal dominant hyper-IgE syndrome.
Milner JD, Brenchley JM, Laurence A, Freeman AF, Hill BJ, Elias KM, Kanno Y, Spalding C, Elloumi HZ, Paulson ML, Davis J, Hsu A, Asher AI, O'Shea J, Holland SM, Paul WE, Douek DC.
Nature. 2008 Mar 12.

Regulatory T-cell depletion does not prevent emergence of new CD25+ FOXP3+ lymphocytes after antigen stimulation in culture.
Melenhorst JJ, Scheinberg P, Lu J, Ambrozak DR, Sosa E, Zhao L, Hensel NF, Savani BN, Douek DC, Price DA, Barrett AJ.
Cytotherapy. 2008;10(2):152-64.


February European Journal of Immunology
Polyfunctional T cell responses are a hallmark of HIV-2 infection.
Duvall MG, Precopio ML, Ambrozak DA, Jaye A, McMichael AJ, Whittle HC, Roederer M, Rowland-Jones SL, Koup RA.
Eur J Immunol. 2008 Feb;38(2):350-63.M

Nature Immunology
The challenges of eliciting neutralizing antibodies to HIV-1 and to influenza virus.
Karlsson Hedestam GB, Fouchier RA, Phogat S, Burton DR, Sodroski J, Wyatt RT.
Nat Rev Microbiol. 2008 Feb;6(2):143-55. Review.

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Last Updated March 10, 2009