2012-2013 Publications

Baker, C. M., W. A. Comrie, Y. M. Hyun, H. L. Chung, C. A. Fedorchuk, K. Lim, C. Brakebusch, J. L. McGrath, R. E. Waugh, M. Meier-Schellersheim, and M. Kim. 2012. Opposing roles for RhoH GTPase during T-cell migration and activation. Proceedings of The National Academy of Sciences of the United States of America 109:10474-10479.

Bello-Irizarry, S. N., J. Wang, K. Olsen, F. Gigliotti, and T. W. Wright. 2012. The Alveolar epithelial cell chemokine response to pneumocystis requires adaptor molecule MyD88 and interleukin-1 receptor but not toll-like receptor 2 or 4. Infection and immunity 80:39123920.

Butts, A., and D. J. Krysan. 2012. Antifungal drug discovery: something old and something new. PLoS pathogens 8:e1002870.

Chaves, F. A., A. H. Lee, J. L. Nayak, K. A. Richards, and A. J. Sant. 2012. The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. Journal of immunology (Baltimore, Md. : 1950) 188:4235-4248.

Davidson, D. C., M. P. Hirschman, A. Sun, M. V. Singh, K. Kasischke, and S. B. Maggirwar. 2012. Excess Soluble CD40L Contributes to Blood Brain Barrier Permeability In Vivo: Implications for HIV-Associated Neurocognitive Disorders. PloS one 7:e51793.

Gigliotti, F., and T. W. Wright. 2012. Pneumocystis: where does it live? PLoS pathogens 8:e1003025.

Kaminski, D. A., C. Wei, Y. Qian, A. F. Rosenberg, and I. Sanz. 2012. Advances in human B cell phenotypic profiling. Frontiers in immunology 3:302.

Keefer, M. C., J. Gilmour, P. Hayes, D. Gill, J. Kopycinski, H. Cheeseman, M. Cashin-Cox, M.
Naarding, L. Clark, N. Fernandez, C. A. Bunce, C. M. Hay, S. Welsh, W. Komaroff, L. Hachaambwa, T. Tarragona-Fiol, E. Sayeed, D. Zachariah, J. Ackland, K. Loughran, B. Barin, E. Cormier, J. H. Cox, P. Fast, and J. L. Excler. 2012. A phase I double blind, placebo controlled, randomized study of a multigenic HIV-1 adenovirus subtype 35 vector vaccine in healthy uninfected adults. PloS one 7:e41936.

Kennedy, S. D., R. Kierzek, and D. H. Turner. 2012. Novel conformation of an RNA structural
switch. Biochemistry 51:9257-9259.

Kim, B., L. A. Nguyen, W. Daddacha, and J. A. Hollenbaugh. 2012. Tight interplay among SAMHD1 protein level, cellular dNTP levels, and HIV-1 proviral DNA synthesis kinetics in human primary monocyte-derived macrophages. The Journal of biological chemistry 287:21570-21574.

Leddon, S. A., and A. J. Sant. 2012. The peptide specificity of the endogenous T follicular helper cell repertoire generated after protein immunization. PloS one 7:e46952.

Luque, A. E., R. Corales, R. J. Fowler, J. Dimarco, A. van Keken, P. Winters, M. C. Keefer, and K.
Fiscella. 2012. Bridging the Digital Divide in HIV Care: A Pilot Study of an iPod Personal Health Record. Journal of the International Association of Physicians in AIDS Care (Chicago, Ill. : 2002).

Mallari, A. O., T. M. Schwartz, A. E. Luque, P. S. Polashenski, S. M. Rauh, and R. B. Corales. 2012. Anal cancer screening in HIV-infected patients: is it time to screen them all?Diseases of the colon and rectum 55:1244-1250

Marker, D. F., J. M. Puccini, T. E. Mockus, J. Barbieri, S. M. Lu, and H. A. Gelbard. 2012. LRRK2 kinase inhibition prevents pathological microglial phagocytosis in response to HIV1 Tat protein. Journal of neuroinflammation 9:261.

Mock, D. J., J. A. Hollenbaugh, W. Daddacha, M. G. Overstreet, C. A. Lazarski, D. J. Fowell, and B.
Kim. 2012. Leishmania induces survival, proliferation and elevated cellular dNTP levels in human monocytes promoting acceleration of HIV co-infection. PLoS pathogens 8:e1002635.

Polesskaya, O., A. Sun, G. Salahura, J. N. Silva, S. Dewhurst, and K. Kasischke. 2012. Detection of microregional hypoxia in mouse cerebral cortex by two-photon imaging of endogenous NADH fluorescence. Journal of visualized experiments : JoVE.

Richards, M. S., and M. M. Doyley. 2012. Non-Rigid Image Registration Based Strain Estimator for Intravascular Ultrasound Elastography. Ultrasound in medicine & biology.

Salter, J. D., G. M. Lippa, I. A. Belashov, and J. E. Wedekind. 2012. Core-binding factor beta increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry 51:8702-8704.

Sant, A. J., and A. McMichael. 2012. Revealing the role of CD4(+) T cells in viral immunity. The
Journal of experimental medicine 209:1391-1395.

Schmidt, C., C. Smith, B. Barin, A. Bakhtyari, P. A. Bart, L. G. Bekker, E. Chomba, N. Clumeck, D.
Ho, A. Hoosen, W. Jaoko, P. Kaleebu, E. Karita, M. C. Keefer, J. van Lunzen, A. McMichael, S.
Mehendale, B. Peters, V. D. Ramanathan, A. Robinson, J. Rockstroh, E. Vardas, E. Vets, J.
Weber, B. S. Graham, S. Than, J. L. Excler, S. Kochhar, M. Ho, A. Heald, and P. E. Fast. 2012.
Background morbidity in HIV vaccine trial participants from various geographic regions as assessed by unsolicited adverse events. Human vaccines & immunotherapeutics 8:630-638.

Seetin, M. G., and D. H. Mathews. 2012. RNA structure prediction: an overview of methods.
Methods in molecular biology (Clifton, N.J.) 905:99-122.

Seetin, M. G., and D. H. Mathews. 2012. TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinformatics (Oxford, England) 28:792-798.

Silva, J., O. Polesskaya, W. Knight, J. T. Zheng, M. Granger, T. Lopez, F. Ontiveros, C. Feng, C.
Yan, K. A. Kasischke, and S. Dewhurst. 2012. Transient hypercapnia reveals an underlying
cerebrovascular pathology in a murine model for HIV-1 associated neuroinflammation: role of NO
cGMP signaling and normalization by inhibition of cyclic nucleotide phosphodiesterase-5. Journal of neuroinflammation 9:253.

St Gelais, C., S. de Silva, S. M. Amie, C. M. Coleman, H. Hoy, J. A. Hollenbaugh, B. Kim, and L. Wu.2012. SAMHD1 restricts HIV-1 infection in dendritic cells (DCs) by dNTP depletion, but its
expression in DCs and primary CD4+ T-lymphocytes cannot be upregulated by interferons.
Retrovirology 9:105.

Sukhera, J., C. Cerulli, B. A. Gawinski, and D. Morse. 2012. Bridging Prevention and Health:
Exploring Community Perceptions of Intimate Partner Violence in Rural Honduras. Journal of family violence 27:707-714.

Walsh, S. R., M. S. Seaman, L. E. Grandpre, C. Charbonneau, K. E. Yanosick, B. Metch, M. C.
Keefer, R. Dolin, and L. R. Baden. 2012. Impact of anti-orthopoxvirus neutralizing antibodies
induced by a heterologous prime-boost HIV-1 vaccine on insert-specific immune responses. Vaccine 31:114-119.

Xu, Z., A. Almudevar, and D. H. Mathews. 2012. Statistical evaluation of improvement in RNA
secondary structure prediction. Nucleic acids research 40:e26.

Zhu, T., J. Zhong, R. Hu, M. Tivarus, S. Ekholm, J. Harezlak, H. Ombao, B. Navia, R. Cohen, and G.
Schifitto. 2012. Patterns of white matter injury in HIV infection after partial immune reconstitution: a DTI tract-based spatial statistics study. Journal of neurovirology.

Amie, S. M., E. Noble, and B. Kim. 2013. Intracellular nucleotide levels and the control of retroviral infections. Virology 436:247-254.

Jacobs, A. C., L. Didone, J. Jobson, M. K. Sofia, D. Krysan, and P. M. Dunman. 2013. Adenylate kinase release as a high-throughput-screening-compatible reporter of bacterial lysis for
identification of antibacterial agents. Antimicrobial agents and chemotherapy 57:26-36.

Jones, M. C., J. J. Kobie, and L. A. Delouise. 2013. Characterization of cell seeding and specific capture of B cells in microbubble well arrays. Biomedical microdevices.

Kakinami, L., R. C. Block, M. J. Adams, S. E. Cohn, B. Maliakkal, and S. G. Fisher. 2013.
Risk of cardiovascular disease in HIV, hepatitis C, or HIV/hepatitis C patients compared to the general population. International journal of clinical practice 67:6-13.

Mathew, E., F. X. Ding, F. Naider, and M. E. Dumont. 2013. Functional fusions of T4 lysozyme in the third intracellular loop of a G protein-coupled receptor identified by a random screening approach in yeast. Protein engineering, design & selection : PEDS 26:59-71.

Mitchell, C., J. E. Balkus, J. McKernan-Mullin, S. E. Cohn, A. E. Luque, C. Mwachari, C. R. Cohen, R. Coombs, L. M. Frenkel, and J. Hitti. 2013. Associations Between Genital Tract Infections, Genital Tract Inflammation, and Cervical Cytobrush HIV-1 DNA in US Versus Kenyan Women. Journal of acquired immune deficiency syndromes (1999) 62:143-148

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