Dr Nitin Saksena - Westmead Millennium Institute

Dr Nitin Saksena
T: +61 2 9845 9119
F: +61 2 9845 9100
E: nitin.saksena@sydney.edu.au
2011
2011 - 2010 - 2009 - 2008 - 2007 - 2006 - 2005 - 2004 - 2003 - 2002 - 2001 - 2000 -
Wang, B., Dwyer, D., Soedjono, M., Shi, H., Matlho, K., Ratnamohan, M., Blyth, C., McPhie, K.,
Cunningham, A., Saksena, N. (2011), Evidence of the circulation of pandemic influenza (H1N1)
2009 with D222D/G/N/S hemagglutinin polymorphisms during the first wave of the 2009
influenza pandemic. Journal of clinical virology : the official publication of the Pan American
Society for Clinical Virology. 52, 304-6. [Abstract]
Wu, J., Dwyer, D., Dyer, W., Yang, Y., Wang, B., Saksena, N. (2011), Genome-wide analysis of
primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched
pathways associated with HIV disease. Retrovirology. 8, 18. [Abstract]
Wang, B., Steain, M., Dwyer, D., Cunningham, A., Saksena, N. (2011), Synthetic long
oligonucleotides to generate artificial templates for use as positive controls in molecular assays:
drug resistance mutations in influenza virus as an example. Virology journal. 8, 405. [Abstract]
2010
Saksena NK, Bin Wang, Li Zhou, Maly Soedjono, Yung Shwen Ho and Viviane Conceicao. HIV
reservoirs in vivo and new strategies for possible eradication of HIV from the reservoir sites. In
Press, Journal of HIV and Palliative care, Dove Press. 2, 103-122: 2010.
Westmead Millennium Institute

Lau KA, Bin Wang, Monica Miranda-Saksena, Ross Boadle, Adeeba Kamarulzaman, Kee-Peng Ng
and Nitin K. Saksena. Evidence for possible biological advantages of the newly emerging HIV-1
circulating recombinant form (CRF) from Malaysia - CRF33_01B in comparison to its progenitors-
CRF01_AE and subtype B. In Press- Current HIV Research, USA. 1, 8(3): 159-171; 2010. [Abstract]
Wightman F, Ajantha Solomon, Gabriela Khoury, Justin Green, Lachlan Gray, Paul R Gorry, Nitin
K. Saksena, Yung Shwen Ho, Jennifer Hoy, Suzanne M Crowe, Paul U Cameron Sharon R Lewin.
Both CD31-positive and CD31-negative naive CD4 T-cells are persistent HIV-infected reservoirs in
individuals receiving antiretroviral therapy. Journal of Infectious Diseases (In Press) 2010.
[Abstract]
Zhou L, Eve Diefenbach, Ben Crossett, Rejane Rua, Bin Wang, Amit Kapur, Bruce J. Brew and
Nitin K. Saksena. First evidence of overlaps between HIV-Associated Dementia (HAD) and nonviral
neurodegenerative diseases: Proteomic analysis of the frontal cortex from HIV+ patients
with and without dementia. Molecular Neurodegeneration (In Press) 2010. [Abstract]
Zhou L, Rua R, Ng T, Vongrad V, Ho YS, Geczy C, Hsu K, Brew BJ, Saksena NK.Evidence for
predilection of macrophage infiltration patterns in the deeper midline and mesial temporal
structures of the brain uniquely in patients with HIV-associated dementia. BMC Infectious
Diseases;9:192. 2010. [Abstract]
Wade J, Sterjovski J, Gray L, Roche M, Chiavaroli L, Ellett A, Jakobsen MR, Cowley D, Pereira Cda
F, Saksena N, Wang B, Purcell DF, Karlsson I, Fenyö EM, Churchill M, Gorry PR. Enhanced CD4+
cellular apoptosis by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with
progressive HIV-1 infection. Virology. 2010 Jan 20;396(2):246-55.
Wang B, Dwyer DE, Blyth CC, Soedjono M, Shi H, Kesson A, Ratnamohan M, McPhie K,
Cunningham AL, Saksena NK Detection of the rapid emergence of the H275Y mutation
associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections.
Antiviral Res. 2010 Jul;87(1):16-21. Epub 2010 Apr 10. [Abstract]
Yoo, P., Shwen Ho, Y., Ng, J., Charleston, M., Saksena, N., Yang, P., Zomaya, A. (2010),
Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV
structural gp120 profiles. BMC Genomics. 11, S22. [Abstract]
2009
Gray, L., M. Roche, M. J. Churchill, J. Sterjovski, A. Ellett, P. Poumbourios, S. Sherieff, B. Wang, N.
Saksena, D. F. Purcell, S. Wesselingh, A. L. Cunningham, B. J. Brew, D. Gabuzda and P. R. Gorry.
"Tissue-specific sequence alterations in the human immunodeficiency virus type 1 envelope
favoring CCR5 usage contribute to persistence of dual-tropic virus in the brain." J Virol 83(11):
5430-5441.2009.
Saksena, N., J. Q. Wu, K. A. Lau, L. Zhou, M. Soedjono and B. Wang. CD8 Antiviral Soluble Factors
and Human Immunodefieciency Virus (HIV) Control. M. A. Ph.D, Bentham Books (Bentam
Science Publishers): 11-34. 2009.
Westmead Millennium Institute

Steain, M. C., D. E. Dwyer, A. C. Hurt, C. Kol, N. K. Saksena, A. L. Cunningham and B. Wang
(2009). "Detection of influenza A H1N1 and H3N2 mutations conferring resistance to oseltamivir
using rolling circle amplification." Antiviral Res 84(3): 242-248. [Abstract]
van Hal, S. J., B. Herring, Z. Deris, B. Wang, N. K. Saksena and D. E. Dwyer (2009). "HIV-1
integrase polymorphisms are associated with prior antiretroviral drug exposure." Retrovirology
6: 12. [Abstract]
Wang, B., D. E. Dwyer, C. B. Chew, C. Kol, Z. P. He, H. Joshi, M. C. Steain, A. L. Cunningham and N.
K. Saksena (2009). "Sensitive detection of the K103N non-nucleoside reverse transcriptase
inhibitor resistance mutation in treatment-naive HIV-1 infected individuals by rolling circle
amplification." J Virol Methods 161(1): 128-135.
2008
Wu JQ, Wang B, Saksena NK. Transitory viremic surges in an HIV+ elite controller can shift
cellular transcriptome profile: a word of caution for microarray studies. J Virol. 2008 Aug 13.
[Epub ahead of print] PMID: 18701597. [Abstract]
Wu JQ, Dwyer DE, Dyer WB, Yang YH, Wang B, Saksena NK. Transcriptional profiles in CD8+ T
cells from HIV+ progressors on HAART are characterized by coordinated up-regulation of
oxidative phosphorylation enzymes and interferon responses. Virology. 2008Aug 8. [Epub ahead
of print] PMID: 18692859. [Abstract]
Caly L, Saksena NK, Piller SC, Jans DA. Impaired nuclear import and viral incorporation of Vpr
derived from a HIV long-term non-progressor. Retrovirology. 2008 Jul 18;5:67. [Abstract]
Zhou L, Ng T, Yuksel A, Wang B, Dwyer DE and Saksena NK: Absence of HIV infection in the
choroid plexus of two patients who died rapidly with HIV-associated dementia. AIDS Research &
Human Retroviruses, 24(6): 839-843. 2008. [Abstract]
Lau KA Bin Wang, Adeeba Kamarulzaman, Kee-Peng Ng and Nitin K. Saksena. Continuous
crossover(s) events of HIV-1 CRF01_AE and B subtype strains in Malaysia: Evidence of Rapid and
Extensive HIV-1 Evolution in the Region. Current HIV Research, 6(2) 108-16; 2008. [Abstract]
Fujii YR and Saksena NK:”RNA and the Regulation of Gene Expression” (Book Chapter) in “RNA
and the Regulation of Gene Expression: A Hidden Layer of Complexity”, Publisher: Horizon
Scientific Press; Editor: Kevin V. Morris, The Scripps Research Institute, 10550 N. Terrey Pines
Road, La Jolla, CA, 92037. 2008 (In press, January 1, 2008). ISBN 1904455255, 9781904455257;
228 pages.
Saksena NK, Wu JQ, Potter SJ, Wilkinson J and Wang B. HIV interaction with the CD8+ T cells.
Current HIV Research (Peer Reviewed) 6(1); 1-9: 2008. [Abstract]
Ho YS, Abecasis AB, Theys K, Deforche K, Dwyer DE, Charleston M, Vandamme AM, Saksena
NK.HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.
Virol J. 2008 Jan 23;5(1):14 [Epub ahead of print].
Steain MC, Wang B and Saksena NK. The possible contribution of HIV-induced syncytia to the
generation of intersubtype recombinants in vitro. AIDS, 22(9)1009-17; 2008). [Abstract]
Westmead Millennium Institute

Jing Qin Wu, Wayne B. Dyer, Jeremy Chrisp, Larissa Belov, Bin Wang and Nitin K. Saksena.
Longitudinal Microarray Analysis of Cell Surface Antigens on Peripheral Blood Mononuclear Cells
from HIV+ Individuals on Highly Active Antiretroviral Therapy. Retrovirology, 5: 24 2008.
[Abstract]
2007
Saksena NK, Rhodes B, Wang B and Soriano V. Elite HIV controllers: Myth or a reality. (Review)
AIDS Reviews 9: 195-207: 2007. [Abstract]
Lau KA, Wang B and Saksena NK. Emerging trends of HIV epidemiology in Asia. (Review) AIDS
Reviews 9; 218-229: 2007. [Abstract]
Lau K, Wang B, Kamarulzaman A, Ng KP, and Saksena NK. Near full-length sequence analysis of
HIV-1 CRF33_01B/B Intersubtype recombinant from Malaysia: Evidence of secondary
recombinant derived from CRF33_01B. AIDS Research & Human Retroviruses 23, 1139-1143;
2007. [Abstract]
Wang YM, Wang B, Dyer WB, Lachireddy K, Peng NG and Saksena NK. Evidence for
predominance of CCR5-using HIV-1 strains during HAART. Current HIV Research 5, 221-234,
2007. [Abstract]
Wang YM, Dyer WB, Workman, C, Wang B, Ng KP, Lachireddy K, Chew CB, Sullivan J and Saksena
NK. Drug resistance and viral evolution in plasma and peripheral blood cells during structured
treatment interruption (STI) and non-interrupted HAART. Current HIV Research 2, 235-250,
2007. [Abstract]
Wang B, Lau KA, Ong LY, Shah M, Steain MC, Foley B, Dwyer DE, Chew CB, Kamarulzaman A, Ng
KP and Saksena NK. Complex patterns of the HIV-1 epidemic in Kuala Lumpur, Malaysia:
Evidence for expansion of circulating recombinant form CRF33_01B and detection of multiple
other recombinants. Virology 367, 388-397; 2007. [Abstract]
Sterjovski J, Churchill MJ, Ellett A, Gray LR, Roche MJ, Dunfee RL, Purcell DF, Saksena N, Wang B,
Sonza S, Wesselingh SL, Karlsson I, Fenyo EM, Gabuzda D, Cunningham AL, Gorry PR. Asn 362 in
gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein
variants from patients with AIDS. Retrovirology. Dec 12;4(1):89 [Epub ahead of print] 2007.
Wu JQ, Wang B, Belov L, Chrisp J, Learmont J, Dyer WB, Zaunders J, Cunningham AL, Dwyer DE,
Saksena NK. Antibody microarray analysis of cell surface antigens on CD4+ and CD8+ T cells from
HIV+ individuals correlates with disease stages. Retrovirology. Nov 26;4(1):83 [Epub ahead of
print] 2007.
Sivakumaran H, Wang B, Gill MJ, Beckholdt B, Saksena NK, Harrich D. Functional relevance of
nonsynonymous mutations in the HIV-1 tat gene within an epidemiologically-linked transmission
cohort. Virology J. Oct 25;4(1):107 [Epub ahead of print] 2007.
2006
Westmead Millennium Institute

Arriaga, M, Carr, J, Li, P, Wang, B, Saksena, N. Interaction between HIV-1 and APOBEC3
sub-family of proteins. Current HIV research. 2006; 4:401-9 [Abstract]
Steain, M, Wang, B, Saksena, N. Analysis of HIV-1 sequences vertically transmitted to
infants in Kisumu, Kenya. Journal of clinical virology : the official publication of the Pan
American Society for Clinical Virology. 2006; 36:298-302 [Abstract]
Potter, S, Lemey, P, Dyer, W, Sullivan, J, Chew, C, Vandamme, A, Dwyer, D, Saksena, N.
Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes
of patients receiving HAART. Virology. 2006; 348:35-46 [Abstract]
Gray, L, Churchill, M, Keane, N, Sterjovski, J, Ellett, A, Purcell, D, Poumbourios, P, Kol, C,
Wang, B, Saksena, N, Wesselingh, S, Price, P, French, M, Gabuzda, D, Gorry, P. Genetic
and functional analysis of R5X4 human immunodeficiency virus type 1 envelope
glycoproteins derived from two individuals homozygous for the CCR5 Delta 32 allele.
Journal of Virology. 2006; 80:3684-3691 [Abstract]
Verity, E, Williams, L, Haddad, D, Choy, V, O'Loughlin, C, Chatfield, C, Saksena, N,
Cunningham, A, Gelder, F, McPhee, D. Broad neutralization and complement-mediated
lysis of HIV-1 by (PE)HRG214, a novel caprine anti-HIV-1 polyclonal antibody. Aids. 2006;
20:505-515 [Abstract]
Shah, M, Smit, T, Morgello, S, Tourtellotte, W, Gelman, B, Brew, B, Saksena, N. Env gp120
sequence analysis of HIV type 1 strains from diverse areas of the brain shows preponderance of
CCR5 usage. AIDS research and human retroviruses. 2006; 22:177-81 [Abstract]
2005
Steain, M, Wang, B, Yang, C, Shi, Y, Nahlen, B, Lal, R, Saksena, N. HIV type 1 sequence
diversity and dual infections in Kenya. AIDS research and human retroviruses. 2005;
21:882-5 [Abstract]
Cali, L, Wang, B, Mikhail, M, Gill, M, Beckthold, B, Salemi, M, Jans, D, Piller, S, Saksena,
N. Evidence for host-driven selection of the HIV type 1 vpr gene in vivo during HIV
disease progression in a transfusion-acquired cohort. AIDS research and human
retroviruses. 2005; 21:728-33 [Abstract]
Chew, C, Potter, S, Wang, B, Wang, Y, Shaw, C, Dwyer, D, Saksena, N. Assessment of
drug resistance mutations in plasma and peripheral blood mononuclear cells at different
plasma viral loads in patients receiving HAART. Journal of clinical virology: the official
publication of the Pan American Society for Clinical Virology. 2005; 33:206-16 [Abstract]
Mikhail, M, Wang, B, Lemey, P, Beckholdt, B, Vandamme, A, Gill, M, Saksena, N. Fulllength
HIV type 1 genome analysis showing evidence for HIV type 1 transmission from a
nonprogressor to two recipients who progressed to AIDS. AIDS research and human
retroviruses. 2005; 21:575-9 [Abstract]
Westmead Millennium Institute

Wang, B, Potter, S, Lin, Y, Cunningham, A, Dwyer, D, Su, Y, Ma, X, Hou, Y, Saksena, N.
Rapid and sensitive detection of severe acute respiratory syndrome coronavirus by
rolling circle amplification. Journal of clinical microbiology. 2005; 43:2339-44 [Abstract]
Saksena, N, Smit, T. HAART & the molecular biology of AIDS dementia complex. The
Indian journal of medical research. 2005; 121:256-69 [Abstract]
Saksena, N, Wang, B, Steain, M, Yang, R, Zhang, L. Snapshot of HIV pathogenesis in
China. Cell research. 2005; 15:953-61 [Abstract]
Mikhail, M, Wang, B, Lemey, P, Beckthold, B, Vandamme, A, Gill, M, Saksena, N. Role of viral
evolutionary rate in HIV-1 disease progression in a linked cohort. Retrovirology. 2005;
2:41 [Abstract]
2004
Smit, T, Brew, B, Tourtellotte, W, Morgello, S, Gelman, B, Saksena, N. Independent
evolution of human immunodeficiency virus (HIV) drug resistance mutations in diverse
areas of the brain in HIV-infected patients, with and without dementia, on antiretroviral
treatment. Journal of virology. 2004; 78:10133-48 [Abstract]
Potter, S, Lemey, P, Achaz, G, Chew, C, Vandamme, A, Dwyer, D, Saksena, N. HIV-1
compartmentalization in diverse leukocyte populations during antiretroviral therapy.
Journal of leukocyte biology. 2004; 76:562-70 [Abstract]
Potter, S, Chew, C, Steain, M, Dwyer, D, Saksena, N. Obstacles to successful
antiretroviral treatment of HIV-1 infection: problems & perspectives. The Indian journal
of medical research. 2004; 119:217-37 [Abstract]
Zaunders, J, Dyer, W, Wang, B, Munier, M, Miranda-Saksena, M, Newton, R, Moore, J,
Mackay, C, Cooper, D, Saksena, N, Kelleher, A. Identification of circulating antigenspecific
CD4+ T lymphocytes with a CCR5+, cytotoxic phenotype in an HIV-1 long-term
nonprogressor and in CMV infection. Blood. 2004; 103:2238-47 [Abstract]
2003
Otake, K, Omoto, S, Yamamoto, T, Okuyama, H, Okada, H, Okada, N, Kawai, M, Saksena,
N, Fujii, Y. HIV-1 Nef protein in the nucleus influences adipogenesis as well as viral
transcription through the peroxisome proliferator-activated receptors. AIDS (London,
England). 2004; 18:189-98 [Abstract]
Omoto, S, Ito, M, Tsutsumi, Y, Ichikawa, Y, Okuyama, H, Brisibe, E, Saksena, N, Fujii, Y. HIV-1 nef
suppression by virally encoded microRNA. Retrovirology. 2004; 1:44 [Abstract]
Lemey, P, Salemi, M, Wang, B, Duffy, M, Hall, W, Saksena, N, Vandamme, A. Site
stripping based on likelihood ratio reduction is a useful tool fo evaluate the impact of
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non-clock-like behavior on viral phylogenetic reconstructions. Fems Immunology And
Medical Microbiology. 2003; 39:125-132
Lemey, P, Pybus, O, Wang, B, Saksena, N, Salemi, M, Vandamme, A. Tracing the origin
and history of the HIV-2 epidemic. Proceedings Of The National Academy Of Sciences Of
The United States Of America. 2003; 100(11):6588-6592
Potter, S, Dwyer, D, Saksena, N. Diffential cellular distribution of HIV-1 drug resistance in
vivo: evidence for infection of CD8+ T cells during HAART. Virology. 2003; 305:339-352
Wang, B, Mikhail, M, Dyer, W, Zaunders, J, Kelleher, A, Saksena, N. First demonstration of a lack
of viral sequence evolution in a nonprogressor, defining replication-incompetent HIV-1
infection. Virology. 2003; 312:135-150
2002
Wang, B, Dyer, W, Zaunders, J, Mikhail, M, Sullivan, J, Williams, L, Haddad, D, Harris, G, Holt, J,
Cooper, D, Miranda-Saksena, M, Boadle, R, Kelleher, A, Saksena, N. Comprehensive analyses of a
unique HIV-1-infected nonprogressor reveal a complex association of immunobiological
mechanisms in the context of replication-incompetent infection. Virology. 2002; 304:246-
64 [Abstract]
2001
Birch, M, Learmont, J, Dyer, W, Deacon, N, Zaunders, J, Saksena, N, Cunningham, A, Mills, J,
Sullivan, J. An examination of signs of disease progression in survivors of the Sydney Blood Bank
Cohort (SBBC). Journal of Virology. 2001; 27:273-277
Smit, T, Wang, B, Ng, T, Osborne, R, Brew, B, Saksena, N. Varied Tropism of HIV-1 Isolates
Derived from Different Regions of Adult Brain Cortex Discriminate between Patients with and
without AIDS Dementia Complex (ADC); Evidence for Neurotropic HIV Variants. Virology. 2001;
14(5):1070-1079
2000
Wang, Y, Dyer, W, Workman, C, Wang, B, Sullivan, J, Saksena, N. Molecular evidence for
drug-induced compartmentalization of HIV-1 quasispecies in a patient with periodic
changes to HAART. AIDS (London, England). 2000; 14:2265-72 [Abstract]
Haddad, D, Birch, C, Middleton, T, Dwyer, D, Cunningham, A, Saksena, N. Evidence for
late stage compartmentalization of HIV-1 resistance mutations between lymph node
and peripheral blood mononuclear cells. AIDS. 2000; 14:2273-2281
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Wang, B, Lal, R, Dwyer, D, Miranda Held, M, Boadle, R, Cunningham, A, Saksena, N.
Molecular and biological interactions between two HIV-1 strains from a coinfected
patient reveal the first evidence in favor of viral synergism. Virology. 2000; 274:105-119
Wang, Y, Dyer, W, Workman, C, Wang, B, Sullivan, J, Saksena, N. Molecular evidence for
drug-induced compartmentalization of HIV-1 quasispecies in a patient with periodic
changes to HAART. AIDS. 2000; 14:2265-2272
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