Publications resulting from work performed at the
Genomics Core
If work performed for you at the CFAR Genomics Core results in publication please acknowledge us with the following statement so that we may continue to bring you excellent service: |
"This work was performed with the support of the Genomics Core at the UCSD Center for AIDS Research (AI36214) and the San Diego Veterans Medical Research Foundation."
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Authors in bold refer to past and present members of the CFAR Genomics Core:
2010:
Woelk C.H., Beliakova-Bethell N., Goicoechea M., Zhao Y., Du P., Rought S.E., Lozach J., Pérez-Santiago J., Richman D.D., Smith D.M. and Little S.J. (In Press) Gene Expression Predicts HIV-infected Individuals at Risk of Poor CD4+ T Cell Recovery Before Initiation of Highly Active Antiretroviral Treatment (HAART). AIDS, ##(##):###-###. [Pubmed]
2009:
Chana G., Lucero G., Salaria S., Lozach J., Du P., Woelk C.H. and Everall I. (2009) Upregulation of NRG-1 and VAMP-1 in Human Brain Aggregates Exposed to Clozapine. Schizophrenia Research, 113(2):273-276. [Pubmed]
Chang L.W. & Spitzer N.C. (2009) Spontaneous calcium spike activity in embryonic spinal neurons is regulated by developmental expression of Na+, K+-ATPase b3 subunti. J. Neurosci, 29(24):7877-7885 [Pubmed]
Terry V.H., Johnston I.C.D. & Spina C.A. (In press) CD44 MicroBeads accelerate HIV-1 infection in T cells. Virology, 388(2):294-304 [Pubmed].
Tatro E.T., Everall I.P., Masliah E., Hult B.J., Lucero G., Chana G., Soontornniyomkij V., Achim C.L.; HNRC. (2009) Differential Expression of Immunophilins FKBP51 and FKBP52 in the Frontal Cortex of HIV-Infected Patients with Major Depressive Disorder. J Neuroimmune Pharmacol, 4(2):218-26 [Pubmed]
Smith D.M., May S., Tweeten S., Drumright L., Pacold M.E., Kosakovsky Pond S.L., Pesano R.L., Lie Y.S., Richman D.D., Frost S.D.W., Woelk C.H., and Little S.J. (2009) A Public Health Model for the Molecular Surveillance of HIV Transmission in San Diego, California, AIDS, 23 (2): 225-232. [Pubmed]
2008:
Woelk C.H. & Burczynski M.E. (2008) The clinical relevance of gene expression profiles in peripheral blood mononuclear cells, in Oligonucleotide Array Sequence Analysis, NOVA publishing, New York USA. [NOVA]
Liu L., May S., Richman D.D., Hecht F.M., Markowitz M., Daar E.S., Routy J.P., Margolick J.B., Collier A.C., Woelk C.H., Little S.J. & Smith D.M. (2008) Comparison of algorithms that interpret genotypic HIV-1 drug resistance to determine the prevalence of transmitted drug resistance. AIDS. 22 (7):835-9. [Pubmed]
Gorbach P.M., Drumright L.N., Javanbakht M., Pond S.L., Woelk C.H., Daar E.S. & Little S.J. (2008) Antiretroviral drug resistance and risk behavior among recently HIV-infected men who have sex with men. J Acquir Immune Defic Syndr. 47 (5):639-43. [Pubmed]
Grigorian A., Hurford R., Chao Y. & Patrick C. (2008) Alterations in the Notch4 pathway in cerebral endothelial cells by the HIV aspartyl protease inhibitor, nelfinavir. BMC Neuroscience, 26 (9): 27. [Pubmed]
Koelsch K.K., Liu L., Haubrich R., May S., Havlir D., Günthard H.F., Ignacio C.C., Campos-Soto P., Little S.J., Shafer R., Robbins G.K., D'Aquila R.T., Kawano Y., Young K., Dao P., Spina C.A., Richman D.D. & Wong J.K. (2008) Dynamics of total, linear non-integrated and integrated HIV-1 DNA in vivo and in vitro. J. Infect. Dis., 197 (3): 411-419. [Pubmed]
Shilling, P.D., Saint Marie, R.L., Shoemaker, J.M., Swerdlow, N.R. (2008) Strain differences in the gating-disruptive effects of apomorphine: Relationship to gene expression in nucleus accumbens signaling pathways. Biological Psychiatry, 63:748-758. [Pubmed]
Suckow AT, Comoletti D, Waldrop MA, Mosedale M, Egodage S, Taylor P, Chessler SD. Expression of neurexin, neuroligin, and their cytoplasmic binding partners in the pancreatic beta-cells and the involvement of neuroligin in insulin secretion. Endocrinology. 149(12):6006-17. [Pubmed]
2007:
Feng Z., Davis D.P., Sasik R., Patel H.H., Drummond J.C. & Patel P.M. (2007) Pathway and gene ontology based analysis of gene expression in a rat model of cerebral ischemic tolerance. Brain Research, 1177: 103-123. [Pubmed]
Fuster M.M., Wang L., Castagnola J., Sikora L., Reddi K., Lee P.H., Radek K.A., Schuksz M., Bishop J.R., Gallo R.L., Sriramarao P. & Esko J.D. (2007) Genetic alteration of endothelial heparan sulfate selectively inhibits tumor angiogenesis. J Cell Biol., 177 (3): 539-549. [Pubmed]
Woelk C.H., Frost S.D., Richman D.D., Higley P.E. & Kosakovsky Pond S.L. (2007) Evolution of the interferon alpha gene family in eutherian mammals. Gene, 397 (1-2): 38-50 [Pubmed]
2006:
Chatterji U., Bobardt M.D., Gaskill P., Sheeter D., Fox H. & Gallay P.A. (2006) Trim5-alpha accelerates degradation of cytosolic capsid associated with productive HIV-1 entry. J. Biol. Chem., 281 (48): 37025-37033 [Pubmed]
Hostetler K.Y., Rought S., Aldern K.A., Trahan J., Beadle J.R. and Corbeil J. (2006) Enhanced antiproliferative effects of alkoxyalkyl esters of cidofovir in human cervical cancer cells in vitro. Molecular cancer therapeutics, 5 (1): 156-159. [Pubmed]
Kosakovsky Pond S.L., Posada D., Gravenor M.B., Woelk C.H. & Frost S.D. (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics, 22 (24): 3096-3098. [Pubmed]
Kosakovsky Pond S.L., Posada D., Gravenor M.B., Woelk C.H. & Frost S.D. (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Molecular Biology and Evolution, 23 (10): 1891-1901. [Pubmed]
2005:
Everall I., Salaria S., Roberts E., Corbeil J., Sasik R., Fox H., Grant I., Masliah E. and the HNRC Group. (2005) Methamphetamine stimulates interferon inducible genes in HIV infected brain. Journal of neuroimmunology, 170 (1-2): 158-171. [Pubmed]
Glatt S.J., Everall I.P., Kremen W.S., Corbeil J., Sasik R., Khanlou N., Han M., Liew C.C. and Tsuang M.T. (2005) Comparative gene expression analysis of blood and brain provides concurrent validation of SELENBP1 up-regulation in schizophrenia. Proceedings of the National Academy of Sciences of the United States of America, 102 (43): 15533-15538. [Pubmed]
Naviaux R.K., Good B., McPherson J.D., Steffen D.L., Markusic D., Ransom B. and Corbeil J. (2005) Sand DNA - a genetic library of life at the water's edge. Marine Ecology Progress Series, 301 9-22. [MEPS]
Pillai S.K., Kosakovsky Pond S.L., Woelk C.H., Richman, D.D., Smith D.M. (2005) "Codon Volatility" does not reflect selective pressure on the HIV-1 genome. Virology, 336 (2): 137-143. [Pubmed]
2004:
de Rozieres S., Swan C.H., Sheeter D.A., Clingerman K.J., Lin Y.C., Huitron-Resendiz S., Henriksen S., Torbett B.E. & Elder J.H. (2004) Assessment of FIV-C infection of cats as a function of treatment with the protease inhibitor, TL-3. Retrovirology, 19 (1): 38. [Pubmed]
Huffman D.L., Abrami L., Sasik R., Corbeil J., van der Goot F.G. and Aroian R.V. (2004) Mitogen-activated protein kinase pathways defend against bacterial pore-forming toxins. Proceedings of the National Academy of Sciences of the United States of America, 101 (30): 10995-11000. [Pubmed]
Cunard R., Eto Y., Muljadi J.T., Glass C.K., Kelly C.J., Ricote M. (2004) Repression of IFN-gamma expression by peroxisome proliferator-activated receptor gamma. Journal of Immunology, 172 (12): 7530-7536. [Pubmed]
Li A.C., Binder C.J., Gutierrez A., Brown K.K., Plotkin C.R., Pattison J.W., Valledor A.F., Davis R.A., Willson T.M., Witztum J.L., Palinski W. and Glass C.K. (2004) Differential inhibition of macrophage foam-cell formation and atherosclerosis in mice by PPARalpha, beta/delta, and gamma. The Journal of Clinical Investigation, 114 (11): 1564-1576. [Pubmed]
Li A.C. and Glass C.K. (2004) PPAR- and LXR-dependent pathways controlling lipid metabolism and the development of atherosclerosis. Journal of Lipid Research, 45 (12): 2161-2173. [Pubmed]
Woelk C.H., Ottones F., Plotkin C.R., Pinyi Du, Royer C.D., Rought S.E., Lozach J., Sasik R., Kornbluth R.S., Richman D. and Corbeil J. (2004) Interferon gene expression following HIV-1 infection of monocyte-derived macrophages. AIDS Research and Human Retroviruses, 20 (11): 1210-1222 [Pubmed][Supplementary Figure 1][Supplementary Figure 2][Supplementary Figure 3][DAT & CEL files (MAS 4.0)][CEL files (MAS 5.0)][Excel spreadsheet of results (CORGON)]
Sasik R., Woelk C.H. and Corbeil J. (2004) Microarrays: Truths and Consequences. Journal of Molecular Endocrinology, 33 (1): 1-9 [Pubmed]
Leigh Brown A.J., Frost S.D., Good B., Daar E.S., Simon V., Markowitz M., Collier A.C., Connick E., Conway B., Margolick J.B., Routy J.P., Corbeil J., Hellmann N.S., Richman D.D.and Little S.J. (2004) Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection. Journal of Virology, 78 (5): 2242-2246 [Pubmed]
Lelièvre J.D., Petit F., Perrin L., Mammano F., Arnoult D., Ameisen J.C., Corbeil J., Gervaix A., Estaquier J. (2004) The density of coreceptors at the surface of CD4+ T cells contributes to the extent of human immunodeficiency virus type 1 viral replication-mediated T cell death. AIDS Research and Human Retroviruses, 20 (11): 1230-1243 [Pubmed]
Choisy M., Woelk C.H., Guégan J.F. & Robertson D. L. (2004) A comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. Journal of Virology, 78 (4): 1962-1970. [Pubmed]
2003:
Sheeter D., Du P., Rought S., Richman D. and Corbeil J. (2003) Surface CD4 expression modulated by a cellular factor induced by HIV type 1 infection. AIDS Research and Human Retroviruses, 19 (2): 117-123. [Pubmed]
Zaunders J.J., Moutouh-de Parseval L., Kitada S., Reed J.C., Rought S., Genini D., Leoni L., Kelleher A., Cooper D.A., Smith D.E., Grey P., Estaquier J., Little S., Richman D.D. and Corbeil J. (2003) Polyclonal proliferation and apoptosis of CCR5+ T lymphocytes during primary human immunodeficiency virus type 1 infection: regulation by interleukin (IL)-2, IL-15, and Bcl-2. The Journal of Infectious Diseases, 187 (11): 1735-1747. [Pubmed]
Wang J.P., Rought S.E., Corbeil J. and Guiney D.G. (2003) Gene expression profiling detects patterns of human macrophage responses following Mycobacterium tuberculosis infection. FEMS Immunology and Medical Microbiology, 39 (2): 163-172. [Pubmed]
Fink J.L., Drewes S., Patel H., Welsh J.B., Masys D.R., Corbeil J. and Gribskov M. (2003) 2HAPI: a microarray data analysis system. Bioinformatics, 19 (11): 1443-1445. [Pubmed]
Pillai S., Good B., Richman D. and Corbeil J. (2003) A new perspective on V3 phenotype prediction. AIDS Research and Human Retroviruses, 19 (2): 145-149. [Pubmed]
2002:
Pioletti D.P., Leoni L., Genini D., Takei H., Du P. and Corbeil J. (2002) Gene expression analysis of osteoblastic cells contacted by orthopedic implant particles. Journal of Biomedical Materials Research, 61 (3): 408-420. [Pubmed]
Sasik R., Calvo E. and Corbeil J. (2002) Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinformatics, 18 (12): 1633-1640. [Pubmed]
Ku C.H., Browne M., Gregson P.J., Corbeil J., Pioletti D.P. (2002) Large-scale gene expression analysis of osteoblasts cultured on three different Ti-6Al-4V surface treatments. Biomaterials, 23 (21): 4193-4202. [Pubmed]
Estaquier J., Lelièvre J.D., Petit F, Brunner T., Moutouh-De Parseval L., Richman D.D., Ameisen J.C. and Corbeil J. (2002) Effects of antiretroviral drugs on human immunodeficiency virus type 1-induced CD4(+) T-cell death. Biomaterials, 76 (12): 5966-5973. [Pubmed]
Petit F., Corbeil J., Lelièvre J.D., Moutouh-de Parseval L., Pinon G., Green D.R., Ameisen J.C. and Estaquier J. (2002) Role of CD95-activated caspase-1 processing of IL-1beta in TCR-mediated proliferation of HIV-infected CD4(+) T cells. European Journal of Immunology, 31 (12): 3513-3524. [Pubmed]
Petit F., Arnoult D., Lelièvre J.D., Moutouh-de Parseval L., Hance A.J., Schneider P., Corbeil J., Ameisen J.C. and Estaquier J. (2002) Productive HIV-1 infection of primary CD4+ T cells induces mitochondrial membrane permeabilization leading to a caspase-independent cell death. The Journal of Biological Chemistry, 277 (2): 1477-1487. [Pubmed]
2001:
Corbeil J., Sheeter D., Genini D., Rought S., Leoni L, Du P., Ferguson M, Masys D.R., Welsh J.B., Fink J.L., Sasik R., Huang D., Drenkow J., Richman D.D. and Gingeras T. (2001) Temporal gene regulation during HIV-1 infection of human CD4+ T cells. Genome Research, 11 (7): 1198-1204. [Pubmed]
Genini D., Sheeter D., Rought S., Zaunders J.J., Susin S.A., Kroemer G., Richman D.D., Carson D.A., Corbeil J. and Leoni L.M. (2001) HIV induces lymphocyte apoptosis by a p53-initiated, mitochondrial-mediated mechanism. The FASEB journal, 15 (1): 5-6. [Pubmed]
Zelphati O., Wang Y., Kitada S., Reed J.C., Felgner P.L. and Corbeil J. (2001) Intracellular delivery of proteins with a new lipid-mediated delivery system. The Journal of Biological Chemistry, 276 (37): 35103-35110. [Pubmed]
Masys D.R., Welsh J.B., Lynn Fink J., Gribskov M., Klacansky I., and Corbeil J. (2001) Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics, 17 (4): 319-326. [Pubmed]
2000:
Tighe H., Takabayashi K., Schwartz D., Marsden R., Beck L., Corbeil J., Richman D.D., Eiden J.J. Jr., Spiegelberg H.L. and Raz E. (2000) Conjugation of protein to immunostimulatory DNA results in a rapid, long-lasting and potent induction of cell-mediated and humoral immunity. European Journal of Immunology, 30 (7): 1939-1947. [Pubmed]
1999:
Benedict C.A., Butrovich K.D., Lurain N.S., Corbeil J., Rooney I., Schneider P., Tschopp J. and Ware C.F. (1999) Cutting edge: a novel viral TNF receptor superfamily member in virulent strains of human cytomegalovirus. Journal of Immunology, 13 (2): 6967-6970. [Pubmed]
1998:
Moutouh L., Estaquier J., Richman D.D. and Corbeil J. (1998) Molecular and cellular analysis of human immunodeficiency virus-induced apoptosis in lymphoblastoid T-cell-line-expressing wild-type and mutated CD4 receptors. Journal of Virology, 72 (10): 8061-8072. [Pubmed]
