CHAIN Grant Publications

Publications resulting from the CHAIN Center research





Xue J, Guijas C, Benton HP, Warth B, Siuzdak G. METLIN MS(2) molecular standards database: a broad chemical and biological resource. Nat Methods. 2020;17(10):953-4. Epub 2020/08/26. doi: 10.1038/s41592-020-0942-5. PubMed PMID: 32839599.

Wiesman AI, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. Cereb Cortex. 2020;30(3):1234-43. Epub 2019/09/11. doi: 10.1093/cercor/bhz162. PubMed PMID: 31504270; PMCID: PMC7132912.

Wang W, Smith N, Makarov E, Sun Y, Gebhart CL, Ganesan M, Osna NA, Gendelman HE, Edagwa BJ, Poluektova LY. A long-acting 3TC ProTide nanoformulation suppresses HBV replication in humanized mice. Nanomedicine. 2020;28:102185. Epub 2020/03/29. doi: 10.1016/j.nano.2020.102185. PubMed PMID: 32217146; PMCID: PMC7438263.

Vellichirammal NN, Albahrani A, Banwait JK, Mishra NK, Li Y, Roychoudhury S, Kling MJ, Mirza S, Bhakat KK, Band V, Joshi SS, Guda C. Pan-Cancer Analysis Reveals the Diverse Landscape of Novel Sense and Antisense Fusion Transcripts. Mol Ther Nucleic Acids. 2020;19:1379-98. Epub 2020/03/13. doi: 10.1016/j.omtn.2020.01.023. PubMed PMID: 32160708; PMCID: PMC7044684.

Uppada SB, Madduri LSV, Singu S, Lawson B, Bauer L, Freifeld A, Bhatt VR, Byrareddy SN. Modified Papanicolaou staining for oral swab samples stored long term. Biotech Histochem. 2020:1-5. Epub 2020/08/22. doi: 10.1080/10520295.2020.1804075. PubMed PMID: 32820964; PMCID: PMC7897329.

Trivedi J, Mohan M, Byrareddy SN. Drug Repurposing Approaches to Combating Viral Infections. J Clin Med. 2020;9(11). Epub 2020/11/27. doi: 10.3390/jcm9113777. PubMed PMID: 33238464; PMCID: PMC7700377.

Thurman M, Johnson S, Acharya A, Pallikkuth S, Mahesh M, Byrareddy SN. Biomarkers of Activation and Inflammation to Track Disparity in Chronological and Physiological Age of People Living With HIV on Combination Antiretroviral Therapy. Front Immunol. 2020;11:583934. Epub 2020/11/10. doi: 10.3389/fimmu.2020.583934. PubMed PMID: 33162998; PMCID: PMC7581935.

Tan YD, Xiao P, Guda C. In-depth Mendelian randomization analysis of causal factors for coronary artery disease. Sci Rep. 2020;10(1):9208. Epub 2020/06/10. doi: 10.1038/s41598-020-66027-4. PubMed PMID: 32514076; PMCID: PMC7280530.

Su H, Sravanam S, Gorantla S, Kaminski R, Khalili K, Poluektova L, Gendelman HE, Dash PK. Amplification of Replication Competent HIV-1 by Adoptive Transfer of Human Cells From Infected Humanized Mice. Front Cell Infect Microbiol. 2020;10:38. Epub 2020/03/03. doi: 10.3389/fcimb.2020.00038. PubMed PMID: 32117811; PMCID: PMC7026001.

Singu S, Acharya A, Challagundla K, Byrareddy SN. Impact of Social Determinants of Health on the Emerging COVID-19 Pandemic in the United States. Front Public Health. 2020;8:406. Epub 2020/08/15. doi: 10.3389/fpubh.2020.00406. PubMed PMID: 32793544; PMCID: PMC7385373.

Sil S, Dagur RS, Liao K, Peeples ES, Hu G, Periyasamy P, Buch S. Strategies for the use of Extracellular Vesicles for the Delivery of Therapeutics. J Neuroimmune Pharmacol. 2020;15(3):422-42. Epub 2019/08/29. doi: 10.1007/s11481-019-09873-y. PubMed PMID: 31456107; PMCID: PMC7044028.

Schwab AD, Thurston MJ, Machhi J, Olson KE, Namminga KL, Gendelman HE, Mosley RL. Immunotherapy for Parkinson's disease. Neurobiol Dis. 2020;137:104760. Epub 2020/01/25. doi: 10.1016/j.nbd.2020.104760. PubMed PMID: 31978602; PMCID: PMC7933730.

Rothan HA, Acharya A, Reid SP, Kumar M, Byrareddy SN. Molecular Aspects of COVID-19 Differential Pathogenesis. Pathogens. 2020;9(7). Epub 2020/07/10. doi: 10.3390/pathogens9070538. PubMed PMID: 32640525; PMCID: PMC7400297.

Proskovec AL, Rezich MT, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Association of Epigenetic Metrics of Biological Age With Cortical Thickness. JAMA Netw Open. 2020;3(9):e2015428. Epub 2020/09/15. doi: 10.1001/jamanetworkopen.2020.15428. PubMed PMID: 32926115; PMCID: PMC7490648holding an equity interest in Data4Cure, Inc, and serving on its scientific advisory board, holding an equity interest and serving on the Scientific Advisory Board of Ideaya BioSciences, Inc, and receiving income for sponsored research funding; the terms of these arrangements have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies. Dr Swindells reported receiving grants from ViiVHealthcare outside the submitted work. No other disclosures were reported.

Olwenyi OA, Dyavar SR, Acharya A, Podany AT, Fletcher CV, Ng CL, Reid SP, Byrareddy SN. Immuno-epidemiology and pathophysiology of coronavirus disease 2019 (COVID-19). J Mol Med (Berl). 2020;98(10):1369-83. Epub 2020/08/19. doi: 10.1007/s00109-020-01961-4. PubMed PMID: 32808094; PMCID: PMC7431311.

Olwenyi OA, Acharya A, Routhu NK, Pierzchalski K, Jones JW, Kane MA, Sidell N, Mohan M, Byrareddy SN. Retinoic Acid Improves the Recovery of Replication-Competent Virus from Latent SIV Infected Cells. Cells. 2020;9(9). Epub 2020/09/17. doi: 10.3390/cells9092076. PubMed PMID: 32932813; PMCID: PMC7565696.

Olson KE, Namminga KL, Schwab AD, Thurston MJ, Lu Y, Woods A, Lei L, Shen W, Wang F, Joseph SB, Gendelman HE, Mosley RL. Neuroprotective Activities of Long-Acting Granulocyte-Macrophage Colony-Stimulating Factor (mPDM608) in 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine-Intoxicated Mice. Neurotherapeutics. 2020;17(4):1861-77. Epub 2020/07/09. doi: 10.1007/s13311-020-00877-8. PubMed PMID: 32638217; PMCID: PMC7851309.

Odegaard KE, Schaal VL, Clark AR, Koul S, Gowen A, Sankarasubramani J, Xiao P, Guda C, Lisco SJ, Yelamanchili SV, Pendyala G. Characterization of the intergenerational impact of in utero and postnatal oxycodone exposure. Transl Psychiatry. 2020;10(1):329. Epub 2020/09/25. doi: 10.1038/s41398-020-01012-z. PubMed PMID: 32968044; PMCID: PMC7511347.

Niu M, Morsey B, Lamberty BG, Emanuel K, Yu F, León-Rivera R, Berman JW, Gaskill PJ, Matt SM, Ciborowski PS, Fox HS. Methamphetamine Increases the Proportion of SIV-Infected Microglia/Macrophages, Alters Metabolic Pathways, and Elevates Cell Death Pathways: A Single-Cell Analysis. Viruses. 2020;12(11). Epub 2020/11/18. doi: 10.3390/v12111297. PubMed PMID: 33198269; PMCID: PMC7697917.

Mukadam IZ, Machhi J, Herskovitz J, Hasan M, Oleynikov MD, Blomberg WR, Svechkarev D, Mohs AM, Zhou Y, Dash P, McMillan J, Gorantla S, Garrison J, Gendelman HE, Kevadiya BD. Rilpivirine-associated aggregation-induced emission enables cell-based nanoparticle tracking. Biomaterials. 2020;231:119669. Epub 2019/12/23. doi: 10.1016/j.biomaterials.2019.119669. PubMed PMID: 31865227; PMCID: PMC7334833.

Mishra PK, Tandon R, Byrareddy SN. Diabetes and COVID-19 risk: an miRNA perspective. Am J Physiol Heart Circ Physiol. 2020;319(3):H604-h9. Epub 2020/08/09. doi: 10.1152/ajpheart.00489.2020. PubMed PMID: 32762561; PMCID: PMC7509271.

Mishra NK, Southekal S, Guda C. Prognostic value of biomarkers in the tumor microenvironment of pancreatic ductal adenocarcinoma. Ann Transl Med. 2020;8(10):615. Epub 2020/06/23. doi: 10.21037/atm.2020.03.59. PubMed PMID: 32566552; PMCID: PMC7290607 (available at The authors have no conflicts of interest to declare.

Mishra NK, Niu M, Southekal S, Bajpai P, Elkholy A, Manne U, Guda C. Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles. Front Genet. 2020;11:522125. Epub 2020/11/17. doi: 10.3389/fgene.2020.522125. PubMed PMID: 33193605; PMCID: PMC7606733.

Machhi J, Kevadiya BD, Muhammad IK, Herskovitz J, Olson KE, Mosley RL, Gendelman HE. Harnessing regulatory T cell neuroprotective activities for treatment of neurodegenerative disorders. Mol Neurodegener. 2020;15(1):32. Epub 2020/06/07. doi: 10.1186/s13024-020-00375-7. PubMed PMID: 32503641; PMCID: PMC7275301.

Machhi J, Herskovitz J, Senan AM, Dutta D, Nath B, Oleynikov MD, Blomberg WR, Meigs DD, Hasan M, Patel M, Kline P, Chang RC, Chang L, Gendelman HE, Kevadiya BD. The Natural History, Pathobiology, and Clinical Manifestations of SARS-CoV-2 Infections. J Neuroimmune Pharmacol. 2020;15(3):359-86. Epub 2020/07/23. doi: 10.1007/s11481-020-09944-5. PubMed PMID: 32696264; PMCID: PMC7373339.

Liao K, Niu F, Hu G, Yang L, Dallon B, Villarreal D, Buch S. Morphine-mediated release of miR-138 in astrocyte-derived extracellular vesicles promotes microglial activation. J Extracell Vesicles. 2020;10(1):e12027. Epub 2020/12/12. doi: 10.1002/jev2.12027. PubMed PMID: 33304479; PMCID: PMC7710131.

Liao K, Niu F, Hu G, Guo ML, Sil S, Buch S. HIV Tat-mediated induction of autophagy regulates the disruption of ZO-1 in brain endothelial cells. Tissue Barriers. 2020;8(2):1748983. Epub 2020/04/18. doi: 10.1080/21688370.2020.1748983. PubMed PMID: 32299282; PMCID: PMC7549738.

Liao K, Niu F, Dagur RS, He M, Tian C, Hu G. Intranasal Delivery of lincRNA-Cox2 siRNA Loaded Extracellular Vesicles Decreases Lipopolysaccharide-Induced Microglial Proliferation in Mice. J Neuroimmune Pharmacol. 2020;15(3):390-9. Epub 2019/07/22. doi: 10.1007/s11481-019-09864-z. PubMed PMID: 31325121; PMCID: PMC6980430.

León-Rivera R, Morsey B, Niu M, Fox HS, Berman JW. Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities. mBio. 2020;11(4). Epub 2020/07/30. doi: 10.1128/mBio.01037-20. PubMed PMID: 32723919; PMCID: PMC7387797.

Larabi A, Barnich N, Nguyen HTT. New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD. Autophagy. 2020;16(1):38-51. Epub 2019/07/10. doi: 10.1080/15548627.2019.1635384. PubMed PMID: 31286804; PMCID: PMC6984609.

Lakshmaiah Narayana J, Mishra B, Lushnikova T, Wu Q, Chhonker YS, Zhang Y, Zarena D, Salnikov ES, Dang X, Wang F, Murphy C, Foster KW, Gorantla S, Bechinger B, Murry DJ, Wang G. Two distinct amphipathic peptide antibiotics with systemic efficacy. Proc Natl Acad Sci U S A. 2020;117(32):19446-54. Epub 2020/07/30. doi: 10.1073/pnas.2005540117. PubMed PMID: 32723829; PMCID: PMC7431008.

Kutchy NA, Peeples ES, Sil S, Liao K, Chivero ET, Hu G, Buch S. Extracellular Vesicles in Viral Infections of the Nervous System. Viruses. 2020;12(7). Epub 2020/07/02. doi: 10.3390/v12070700. PubMed PMID: 32605316; PMCID: PMC7411781.

Kumar SRP, Wang X, Avuthu N, Bertolini TB, Terhorst C, Guda C, Daniell H, Herzog RW. Role of Small Intestine and Gut Microbiome in Plant-Based Oral Tolerance for Hemophilia. Front Immunol. 2020;11:844. Epub 2020/06/09. doi: 10.3389/fimmu.2020.00844. PubMed PMID: 32508814; PMCID: PMC7251037.

Kulkarni TA, Bade AN, Sillman B, Shetty BLD, Wojtkiewicz MS, Gautam N, Hilaire JR, Sravanam S, Szlachetka A, Lamberty BG, Morsey BM, Fox HS, Alnouti Y, McMillan JM, Mosley RL, Meza J, Domanico PL, Yue TY, Moore G, Edagwa BJ, Gendelman HE. A year-long extended release nanoformulated cabotegravir prodrug. Nat Mater. 2020;19(8):910-20. Epub 2020/04/29. doi: 10.1038/s41563-020-0674-z. PubMed PMID: 32341511; PMCID: PMC7384935.

Hu G, Niu F, Liao K, Periyasamy P, Sil S, Liu J, Dravid SM, Buch S. HIV-1 Tat-Induced Astrocytic Extracellular Vesicle miR-7 Impairs Synaptic Architecture. J Neuroimmune Pharmacol. 2020;15(3):538-53. Epub 2019/08/12. doi: 10.1007/s11481-019-09869-8. PubMed PMID: 31401755; PMCID: PMC7008083.

Hanna KF, Sayles HR, O'Neill J, White ML, Wilson TW, Swindells S. Incidental Findings on Brain MRI in People with HIV Infection. Sci Rep. 2020;10(1):9474. Epub 2020/06/13. doi: 10.1038/s41598-020-66443-6. PubMed PMID: 32528044; PMCID: PMC7289834.

Guijas C, Montenegro-Burke JR, Cintron-Colon R, Domingo-Almenara X, Sanchez-Alavez M, Aguirre CA, Shankar K, Majumder EL, Billings E, Conti B, Siuzdak G. Metabolic adaptation to calorie restriction. Sci Signal. 2020;13(648). Epub 2020/09/10. doi: 10.1126/scisignal.abb2490. PubMed PMID: 32900879; PMCID: PMC7580877.

Groff BR, Wiesman AI, Rezich MT, O'Neill J, Robertson KR, Fox HS, Swindells S, Wilson TW. Age-related visual dynamics in HIV-infected adults with cognitive impairment. Neurol Neuroimmunol Neuroinflamm. 2020;7(3). Epub 2020/02/28. doi: 10.1212/nxi.0000000000000690. PubMed PMID: 32102916; PMCID: PMC7051212.

Gao G, Li C, Zhu J, Wang Y, Huang Y, Zhao S, Sheng S, Song Y, Ji C, Li C, Yang X, Ye L, Qi X, Zhang Y, Xia X, Zheng JC. Glutaminase 1 Regulates Neuroinflammation After Cerebral Ischemia Through Enhancing Microglial Activation and Pro-Inflammatory Exosome Release. Front Immunol. 2020;11:161. Epub 2020/03/03. doi: 10.3389/fimmu.2020.00161. PubMed PMID: 32117296; PMCID: PMC7020613.

Fan W, Wan Y, Li Q. Interleukin-21 enhances the antibody avidity elicited by DNA prime and MVA boost vaccine. Cytokine. 2020;125:154814. Epub 2019/08/27. doi: 10.1016/j.cyto.2019.154814. PubMed PMID: 31450102.

Dyavar SR, Potts LF, Beck G, Dyavar Shetty BL, Lawson B, Podany AT, Fletcher CV, Amara RR, Papa SM. Transcriptomic approach predicts a major role for transforming growth factor beta type 1 pathway in L-Dopa-induced dyskinesia in parkinsonian rats. Genes Brain Behav. 2020;19(8):e12690. Epub 2020/08/03. doi: 10.1111/gbb.12690. PubMed PMID: 32741046; PMCID: PMC8006569.

Dyavar SR, Mykris TM, Winchester LC, Scarsi KK, Fletcher CV, Podany AT. Hepatocytic transcriptional signatures predict comparative drug interaction potential of rifamycin antibiotics. Sci Rep. 2020;10(1):12565. Epub 2020/07/30. doi: 10.1038/s41598-020-69228-z. PubMed PMID: 32724080; PMCID: PMC7387492.

Dash PK, Kevadiya BD, Su H, Banoub MG, Gendelman HE. Pathways towards human immunodeficiency virus elimination. EBioMedicine. 2020;53:102667. Epub 2020/03/03. doi: 10.1016/j.ebiom.2020.102667. PubMed PMID: 32114397; PMCID: PMC7047153.

Dash PK, Alomar FA, Hackfort BT, Su H, Conaway A, Poluektova LY, Gendelman HE, Gorantla S, Bidasee KR. HIV-1-Associated Left Ventricular Cardiac Dysfunction in Humanized Mice. Sci Rep. 2020;10(1):9746. Epub 2020/06/18. doi: 10.1038/s41598-020-65943-9. PubMed PMID: 32546795; PMCID: PMC7297773.

Dagur RS, Liao K, Sil S, Niu F, Sun Z, Lyubchenko YL, Peeples ES, Hu G, Buch S. Neuronal-derived extracellular vesicles are enriched in the brain and serum of HIV-1 transgenic rats. J Extracell Vesicles. 2020;9(1):1703249. Epub 2020/02/01. doi: 10.1080/20013078.2019.1703249. PubMed PMID: 32002168; PMCID: PMC6968593.

Cornish A, Roychoudhury S, Sarma K, Pramanik S, Bhakat K, Dudley A, Mishra NK, Guda C. Red panda: a novel method for detecting variants in single-cell RNA sequencing. BMC Genomics. 2020;21(Suppl 11):830. Epub 2020/12/30. doi: 10.1186/s12864-020-07224-3. PubMed PMID: 33372593; PMCID: PMC7771073.

Chand S, Jo A, Vellichirammal NN, Gowen A, Guda C, Schaal V, Odegaard K, Lee H, Pendyala G, Yelamanchili SV. Comprehensive Characterization of Nanosized Extracellular Vesicles from Central and Peripheral Organs : Implications for Preclinical and Clinical Applications. ACS Appl Nano Mater. 2020;3(9):8906-19. Epub 2021/01/02. doi: 10.1021/acsanm.0c01654. PubMed PMID: 33385108; PMCID: PMC7771629.

Buch S, Periyasamy P, Thangaraj A, Sil S, Chivero ET, Tripathi A. Opioid-Mediated HIV-1 Immunopathogenesis. J Neuroimmune Pharmacol. 2020;15(4):628-42. Epub 2020/10/09. doi: 10.1007/s11481-020-09960-5. PubMed PMID: 33029670; PMCID: PMC7872067.

Banoub MG, Bade AN, Lin Z, Cobb D, Gautam N, Dyavar Shetty BL, Wojtkiewicz M, Alnouti Y, McMillan J, Gendelman HE, Edagwa B. Synthesis and Characterization of Long-Acting Darunavir Prodrugs. Mol Pharm. 2020;17(1):155-66. Epub 2019/11/20. doi: 10.1021/acs.molpharmaceut.9b00871. PubMed PMID: 31742407; PMCID: PMC7295016.

Avedissian SN, Dyavar SR, Fox HS, Fletcher CV. Pharmacologic approaches to HIV-associated neurocognitive disorders. Curr Opin Pharmacol. 2020;54:102-8. Epub 2020/10/14. doi: 10.1016/j.coph.2020.09.003. PubMed PMID: 33049585; PMCID: PMC7770011.

Arif Y, Wiesman AI, O'Neill J, Embury C, May PE, Lew BJ, Schantell MD, Fox HS, Swindells S, Wilson TW. The age-related trajectory of visual attention neural function is altered in adults living with HIV: A cross-sectional MEG study. EBioMedicine. 2020;61:103065. Epub 2020/10/26. doi: 10.1016/j.ebiom.2020.103065. PubMed PMID: 33099087; PMCID: PMC7585051.

Almikhlafi MA, Stauch KL, Villeneuve LM, Purnell PR, Lamberty BG, Fox HS. Deletion of DJ-1 in rats affects protein abundance and mitochondrial function at the synapse. Sci Rep. 2020;10(1):13719. Epub 2020/08/15. doi: 10.1038/s41598-020-70486-0. PubMed PMID: 32792613; PMCID: PMC7426919.

Acharya A, Olwenyi OA, Thurman M, Pandey K, Morsey BM, Lamberty B, Ferguson N, Callen S, Fang Q, Buch SJ, Fox HS, Byrareddy SN. Chronic morphine administration differentially modulates viral reservoirs in SIVmac251 infected rhesus macaque model. J Virol. 2020;95(5). Epub 2020/12/18. doi: 10.1128/jvi.01657-20. PubMed PMID: 33328304; PMCID: PMC8092838.

Acharya A, Kevadiya BD, Gendelman HE, Byrareddy SN. SARS-CoV-2 Infection Leads to Neurological Dysfunction. J Neuroimmune Pharmacol. 2020;15(2):167-73. Epub 2020/05/25. doi: 10.1007/s11481-020-09924-9. PubMed PMID: 32447746; PMCID: PMC7244399.


Soni D, Bade AN, Gautam N, Herskovitz J, Ibrahim IM, Smith N, Wojtkiewicz MS, Dyavar Shetty BL, Alnouti Y, McMillan J, Gendelman HE, Edagwa BJ. Synthesis of a long acting nanoformulated emtricitabine ProTide. Biomaterials. 2019 Nov;222:119441. doi: 10.1016/j.biomaterials.2019.119441. Epub 2019 Aug 20. PMID: 31472458

Hilaire JR, Bade AN, Sillman B, Gautam N, Herskovitz J, Dyavar Shetty BL, Wojtkiewicz MS, Szlachetka A, Lamberty BG, Sravanam S, Fox HS, Alnouti Y, Dash PK, McMillan JM, Edagwa BJ, Gendelman HE. Creation of a long-acting rilpivirine prodrug nanoformulation.  2019 Sep 3;311-312:201-211. PMID: 31491432

Cao M, Li H, Zhao J, Cui J, Hu G. Identification of age- and gender-associated long noncoding RNAs in the human brain with Alzheimer's disease. Neurobiol Aging. 2019 Sep;81:116-126. doi: 10.1016/j.neurobiolaging.2019.05.023. Epub 2019 Jun 6. PMID: 31280115

Frank I, Acharya A, Routhu NK, Aravantinou M, Harper JL, Maldonado S, Sole Cigoli M, Semova S, Mazel S, Paiardini M, Derby N, Byrareddy SN, Martinelli E. A Tat/Rev Induced Limiting Dilution Assay to Measure Viral Reservoirs in Non-Human Primate Models of HIV Infection. Sci Rep. 2019 Aug 19;9(1):12078. doi: 10.1038/s41598-019-48354-3. PMID: 31427605

Zhao R, Li Y, Gorantla S, Poluektova LY, Lin H, Gao F, Wang H, Zhao J, Zheng JC, Huang Y. Small molecule ONC201 inhibits HIV-1 replication in macrophages via FOXO3a and TRAIL. Antiviral Res. 2019 Aug;168:134-145. doi: 10.1016/j.antiviral.2019.05.015. Epub 2019 May 31. PMID: 31158413

Hu G, Niu F, Liao K, Periyasamy P, Sil S, Liu J, Dravid SM, Buch S. HIV-1 Tat-Induced Astrocytic Extracellular Vesicle miR-7 Impairs Synaptic Architecture. 
J Neuroimmune Pharmacol
. 2019 Aug 10. doi: 10.1007/s11481-019-09869-8. [Epub ahead of print]
PMID: 31401755

Pawlak K, Lech K, Vei A, Burch S, Zieschang S, Jaquet S, Yu F, Harwood E, Morsey B, Fox HS, Ciborowski P. Secreted Metabolome of Human Macrophages Exposed to Methamphetamine. Anal Chem. 2019 Jul 16;91(14):9190-9197. doi: 10.1021/acs.analchem.9b01952. Epub 2019 Jul 2. PMID: 31265257


Liao K, Niu F, Dagur RS, He M, Tian C, Hu G. Intranasal Delivery of lincRNA-Cox2 siRNA Loaded Extracellular Vesicles Decreases Lipopolysaccharide-Induced Microglial Proliferation in Mice. J Neuroimmune Pharmacol. 2019 Jul 20. doi: 10.1007/s11481-019-09864-z. [Epub ahead of print] PMID:31325121

Dash PK, Kaminski R, Bella R, Su H, Mathews S, Ahooyi TM, Chen C, Mancuso P, Sariyer R, Ferrante P, Donadoni M, Robinson JA, Sillman B, Lin Z, Hilaire JR, Banoub M, Elango M, Gautam N, Mosley RL, Poluektova LY, McMillan J, Bade AN, Gorantla S, Sariyer IK, Burdo TH, Young WB, Amini S, Gordon J, Jacobson JM, Edagwa B, Khalili K, Gendelman HE. Sequential LASER ART and CRISPR Treatments Eliminate HIV-1 in a Subset of Infected Humanized Mice. Nat Commun. 2019 Jul 2;10(1):2753. PMID: 31266936

Domingo-Almenara X, Montenegro-Burke JR, Guijas C, Majumder EL, Benton HP, Siuzdak G. 2019. Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics. Anal Chem 91:3246-3253. PMID: 30681830 

He M, Zhang H, Li Y, Tian C, Tang B, Huang Y, Zheng J. 2019. Direct and selective lineage conversion of human fibroblasts to dopaminergic precursors. Neurosci Lett 699:16-23. PMID: 30664902

Gao G, Zhao S, Xia X, Li C, Li C, Ji C, Sheng S, Tang Y, Zhu J, Wang Y, Huang Y, Zheng JC. Glutaminase C Regulates Microglial Activation and Pro-inflammatory Exosome Release: Relevance to the Pathogenesis of Alzheimer's Disease. Front Cell Neurosci. 2019 Jun 28;13:264. doi: 10.3389/fncel.2019.00264. eCollection 2019. PMID: 31316350

Herskovitz J, Gendelman HE 2019 HIV and the Macrophage: From Cell Reservoirs to Drug Delivery to Viral Eradication. J Neuroimmune Pharmacol 14:52-67. PMID: 29572681. PMC6501843

Hu G, Niu F, Liao K, Periyasamy P, Sil S, Liu J, Dravid SM, Buch S (2019) HIV-1 Tat-Induced Astrocytic Extracellular Vesicle miR-7 Impairs Synaptic Architecture. J Neuroimmune Pharmacol. PMID: 31401755

McMillan J, Szlachetka A, Zhou T, Morsey B, Lamberty B, Callen S, Gautam N, Alnouti Y, Edagwa B, Gendelman HE, Fox HS. 2019. Pharmacokinetic testing of a first-generation cabotegravir prodrug in rhesus macaques. Aids 33:585-588. PMID: 30289818

Montenegro-Burke JR, Woldstad CJ, Fang M, Bade AN, McMillan J, Edagwa B, Boska MD, Gendelman HE, Siuzdak G. 2019. Nanoformulated Antiretroviral Therapy Attenuates Brain Metabolic Oxidative Stress. Mol Neurobiol 56:2896-2907. PMID: 30069830

Niu F, Liao K, Hu G, Sil S, Callen S, Guo ML, Yang L, Buch S. 2019. Cocaine-induced release of CXCL10 from pericytes regulates monocyte transmigration into the CNS. J Cell Biol 218:700-721. PMID: 30626719

Periyasamy P, Thangaraj A, Bendi VS, Buch S. 2019. HIV-1 Tat-mediated microglial inflammation involves a novel miRNA-34a-NLRC5-NFkappaB signaling axis. Brain Behav Immun doi:10.1016/j.bbi.2019.03.011. PMID: 30872089

Rinschen MM, Ivanisevic J, Giera M, Siuzdak G (2019) Identification of bioactive metabolites using activity metabolomics. Nat Rev Mol Cell Biol 20:353-367.PMID: 30814649. PMC6613555

Saminathan P, Kevadiya BD, Marker DF, Gendelman HE, Gorantla S, Gelbard HA. 2019. Broad Spectrum Mixed Lineage Kinase Type 3 Inhibition and HIV-1 Persistence in Macrophages. J Neuroimmune Pharmacol 14:44-51. PMID: 30617749

Sil S, Niu F, Tom E, Liao K, Periyasamy P, Buch S. 2019. Cocaine Mediated Neuroinflammation: Role of Dysregulated Autophagy in Pericytes. Mol Neurobiol 56:3576-3590. PMID: 30151726

Stauch KL, Villeneuve LM, Totusek S, Lamberty B, Ciborowski P, Fox HS. 2019. Quantitative Proteomics of Presynaptic Mitochondria Reveal an Overexpression and Biological Relevance of Neuronal MitoNEET in Postnatal Brain Development. Dev Neurobiol 79:370-386. PMID: 31050203

Su H, Cheng Y, Sravanam S, Mathews S, Gorantla S, Poluektova LY, Dash PK, Gendelman HE. 2019. Immune Activations and Viral Tissue Compartmentalization During Progressive HIV-1 Infection of Humanized Mice. Front Immunol 10:340. PMID: 30873181

Taraschenko O, Fox HS, Pittock SJ, Zekeridou A, Gafurova M, Eldridge E, Liu J, Dravid SM, Dingledine R (2019) A mouse model of seizures in anti-N-methyl-d-aspartate receptor encephalitis. Epilepsia 60:452-463. PMID: 30740690. PMC6684284

Zhao R, Li Y, Gorantla S, Poluektova LY, Lin H, Gao F, Wang H, Zhao J, Zheng JC, Huang Y. 2019. Small molecule ONC201 inhibits HIV-1 replication in macrophages via FOXO3a and TRAIL. Antiviral Res 168:134-145. PMID: 31158413


Gu CJ, Borjabad A, Hadas E, Kelschenbach J, Kim BH, Chao W, Arancio O, Suh J, Polsky B, McMillan J, Edagwa B, Gendelman HE, Potash MJ, Volsky DJ. 2018. EcoHIV infection of mice establishes latent viral reservoirs in T cells and active viral reservoirs in macrophages that are sufficient for induction of neurocognitive impairment. PLoS Pathog 14:e1007061. PMID: 29879225

Hu G, Liao K, Niu F, Yang L, Dallon BW, Callen S, Tian C, Shu J, Cui J, Sun Z, Lyubchenko YL, Ka M, Chen XM, Buch S. 2018. Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration. Mol Ther Nucleic Acids 13:450-463. PMID: 30388619

Lew BJ, McDermott TJ, Wiesman AI, O'Neill J, Mills MS, Robertson KR, Fox HS, Swindells S, Wilson TW. 2018. Neural dynamics of selective attention deficits in HIV-associated neurocognitive disorder. Neurology 91:e1860-e1869. PMID: 30333162

Lin Z, Gautam N, Alnouti Y, McMillan J, Bade AN, Gendelman HE, Edagwa B. 2018. ProTide generated long-acting abacavir nanoformulations. Chem Commun (Camb) 54:8371-8374. PMID: 29995046 

Ottemann BM, Helmink AJ, Zhang W, Mukadam I, Woldstad C, Hilaire JR, Liu Y, McMillan JM, Edagwa BJ, Mosley RL, Garrison JC, Kevadiya BD, Gendelman HE. 2018. Bioimaging predictors of rilpivirine biodistribution and antiretroviral activities. Biomaterials 185:174-193. PMID: 30245386

Tso FY, Kang G, Kwon EH, Julius P, Li Q, West JT, Wood C. 2018. Brain is a potential sanctuary for subtype C HIV-1 irrespective of ART treatment outcome. PLoS One 13:e0201325. PMID: 30040863 

Thangaraj A, Periyasamy P, Liao K, Bendi VS, Callen S, Pendyala G, Buch S. HIV-1 TAT-mediated microglial activation: role of mitochondrial dysfunction and defective mitophagy. Autophagy. 2018;14(9):1596-1619. doi: 10.1080/15548627.2018.1476810. Epub 2018 Jul 26. PMID: 29966509; PubMed Central PMCID: PMC6135576.

Brenza TM, Schlichtmann BW, Bhargavan B, Vela Ramirez JE, Nelson RD, Panthani MG, McMillan JM, Kalyanaraman B, Gendelman HE, Anantharam V, Kanthasamy AG, Mallapragada SK, Narasimhan B, Kanmogne GD (2018) Biodegradable polyanhydride-based nanomedicines for blood to brain drug delivery. Journal of biomedical materials research Part A 106:2881-2890. PMID: 30369055

Domingo-Almenara X, Montenegro-Burke JR, Benton HP, Siuzdak G (2018) Annotation: A Computational Solution for Streamlining Metabolomics Analysis. Analytical chemistry 90:480-489. PMID: 29039932 PMCID: PMC5750104 

Kiyota T, Machhi J, Lu Y, Dyavarshetty B, Nemati M, Zhang G, Mosley RL, Gelbard HA, Gendelman HE (2018) URMC-099 facilitates amyloid-beta clearance in a murine model of Alzheimer's disease. Journal of neuroinflammation 15:137. PMID: 29729668 PMCID: PMC5935963

McMillan J, Szlachetka A, Zhou T, Morsey B, Lamberty B, Callen S, Gautam N, Alnouti Y, Edagwa B, Gendelman HE, Fox HS (2018a) Pharmacokinetic testing of a first generation cabotegravir prodrug in rhesus macaques. AIDS (London, England). PMID: 30289818

Guijas C, Montenegro-Burke JR, Warth B, Spilker ME, Siuzdak G. Metabolomics activity screening for identifying metabolites that modulate phenotype. Nat Biotechnol. 2018;36(4):316-20. Epub 2018/04/06. doi: 10.1038/nbt.4101. PubMed PMID: 29621222; PubMed Central PMCID: PMC5937131.

Hu G, Liao K, Niu F, Yang L, Dallon BW, Callen S, Tian C, Shu J, Cui J, Sun Z, Lyubchenko YL, Ka M, Chen XM, Buch S. Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration. Mol Ther Nucleic Acids. 2018;13:450-63. Epub 2018/11/06. doi: 10.1016/j.omtn.2018.09.019. PubMed PMID: 30388619; PubMed Central PMCID: PMC6202788.

Kevadiya BD, Ottemann BM, Thomas MB, Mukadam I, Nigam S, McMillan J, Gorantla S, Bronich TK, Edagwa B, Gendelman HE. Neurotheranostics as personalized medicines. Adv Drug Deliv Rev. 2018. Epub 2018/11/14. doi: 10.1016/j.addr.2018.10.011. PubMed PMID: 30421721.

Ottemann BM, Helmink AJ, Zhang W, Mukadam I, Woldstad C, Hilaire JR, Liu Y, McMillan JM, Edagwa BJ, Mosley RL, Garrison JC, Kevadiya BD, Gendelman HE.. Bioimaging predictors of rilpivirine biodistribution and antiretroviral activities. Biomaterials. 2018;185:174-93. Epub 2018/09/25. doi: 10.1016/j.biomaterials.2018.09.018. PubMed PMID: 30245386.

Periyasamy P, Thangaraj A, Guo ML, Hu G, Callen S, Buch S (2018) Epigenetic Promoter DNA Methylation of miR-124 Promotes HIV-1 Tat-Mediated Microglial Activation via MECP2-STAT3 Axis. The Journal of neuroscience : the official journal of the Society for Neuroscience 38:5367-5383. PMID: 29760177 PMCID: PMC5990983.

Sathyanesan M, Watt MJ, Haiar JM, Scholl JL, Davies SR, Paulsen RT, Wiederin J, Ciborowski P, Newton SS (2018) Carbamoylated erythropoietin modulates cognitive outcomes of social defeat and differentially regulates gene expression in the dorsal and ventral hippocampus. Translational psychiatry 8:113. PMID: 29884778 PMCID: PMC5993867.

Schutt CR, Gendelman HE, Mosley RL. Tolerogenic bone marrow-derived dendritic cells induce neuroprotective regulatory T cells in a model of Parkinson's disease. Mol Neurodegener. 2018;13(1):26. Epub 2018/05/23. doi: 10.1186/s13024-018-0255-7. PubMed PMID: 29783988; PubMed Central PMCID: PMC5963189. 

Sil S, Niu F, Tom E, Liao K, Periyasamy P, Buch S. Cocaine Mediated Neuroinflammation: Role of Dysregulated Autophagy in Pericytes. Mol Neurobiol. 2018. Epub 2018/08/29. doi: 10.1007/s12035-018-1325-0. PubMed PMID: 30151726.

Spooner RK, Wiesman AI, Mills MS, O'Neill J, Robertson KR, Fox HS, Swindells S, Wilson TW. Aberrant oscillatory dynamics during somatosensory processing in HIV-infected adults. Neuroimage Clin. 2018;20:85-91. Epub 2018/08/11. doi: 10.1016/j.nicl.2018.07.009. PubMed PMID: 30094159; PubMed Central PMCID: PMC6070689.

Thomas MB, Gnanadhas DP, Dash PK, Machhi J, Lin Z, McMillan J, Edagwa B, Gelbard H, Gendelman HE, Gorantla S (2018) Modulating cellular autophagy for controlled antiretroviral drug release. Nanomedicine (London, England) 13:2139-2154. PMID: 30129397 PMCID: PMC6219451

Wiesman AI, O'Neill J, Mills MS, Robertson KR, Fox HS, Swindells S, et al. Aberrant occipital dynamics differentiate HIV-infected patients with and without cognitive impairment. Brain. 2018;141(6):1678-90. Epub 2018/04/20. doi: 10.1093/brain/awy097. PubMed PMID: 29672678; PubMed Central PMCID: PMC5972635.

Yang L, Niu F, Yao H, Liao K, Chen X, Kook Y, et al. Exosomal miR-9 Released from HIV Tat Stimulated Astrocytes Mediates Microglial Migration. J Neuroimmune Pharmacol. 2018;13(3):330-44. Epub 2018/03/03. doi: 10.1007/s11481-018-9779-4. PubMed PMID: 29497921; PubMed Central PMCID: PMCPMC6082702.

Dave RS, Jain P, Byrareddy SN. Functional Meningeal Lymphatics and Cerebrospinal Fluid Outflow. Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology. 2018;13(2):123-5. Epub 2018/02/22. doi: 10.1007/s11481-018-9778-5. PubMed PMID: 29464588.

Dyavar SR, Ye Z, Byrareddy SN, Scarsi KK, Winchester LC, Weinhold JA, et al. Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay. Scientific reports. 2018;8(1):3626. Epub 2018/02/28. doi: 10.1038/s41598-018-21882-0. PubMed PMID: 29483619; PubMed Central PMC5827666.

Kevadiya BD, Woldstad C, Ottemann BM, Dash P, Sajja BR, Lamberty B, et al. Multimodal Theranostic Nanoformulations Permit Magnetic Resonance Bioimaging of Antiretroviral Drug Particle Tissue-Cell Biodistribution. Theranostics. 2018;8(1):256-76. Epub 2018/01/02. doi: 10.7150/thno.22764. PubMed PMID: 29290806; PubMed Central PMC5743473. 

McMillan J, Szlachetka A, Slack L, Sillman B, Lamberty B, Morsey B, et al. Pharmacokinetics of a Long-Acting Nanoformulated Dolutegravir Prodrug in Rhesus Macaques. Antimicrobial agents and chemotherapy. 2018;62(1). Epub 2017/10/25. doi: 10.1128/aac.01316-17. PubMed PMID: 29061742; PubMed Central PMC5740312.

Olson KE, Bade AN, Namminga KL, Potash MJ, Mosley RL, Poluektova LY, et al. Persistent EcoHIV infection induces nigral degeneration in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-intoxicated mice. Journal of neurovirology. 2018. Epub 2018/03/30. doi: 10.1007/s13365-018-0629-1. PubMed PMID: 29594983.

Sillman B, Bade AN, Dash PK, Bhargavan B, Kocher T, Mathews S, et al. Creation of a long-acting nanoformulated dolutegravir. Nature communications. 2018;9(1):443. Epub 2018/02/07. doi: 10.1038/s41467-018-02885-x. PubMed PMID: 29402886; PubMed Central PMC5799307.

Sillman B, Woldstad C, McMillan J, Gendelman HE. Neuropathogenesis of human immunodeficiency virus infection. Handbook of clinical neurology. 2018;152:21-40. Epub 2018/04/02. doi: 10.1016/b978-0-444-63849-6.00003-7. PubMed PMID: 29604978.

Zhou T, Lin Z, Puligujja P, Palandri D, Hilaire J, Arainga M, et al. Optimizing the preparation and stability of decorated antiretroviral drug nanocrystals. Nanomedicine (London, England). 2018. Epub 2018/03/20. doi: 10.2217/nnm-2017-0381. PubMed PMID: 29553879.

Zhou T, Su H, Dash P, Lin Z, Dyavar Shetty BL, Kocher T, et al. Creation of a nanoformulated cabotegravir prodrug with improved antiretroviral profiles. Biomaterials. 2018;151:53-65. Epub 2017/10/24. doi: 10.1016/j.biomaterials.2017.10.023. PubMed PMID: 29059541; PubMed Central PMC5926202.


Hu G, Liao K, Yang L, Pendyala G, Kook Y, Fox HS, Buch S. Tat-Mediated Induction of miRs-34a & -138 Promotes Astrocytic Activation via Downregulation of SIRT1: Implications for Aging in HAND. J Neuroimmune Pharmacol. 2017 Sep;12(3):420-432. PMID: 28236278

Stauch KL, Emanuel K, Lamberty BG, Morsey B, Fox HS. Central nervous system-penetrating antiretrovirals impair energetic reserve in striatal nerve terminals. J Neurovirol. 2017 Sep 11. doi: 10.1007/s13365-017-0573-5. [Epub ahead of print]. PMID: 28895059

Embury CM, Dyavarshetty B, Lu Y, Wiederin JL, Ciborowski P, Gendelman HE, Kiyota T. Cathepsin B Improves ß-Amyloidosis and Learning and Memory in Models of Alzheimer's Disease. J Neuroimmune Pharmacol. 2017 Jun;12(2):340-352. PMID: 27966067  PMCID: PMC5405105 

Arainga M, Edagwa B, Mosley RL, Poluektova LY, Gorantla S, Gendelman HE. A mature macrophage is a principal HIV-1 cellular reservoir in humanized mice after treatment with long acting antiretroviral therapy. Retrovirology. 2017;14(1):17. Epub 2017/03/11. doi: 10.1186/s12977-017-0344-7. PubMed PMID: 28279181; PMCID: PMC5345240.

Edagwa B, McMillan J, Sillman B, Gendelman HE. Long-acting slow effective release antiretroviral therapy. Expert opinion on drug delivery. 2017:1-11. Epub 2017/01/28. doi: 10.1080/17425247.2017.1288212. PubMed PMID: 28128004; PMCID: PMC5545165.

Embury CM, Dyavarshetty B, Lu Y, Wiederin JL, Ciborowski P, Gendelman HE, Kiyota T. Cathepsin B Improves ss-Amyloidosis and Learning and Memory in Models of Alzheimer's Disease. Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology. 2017;12(2):340-52. Epub 2016/12/15. doi: 10.1007/s11481-016-9721-6. PubMed PMID: 27966067; PMCID: PMC5405105.

Gnanadhas DP, Dash PK, Sillman B, Bade AN, Lin Z, Palandri DL, Gautam N, Alnouti Y, Gelbard HA, McMillan J, Mosley RL, Edagwa B, Gendelman HE, Gorantla S. Autophagy facilitates macrophage depots of sustained-release nanoformulated antiretroviral drugs. The Journal of clinical investigation. 2017;127(3):857-73. Epub 2017/01/31. doi: 10.1172/jci90025. PubMed PMID: 28134625; PMCID: PMC5330738.

Guo D, Zhou T, Arainga M, Palandri D, Gautam N, Bronich T, Alnouti Y, McMillan J, Edagwa B, Gendelman HE. Creation of a Long-Acting Nanoformulated 2',3'-Dideoxy-3'-Thiacytidine. Journal of acquired immune deficiency syndromes. 2017;74(3):e75-e83. Epub 2016/10/19. doi: 10.1097/qai.0000000000001170. PubMed PMID: 27559685; PMCID: PMC5305294.

Hu G, Liao K, Yang L, Pendyala G, Kook Y, Fox HS, Buch S. Tat-Mediated Induction of miRs-34a & -138 Promotes Astrocytic Activation via Downregulation of SIRT1: Implications for Aging in HAND. Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology. 2017;12(3):420-32. Epub 2017/02/27. doi: 10.1007/s11481-017-9730-0. PubMed PMID: 28236278; PMCID: PMC5546000.

Kevadiya BD, Bade AN, Woldstad C, Edagwa BJ, McMillan JM, Sajja BR, Boska MD, Gendelman HE. Development of europium doped core-shell silica cobalt ferrite functionalized nanoparticles for magnetic resonance imaging. Acta biomaterialia. 2017;49:507-20. Epub 2016/12/06. doi: 10.1016/j.actbio.2016.11.071. PubMed PMID: 27916740; PMCID: PMC5501313.

Shahnaz G, Edagwa BJ, McMillan J, Akhtar S, Raza A, Qureshi NA, Yasinzai M, Gendelman HE. Development of mannose-anchored thiolated amphotericin B nanocarriers for treatment of visceral leishmaniasis. Nanomedicine (London, England). 2017;12(2):99-115. Epub 2016/11/24. doi: 10.2217/nnm-2016-0325. PubMed PMID: 27879160; PMCID: PMC5144491.

Wilson TW, Proskovec AL, Heinrichs-Graham E, O'Neill J, Robertson KR, Fox HS, Swindells S. Aberrant Neuronal Dynamics during Working Memory Operations in the Aging HIV-Infected Brain. Scientific reports. 2017;7:41568. Epub 2017/02/06. doi: 10.1038/srep41568. PubMed PMID: 28155864; PMCID: PMC5290733


Arainga M, Su H, Poluektova LY, Gorantla S, Gendelman HE. HIV-1 cellular and tissue replication patterns in infected humanized mice. Scientific reports. 2016;6:23513. Epub 2016/03/22. doi: 10.1038/srep23513. PubMed PMID: 26996968; PMCID: PMC4800734.

Bade AN, Gorantla S, Dash PK, Makarov E, Sajja BR, Poluektova LY, Luo J, Gendelman HE, Boska MD, Liu Y. Manganese-Enhanced Magnetic Resonance Imaging Reflects Brain Pathology During Progressive HIV-1 Infection of Humanized Mice. Molecular neurobiology. 2016;53(5):3286-97. Epub 2015/06/13. doi: 10.1007/s12035-015-9258-3. PubMed PMID: 26063593; PMCID: PMC4676748.

Burns A, Ciborowski P. Acute exposure to methamphetamine alters TLR9-mediated cytokine expression in human macrophage. Immunobiology. 2016 Feb;221(2):199-207. PubMed PMID: 26387832; PubMed Central PMCID: PMC4688157.

Dong W, Embury CM, Lu Y, Whitmire SM, Dyavarshetty B, Gelbard HA, Gendelman HE, Kiyota T. The mixed-lineage kinase 3 inhibitor URMC-099 facilitates microglial amyloid-beta degradation. Journal of neuroinflammation. 2016;13(1):184. Epub 2016/07/13. doi: 10.1186/s12974-016-0646-z. PubMed PMID: 27401058; PMCID: PMC4940949.

Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell. 2016 Apr 21;62(2):157-68. PMID: 27105112. PMCID: PMC4995115.

Heinrichs-Graham E, Wilson TW. Is an absolute level of cortical beta suppression required for proper movement? Magnetoencephalographic evidence from healthy aging. NeuroImage. 2016; 134:514-21. NIHMSID: NIHMS783164 PubMed [journal] PMID: 27090351, PMCID: PMC4912897

Hu G, Yang L, Cai Y, Niu F, Mezzacappa F, Callen S, Fox HS, Buch S. Emerging roles of extracellular vesicles in neurodegenerative disorders: focus on HIV-associated neurological complications. Cell death & disease. 2016;7(11):e2481. Epub 2016/11/25. doi: 10.1038/cddis.2016.336. PubMed PMID: 27882942; PMCID: PMC5260908.

Ivanisevic J, Stauch KL, Petrascheck M, Benton HP, Epstein AA, Fang M, Gorantla S, Tran M, Hoang L, Kurczy ME, Boska MD, Gendelman HE, Fox HS, Siuzdak G. Metabolic drift in the aging brain. Aging (Albany NY). 2016 May;8(5):1000-20. PMID: 27182841; PMCID: PMC4931850

Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hoffree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Molecular neurodegeneration. 2016;11:31. Epub 2016/04/27. doi: 10.1186/s13024-016-0095-2. PubMed PMID: 27112350; PMCID: PMC4845325.

Li W, Tong HI, Gorantla S, Poluektova LY, Gendelman HE, Lu Y. Neuropharmacologic Approaches to Restore the Brain's Microenvironment. Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology. 2016;11(3):484-94. Epub 2016/06/29. doi: 10.1007/s11481-016-9686-5. PubMed PMID: 27352074; PMCID: PMC4985494.

Olson KE, Bade AN, Schutt CR, Dong J, Shandler SJ, Boska MD, Mosley RL, Gendelman HE, Liu Y. Manganese-Enhanced Magnetic Resonance Imaging for Detection of Vasoactive Intestinal Peptide Receptor 2 Agonist Therapy in a Model of Parkinson's Disease. Neurotherapeutics. 2016 Jul;13(3):635-46.PMID: 27329163; PubMed Central PMCID: PMC4965412.

Olson KE, Gendelman HE. Immunomodulation as a neuroprotective and therapeutic strategy for Parkinson's disease. Curr Opin Pharmacol. 2016 Feb;26:87-95. PubMed PMID: 26571205; PubMed Central PMCID: PMC4716884.

Proskovec AL, Heinrichs-Graham E, Wilson TW. Aging modulates the oscillatory dynamics underlying successful working memory encoding and maintenance. Human Brain Mapping. 2016; 37(6):2348-61. NIHMSID: NIHMS764788 PubMed [journal] PMID: 26991358, PMCID: PMC4867257 

Sajja BR, Bade AN, Zhou B, Uberti MG, Gorantla S, Gendelman HE, Boska MD, Liu Y. Generation and Disease Model Relevance of a Manganese Enhanced Magnetic Resonance Imaging-Based NOD/scid-IL-2Rγ c (null) Mouse Brain Atlas. J Neuroimmune Pharmacol. 2016 Mar;11(1):133-41. PubMed PMID: 26556033. PubMed Central PMCID: PMC4871948.

Singh D, McMillan J, Hilaire J, Gautam N, Palandri D, Alnouti Y, Gendelman HE, Edagwa B. Development and characterization of a long-acting nanoformulated abacavir prodrug. Nanomedicine (London, England). 2016;11(15):1913-27. Epub 2016/07/28. doi: 10.2217/nnm-2016-0164. PubMed PMID: 27456759; PMCID: PMC4996153.

Villeneuve LM, Purnell PR, Stauch KL, Callen SE, Buch SJ, Fox HS. HIV-1 transgenic rats display mitochondrial abnormalities consistent with abnormal energy generation and distribution. J Neurovirol. 2016 Feb 3. PubMed PMID: 26843384; [Epub ahead of print] PubMed Central PMCID: PMC4972699.

Wilson TW, Heinrichs-Graham E, Proskovec AL, McDermott TJ. Neuroimaging with magnetoencephalography: A dynamic view of brain pathophysiology. Translational Research. 2016; 175:17-36. NIHMSID: NIHMS754631 PubMed [journal] PMID: 26874219, PMCID: PMC4959997

Yang L, Yao H, Chen X, Cai Y, Callen S, Buch S. Role of Sigma Receptor in Cocaine-Mediated Induct ion of Glial Fibrillary Acidic Protein: Implications for HAND. Mol Neurobiol. 2016 Mar;53(2):1329-42. PubMed PMID: 25631712; PubMed Central PMCID: PMC4519438.

Zhang G, Guo D, Dash PK, Araínga M, Wiederin JL, Haverland NA, Knibbe-Hollinger J, Martinez-Skinner A, Ciborowski P, Goodfellow VS, Wysocki TA, Wysocki BJ, Poluektova LY, Liu XM, McMillan JM, Gorantla S, Gelbard HA, Gendelman HE. The mixed lineage kinase-3 inhibitor URMC-099 improves therapeutic outcomes for long-acting antiretroviral therapy. Nanomedicine. 2016. Jan;12(1):109-22. PubMed PMID: 26472049; PubMed Central PMCID: PMC4728028.

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Araínga M, Guo D, Wiederin J, Ciborowski P, McMillan J, Gendelman HE. Opposing regulation of endolysosomal pathways by long-acting nanoformulated antiretroviral therapy and HIV-1 in human macrophages. Retrovirology. 2015 Jan 22;12:5. PubMed PMID: 25608975; PubMed Central PMCID: PMC4307176.

Bade AN, Gorantla S, Dash PK, Makarov E, Sajja BR, Poluektova LY, Luo J, Gendelman HE, Boska MD, Liu Y. Manganese- Enhanced Magnetic Resonance Imaging Reflects Brain Pathology During Progressive HIV-1 Infection of Humanized Mice. Mol Neurobiol. 2015 Jul;53(5):3286-97. PMID: 26063593. PubMed Central PMCID: PMC4676748

Bade AN, Zhou B, McMillan J, Narayanasamy P, Veerubhotla R, Gendelman HE, Boska MD, Liu Y. Potential of N-acetylated-para-aminosalicylic acid to accelerate manganese enhancement decline for long-term MEMRI in rodent brain. J Neurosci Methods. 2015 Aug 15;251:92-8. PubMed PMID: 26004847; PubMed Central PMCID: PMC4500662.

Bai Y, Zhu X, Chao J, Zhang Y, Qian C, Li P, Liu D, Han B, Zhao L, Zhang J, Buch S, Teng G, Hu G, Yao H. Pericytes contribute to the disruption of the cerebral endothelial barrier via increasing VEGF expression: implications for stroke. PLoS One. 2015;10(4):e0124362. PubMed PMID: 25884837; PubMed Central PMCID: PMC4401453.

Benton HP, Ivanisevic J, Mahieu NG, Kurczy ME, Johnson CH, Franco L, Rinehart D, Valentine E, Gowda H, Ubhi BK, Tautenhahn R, Gieschen A, Fields MW, Patti GJ, Siuzdak G. Autonomous metabolomics for rapid metabolite identification in global profiling. Anal Chem. 2015 Jan 20;87(2):884-91. PubMed PMID: 25496351; PubMed Central PMCID: PMC4303330.

Benton PH, Ivanisevic J, Rinehart D, Epstein A, Kurczy ME, Boska MD, Gendelman HE, Siuzdak G. An Interactive Cluster Heat Map to Visualize and Explore Multidimensional Metabolomic Data. Metabolomics. 2015 Aug 1;11(4):1029-1034. PubMed PMID: 26195918; PubMed Central PMCID: PMC4505375.

Cserhati MF, Pandey S, Beaudoin JJ, Baccaglini L, Guda C, Fox HS. The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies. Database (Oxford). 2015;2015:bav074. PubMed PMID: 26228431; PubMed Central PMCID: PMC4520230.

Donnelly MR, Ciborowski P. Proteomics, biomarkers, and HIV-1: A current perspective. Proteomics Clin Appl. 2015 Feb;10(2):110-25. PubMed PMID: 26033875; PubMed Central PMCID: PMC4666820.

Gendelman HE, Anantharam V, Bronich T, Ghaisas S, Jin H, Kanthasamy AG, Liu X, McMillan J, Mosley RL, Narasimhan B, Mallapragada SK. Nanoneuromedicines for degenerative, inflammatory, and infectious nervous system diseases. Nanomedicine. 2015 Apr;11(3):751-67. PubMed PMID: 25645958; PubMed Central PMCID: PMC4387001.

Gendelman HE, Mosley RL. A Perspective on Roles Played by Innate and Adaptive Immunity in the Pathobiology of Neurodegenerative Disorders. J Neuroimmune Pharmacol. 2015 Dec;10(4):645-50. PubMed PMID: 26520433; PubMed Central PMCID: PMC4662620.

Gruol DL. IL-6 regulation of synaptic function in the CNS. Neuropharmacology. 2015 Sep;96(Pt A):42-54. PMID: 25445486. PubMed Central PMC4446251.

Guo ML, Liao K, Periyasamy P, Yang L, Cai Y, Callen SE, Buch S. Cocaine-mediated microglial activation involves the ER stress- autophagy axis. Autophagy. 2015 Jul 3;11(7):995-1009. PubMed PMID: 26043790. PMCID: PMC4590604.

Johnson CH, Dejea CM, Edler D, Hoang LT, Santidrian AF, Felding BH, Ivanisevic J, Cho K, Wick EC, Hechenbleikner EM, Uritboonthai W, Goetz L, Casero RA Jr, Pardoll DM, White JR, Patti GJ, Sears CL, Siuzdak G. Metabolism links bacterial biofilms and colon carcinogenesis. Cell Metab. 2015 Jun 2;21(6):891-7. PubMed PMID: 25959674; PubMed Central PMCID: PMC4456201.

Johnson CH, Ivanisevic J, Benton HP, Siuzdak G. Bioinformatics: the next frontier of metabolomics. Anal Chem. 2015 Jan 6;87(1):147-56. PubMed PMID: 25389922; PubMed Central PMCID: PMC4287838.

Johnson CH, Patti GJ, Courade JP, Shriver LP, Hoang LT, Manchester M, Siuzdak G. Alterations in Spinal Cord Metabolism during Treatment of Neuropathic Pain. J Neuroimmune Pharmacol. 2015 Sep;10(3):396-401. PMID: 26232265. PubMed Central PMCID: PMC4548716.

Kelso ML, Elliott BR, Haverland NA, Mosley RL, Gendelman HE. Granulocyte-macrophage colony stimulating factor exerts protective and immunomodulatory effects in cortical trauma. J Neuroimmunol. 2015 Jan 15;278:162-73. PubMed PMID: 25468272; PubMed Central PMCID: PMC4297700.

Kiyota T, Morrison CM, Tu G, Dyavarshetty B, Weir RA, Zhang G, Xiong H, Gendelman HE. Presenilin-1 familial Alzheimer's disease mutation alters hippocampal neurogenesis and memory function in CCL2 null mice. Brain Behav Immun. 2015 Oct;49:311-2. PubMed PMID: 26112421; PubMed Central PMCID: PMC4567522.

Kiyota T, Zhang G, Morrison CM, Bosch ME, Weir RA, Lu Y, Dong W, Gendelman HE. AAV2/1 CD74 Gene Transfer Reduces β-amyloidosis and Improves Learning and Memory in a Mouse Model of Alzheimer's Disease. Mol Ther. 2015 Nov;23(11):1712-21. PubMed PMID: 26227349. PubMed Central PMCID: PMC4817947.

Kurczy ME, Northen TR, Trauger SA, Siuzdak G. Nanostructure imaging mass spectrometry: the role of fluorocarbons in metabolite analysis and yoctomole level sensitivity. Methods Mol Biol. 2015;1203:141-9. PubMed PMID: 25361674. PubMed Central PMCID: PMC4755109.

Kurczy ME, Zhu ZJ, Ivanisevic J, Schuyler AM, Lalwani K, Santidrian AF, David JM, Giddabasappa A, Roberts AJ, Olivos HJ, O'Brien PJ, Franco L, Fields MW, Paris LP, Friedlander M, Johnson CH, Epstein AA, Gendelman HE, Wood MR, Felding BH, Patti GJ, Spilker ME, Siuzdak G. Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids. Nat Commun. 2015 Jan 20;6:5998. PubMed PMID: 25601659; PubMed Central PMCID: PMC4454288.

Li T, Gendelman HE, Zhang G, Puligujja P, McMillan JM, Bronich TK, Edagwa B, Liu XM, Boska MD. Magnetic resonance imaging of folic acid-coated magnetite nanoparticles reflects t issue biodistribution of long-acting antiretroviral therapy. Int J Nanomedicine. 2015;10:3779-90. PubMed PMID: 26082630; PubMed Central PMCID: PMC4461087.

Mallapragada SK, Brenza TM, McMillan JM, Narasimhan B, Sakaguchi DS, Sharma AD, Zbarska S, Gendelman HE. Enabling nanomaterial, nanofabrication and cellular technologies for nanoneuromedicines. Nanomedicine. 2015 Apr;11(3):715-29. PubMed PMID: 25652894; PubMed Central PMCID: PMC4628726.

Marcondes MC, Morsey B, Emanuel K, Lamberty BG, Flynn CT, Fox HS. CD8+ T cells maintain suppression of simian immunodeficiency virus in the central nervous system. J Infect Dis. 2015 Jan 1;211(1):40-4. PubMed PMID: 25035516; PubMed Central PMCID: PMC4334822.

Martinez-Skinner AL, Araínga MA, Puligujja P, Palandri DL, Baldridge HM, Edagwa BJ, McMillan JM, Mosley RL, Gendelman HE. Cellular Responses and Tissue Depots for Nanoformulated Antiretroviral Therapy. PLoS One. 2015;10(12):e0145966. PubMed PMID: 26716700; PubMed Central PMCID: PMC4696780

Niu F, Yao H, Liao K, Buch S. HIV Tat 101-mediated loss of pericytes at the blood-brain barrier involves PDGF-BB. Ther Targets Neurol Dis. 2015;2(1)PubMed PMID: 26023685; PubMed Central PMCID: PMC4444060.

Olson KE, Kosloski-Bilek LM, Anderson KM, Diggs BJ, Clark BE, Gledhill JM Jr, Shandler SJ, Mosley RL, Gendelman HE. Selective VIP Receptor Agonists Facilitate Immune Transformation for Dopaminergic Neuroprotection in MPTP-Intoxicated Mice. J Neurosci. 2015 Dec 16;35(50):16463-78. PMID: 26674871. PubMed Central PMCID: PMC4679826

Pendyala G, Periyasamy P, Callen S, Fox HS, Lisco SJ, Buch SJ. Chronic SIV and morphine treatment increases heat shock protein 5 expression at the synapse. J Neurovirol. 2015 Oct;21(5):592-8. PubMed PMID: 26037114; PubMed Central PMCID: PMC4618049.

Puligujja P, Araínga M, Dash P, Palandri D, Mosley RL, Gorantla S, Poluektova L, McMillan J, Gendelman HE. Pharmacodynamics of folic acid receptor targeted antiretroviral nanotherapy in HIV-1- infected humanized mice. Antiviral Res. 2015 Aug;120:85-8. PubMed PMID: 26026666; PubMed Central PMCID: PMC4492829.

Puligujja P, Balkundi SS, Kendrick LM, Baldridge HM, Hilaire JR, Bade AN, Dash PK, Zhang G, Poluektova LY, Gorantla S, Liu XM, Ying T, Feng Y, Wang Y, Dimitrov DS, McMillan JM, Gendelman HE. Pharmacodynamics of long-acting folic acid-receptor targeted ritonavir-boosted atazanavir nanoformulations. Biomaterials. 2015 Feb;41:141-50. PubMed PMID: 25522973; PubMed Central PMCID: PMC4272445.

Ross KA, Brenza TM, Binnebose AM, Phanse Y, Kanthasamy AG, Gendelman HE, Salem AK, Bartholomay LC, Bellaire BH, Narasimhan B. Nano-enabled delivery of diverse payloads across complex biological barriers. J Control Release. 2015 Dec 10;219:548-59. PubMed PMID: 26315817; PubMed Central PMCID: PMC4656048.

Stauch KL, Purnell PR, Villeneuve LM, Fox HS. Data for mitochondrial proteomic alterations in the aging mouse brain. Data Brief. 2015 Sep;4:127-9. PubMed PMID: 26217775; PubMed Central PMCID: PMC4510433.

Stauch KL, Purnell PR, Villeneuve LM, Fox HS. Proteomic analysis and functional characterization of mouse brain mitochondria during aging reveal alterations in energy metabolism. Proteomics. 2015 May;15(9):1574-86. PubMed PMID: 25546256; PubMed Central PMCID: PMC4465935.

Thapa I, Fox HS, Bastola D. Coexpression Network Analysis of miRNA-142 Overexpression in Neuronal Cells. Biomed Res Int. 2015;2015:921517. PMID: 26539539. PubMed Central PMCID: PMCID: PMC4619910.

Wilson TW, Heinrichs-Graham E, Becker KM, Aloi J, Robertson KR, Sandkovsky U, White ML, O'Neill J, Knott NL, Fox HS, Swindells S. Multimodal neuroimaging evidence of alterations in cortical structure and function in HIV-infected older adults. Hum Brain Mapp. 2015 Mar;36(3):897-910. PubMed PMID: 25376125; PubMed Central PMCID: PMC4491915.

Yelamanchili SV, Lamberty BG, Rennard DA, Morsey BM, Hochfelder CG, Meays BM, Levy E, Fox HS. MiR-21 in Extracellular Vesicles Leads to Neurotoxicity via TLR7 Signaling in SIV Neurological Disease. PLoS Pathog. 2015 Jul;11(7):e1005032. PubMed PMID: 26154133; PubMed Central PMCID: PMC4496044.

Zhang Y, Lv X, Bai Y, Zhu X, Wu X, Chao J, Duan M, Buch S, Chen L, Yao H. Involvement of sigma-1 receptor in astrocyte activation induced by methamphetamine via up-regulation of its own expression. J Neuroinflammation. 2015 Feb 17;12:29. PubMed PMID: 25889537; PubMed Central PMCID: PMC4340104.

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Al-Harthi L, Buch S, Geiger JD, Gendelman HE, He JJ, Jordan- Sciutto KL, Kolson DL, Rappaport J, Roy S, Zheng J, Fox HS. Cellular Interactions and Signaling in neuroAIDS: Emerging Issues Colloquium. J Neuroimmune Pharmacol. 2014 Jun;9(3):269-76. PubMed PMID: 24789373; PubMed Central PMCID: PMC4104811.

Boska MD, Dash PK, Knibbe J, Epstein AA, Akhter SP, Fields N, High R, Makarov E, Bonasera S, Gelbard HA, Poluektova LY, Gendelman HE, Gorantla S. Associations between brain microstructures, metabolites, and cognitive deficits during chronic HIV-1 infection of humanized mice. Mol Neurodegener. 2014 Dec 18;9:58. PubMed PMID: 25523827; PubMed Central PMCID: PMC4297430.

Chao J, Yang L, Yao H, Buch S. Platelet-derived growth factor-BB restores HIV Tat -mediated impairment of neurogenesis: role of GSK-3β/β-catenin. J Neuroimmune Pharmacol. 2014 Mar;9(2):259-68. PubMed PMID: 24248537; PubMed Central PMCID: PMC4183349.

Crabtree KL, Wojcicki JM, Minhas V, Smith DR, Kankasa C, Mitchell CD, Wood C. Risk factors for early childhood infection of human herpesvirus-8 in Zambian children: the role of early childhood feeding practices. Cancer Epidemiol Biomarkers Prev. 2014 Feb;23(2):300-8. PubMed PMID: 24296855; PubMed Central PMCID: PMC3939055.

Dempsey KM, Ali HH. Identifying aging-related genes in mouse hippocampus using gateway nodes. BMC Syst Biol. 2014 May 27;8:62. PubMed PMID: 24886704; PubMed Central PMCID: PMC4057599.

Duan M, Yao H, Cai Y, Liao K, Seth P, Buch S. HIV-1 Tat disrupts CX3CL1-CX3CR1 axis in microglia via the NF-κBYY1 pathway. Curr HIV Res. 2014;12(3):189-200. PubMed PMID: 24862326. PMCID: PMC5003019

Edagwa BJ, Zhou T, McMillan JM, Liu XM, Gendelman HE. Development of HIV reservoir targeted long acting nanoformulated antiretroviral therapies. Curr Med Chem. 2014;21(36):4186-98. PubMed PMID: 25174930; PubMed Central PMCID: PMC4281174.

Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. An integrated map of HIV-human protein complexes that facilitate viral infection. PLoS One. 2014;9(5):e96687. PubMed PMID: 24817247; PubMed Central PMCID: PMC4016004.

Gendelman HE, Balogh LP, Bawa R, Bradbury M, Chang EH, Chiu W, Farokhzad O, Foldvari M, Lanza G, Wang K. The 4th Annual Meeting of the American Society for Nanomedicine. J Neuroimmune Pharmacol. 2014 Mar;9 Suppl 1:S1-3. PubMed PMID: 24550132. PubMed Central PMCID: PMC3951957.

Gendelman HE, Gelbard HA. Adjunctive and long-acting nanoformulated antiretroviral therapies for HIV-associated neurocognitive disorders. Curr Opin HIV AIDS. 2014 Nov;9(6):585- 90. PubMed PMID: 25226025; PubMed Central PMCID: PMC4231201.

Gowda H, Ivanisevic J, Johnson CH, Kurczy ME, Benton HP, Rinehart D, Nguyen T, Ray J, Kuehl J, Arevalo B, Westenskow PD, Wang J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem. 2014 Jul 15;86(14):6931-9. PubMed PMID: 24934772; PubMed Central PMCID: PMC4215863.

Guo D, Li T, McMillan J, Sajja BR, Puligujja P, Boska MD, Gendelman HE, Liu XM. Small magnetite antiretroviral therapeutic nanoparticle probes for MRI of drug biodistribution. Nanomedicine (Lond). 2014 Jul;9(9):1341-52. PubMed PMID: 23905578; PubMed Central PMCID: PMC3909560.

Guo D, Zhang G, Wysocki TA, Wysocki BJ, Gelbard HA, Liu XM, McMillan JM, Gendelman HE. Endosomal trafficking of nanoformulated antiretroviral therapy facilitates drug particle carriage and HIV clearance. J Virol. 2014 Sep 1;88(17):9504-13. PubMed PMID: 24920821; PubMed Central PMCID: PMC4136325.

Haverland NA, Fox HS, Ciborowski P. Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages. J Proteome Res. 2014 Apr 4;13(4):2109-19. PubMed PMID: 24564501; PubMed Central PMCID: PMC3993959.

Ivanisevic J, Epstein AA, Kurczy ME, Benton PH, Uritboonthai W, Fox HS, Boska MD, Gendelman HE, Siuzdak G. Brain region mapping using global metabolomics. Chem Biol. 2014 Nov 20;21(11):1575-84. PubMed PMID: 25457182; PubMed Central PMCID: PMC4304924.

Johnson CH, Fisher TS, Hoang LT, Felding BH, Siuzdak G, O'Brien PJ. Luciferase does not Alter Metabolism in Cancer Cells. Metabolomics. 2014 Jun 1;10(3):354-360. PubMed PMID: 24791164; PubMed Central PMCID: PMC4002053.

Ma R, Yang L, Niu F, Buch S. HIV Tat-Mediated Induction of Human Brain Microvascular Endothelial Cell Apoptosis Involves Endoplasmic Reticulum Stress and Mitochondrial Dysfunction. Mol Neurobiol. 2014 Nov 20;PubMed PMID: 25409632. PubMed Central PMC4787264.

Niu F, Yao H, Zhang W, Sutliff RL, Buch S. Tat 101-mediated enhancement of brain pericyte migration involves platelet-derived growth factor subunit B homodimer: implications for human immunodeficiency virus-associated neurocognitive disorders. J Neurosci. 2014 Aug 27;34(35):11812-25. PubMed PMID: 25164676; PubMed Central PMCID: PMC4145180.

Patti GJ, Tautenhahn R, Johannsen D, Kalisiak E, Ravussin E, Brüning JC, Dillin A, Siuzdak G. Meta-analysis of global metabolomic data identifies metabolites associated with life- span extension. Metabolomics. 2014 Aug 1;10(4):737-743. PubMed PMID: 25530742; PubMed Central PMCID: PMC4267291.

Purnell PR, Fox HS. Efavirenz induces neuronal autophagy and mitochondrial alterations. J Pharmacol Exp Ther. 2014 Nov;351(2):250-8. PubMed PMID: 25161171; PubMed Central PMCID: PMC4201278.

Rinehart D, Johnson CH, Nguyen T, Ivanisevic J, Benton HP, Lloyd J, Arkin AP, Deutschbauer AM, Patti GJ, Siuzdak G. Metabolomic data streaming for biology-dependent data acquisition. Nat Biotechnol. 2014 Jun;32(6):524-7. PubMed PMID: 24911492; PubMed Central PMCID: PMC4112958.

Sabouri AH, Marcondes MC, Flynn C, Berger M, Xiao N, Fox HS, Sarvetnick NE. TLR signaling controls lethal encephalitis in WNV- infected brain. Brain Res. 2014 Jul 29;1574:84-95. PubMed PMID: 24928618; PubMed Central PMCID: PMC4099315.

Stauch KL, Purnell PR, Fox HS. Aging synaptic mitochondria exhibit dynamic proteomic changes while maintaining bioenergetic function. Aging (Albany NY). 2014 Apr;6(4):320-34. PubMed PMID: 24827396; PubMed Central PMCID: PMC4032798.

Stauch KL, Purnell PR, Fox HS. Quantitative proteomics of synaptic and nonsynaptic mitochondria: insights for synaptic mitochondrial vulnerability. J Proteome Res. 2014 May 2;13(5):2620-36. PubMed PMID: 24708184; PubMed Central PMCID: PMC4015687.

Tong J, Buch S, Yao H, Wu C, Tong HI, Wang Y, Lu Y. Monocytes-derived macrophages mediated stable expression of human brain-derived neurotrophic factor, a novel therapeutic strategy for neuroAIDS. PLoS One. 2014;9(2):e82030. PubMed PMID: 24505242; PubMed Central PMCID: PMC3914783.

Villeneuve LM, Purnell PR, Boska MD, Fox HS. Early Expression of Parkinson's Disease-Related Mitochondrial Abnormalities in PINK1 Knockout Rats. Mol Neurobiol. 2014 Nov 25;PubMed PMID: 25421206; PubMed Central PMCID: PMC4442772. [Epub ahead of print]

Villeneuve LM, Stauch KL, Fox HS. Proteomic analysis of the mitochondria from embryonic and postnatal rat brains reveals response to developmental changes in energy demands. J Proteomics. 2014 Sep 23;109:228-39. PubMed PMID: 25046836; PubMed Central PMCID: PMC4253732.

Wooden J, Ciborowski P. Chromatin immunoprecipitation for human monocyte derived macrophages. Methods. 2014 Dec;70(2-3):89-96. PubMed PMID: 25220915; PubMed Central PMCID: PMC4268110.

Yao H, Ma R, Yang L, Hu G, Chen X, Duan M, Kook Y, Niu F, Liao K, Fu M, Hu G, Kolattukudy P, Buch S. MiR-9 promotes microglial activation by targeting MCPIP1. Nat Commun. 2014 Jul 14;5:4386. PubMed PMID: 25019481; PubMed Central PMCID: PMC4104446.

Yelamanchili SV, Morsey B, Harrison EB, Rennard DA, Emanuel K, Thapa I, Bastola DR, Fox HS. The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins. Cell Death Dis. 2014 Jan 9;5:e982. PubMed PMID: 24407235; PubMed Central PMCID: PMC4040694.

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Bade AN, Zhou B, Epstein AA, Gorantla S, Poluektova LY, Luo J, Gendelman HE, Boska MD, Liu Y. Improved visualization of neuronal injury following glial activation by manganese enhanced MRI. J Neuroimmune Pharmacol. 2013 Sep;8(4):1027-36. PubMed PMID: 23729245; PubMed Central PMCID: PMC3746563.

Becker KM, Heinrichs-Graham E, Fox HS, Robertson KR, Sandkovsky U, O'Neill J, Swindells S, Wilson TW. Decreased MEG beta oscillations in HIV-infected older adults during the resting state. J Neurovirol. 2013 Dec;19(6):586-94. PubMed PMID: 24297500; PubMed Central PMCID: PMC3913174.

Blankman JL, Long JZ, Trauger SA, Siuzdak G, Cravatt BF. ABHD12 controls brain lysophosphatidylserine pathways that are deregulated in a murine model of the neurodegenerative disease PHARC. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1500-5. PubMed PMID: 23297193; PubMed Central PMCID: PMC3557017.

Chao J, Yang L, Buch S, Gao L. Angiotensin I increased neuronal stem cell proliferation: role of AT2R. PLoS One. 2013;8(5):e63488. PubMed PMID: 23691054; PubMed Central PMCID: PMC3655161.

Chaudhuri AD, Yelamanchili SV, Fox HS. Combined fluorescent in situ hybridization for detection of microRNAs and immunofluorescent labeling for cell-type markers. Front Cell Neurosci. 2013;7:160. PubMed PMID: 24065888; PubMed Central PMCID: PMC3779857.

Chaudhuri AD, Yelamanchili SV, Fox HS. MicroRNA-142 reduces monoamine oxidase A expression and activity in neuronal cells by downregulating SIRT1. PLoS One. 2013;8(11):e79579. PubMed PMID: 24244526; PubMed Central PMCID: PMC3823651.

Chaudhuri AD, Yelamanchili SV, Marcondes MC, Fox HS. Up- regulation of microRNA-142 in simian immunodeficiency virus encephalitis leads to repression of sirtuin1. FASEB J. 2013 Sep;27(9):3720-9. PubMed PMID: 23752207; PubMed Central PMCID: PMC3752547.

Costa BM, Yao H, Yang L, Buch S. Role of endoplasmic reticulum (ER) stress in cocaine-induced microglial cell death. J Neuroimmune Pharmacol. 2013 Jun;8(3):705-14. PubMed PMID: 23404095; PubMed Central PMCID: PMC3663878.

Del Debbio CB, Peng X, Xiong H, Ahmad I. Adult ciliary epithelial stem cells generate functional neurons and differentiate into both early and late born retinal neurons under non-cell autonomous influences. BMC Neurosci. 2013 Oct 22;14:130. PubMed PMID: 24148749; PubMed Central PMCID: PMC3856605.

Drabik A, Bodzoń-Kułakowska A, Suder P, Ciborowski P, Silberring J. iTRAQ analysis with Paul ion t rap-obstacle solved. J Proteome Res. 2013 Oct 4;12(10):4607-11. PubMed PMID: 23991718.

Duan M, Yao H, Hu G, Chen X, Lund AK, Buch S. HIV Tat induces expression of ICAM-1 in HUVECs: implications for miR-221/-222 in HIV-associated cardiomyopathy. PLoS One. 2013;8(3):e60170. PubMed PMID: 23555914; PubMed Central PMCID: PMC3610892.

Epstein AA, Narayanasamy P, Dash PK, High R, Bathena SP, Gorantla S, Poluektova LY, Alnouti Y, Gendelman HE, Boska MD. Combinatorial assessments of brain t issue metabolomics and histopathology in rodent models of human immunodeficiency virus infection. J Neuroimmune Pharmacol. 2013 Dec;8(5):1224- 38. PubMed PMID: 23702663; PubMed Central PMCID: PMC3889226.

Fox HS. Biomarkers for NeuroAIDS: recent progress in the field. J Neuroimmune Pharmacol. 2013 Dec;8(5):1055-8. PubMed PMID: 24292958; PubMed Central PMCID: PMC3901566.

Gautam N, Roy U, Balkundi S, Puligujja P, Guo D, Smith N, Liu XM, Lamberty B, Morsey B, Fox HS, McMillan J, Gendelman HE, Alnouti Y. Preclinical pharmacokinetics and tissue distribution of long-acting nanoformulated antiretroviral therapy. Antimicrob Agents Chemother. 2013 Jul;57(7):3110-20. PubMed PMID: 23612193; PubMed Central PMCID: PMC3697338.

Gelman BB, Lisinicchia JG, Morgello S, Masliah E, Commins D, Achim CL, Fox HS, Kolson DL, Grant I, Singer E, Yiannoutsos CT, Sherman S, Gensler G, Moore DJ, Chen T, Soukup VM. Neurovirological correlation with HIV-associated neurocognitive disorders and encephalitis in a HAART-era cohort. J Acquir Immune Defic Syndr. 2013 Apr 15;62(5):487-95. PubMed PMID: 23242157; PubMed Central PMCID: PMC3664102.

Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013 Jan 24;49(2):359-67. PubMed PMID: 23177740; PubMed Central PMCID: PMC3780611.

Haorah J, Rump TJ, Xiong H. Reduction of brain mitochondrial β- oxidation impairs complex I and V in chronic alcohol intake: the underlying mechanism for neurodegeneration. PLoS One. 2013;8(8):e70833. PubMed PMID: 23967116; PubMed Central PMCID: PMC3742670.

Ivanisevic J, Zhu ZJ, Plate L, Tautenhahn R, Chen S, O'Brien PJ, Johnson CH, Marletta MA, Patti GJ, Siuzdak G. Toward 'omic scale metabolite profiling: a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Anal Chem. 2013 Jul 16;85(14):6876-84. PubMed PMID: 23781873; PubMed Central PMCID: PMC3761963.

Kiyota T, Gendelman HE, Weir RA, Higgins EE, Zhang G, Jain M. CCL2 affects β-amyloidosis and progressive neurocognitive dysfunction in a mouse model of Alzheimer's disease. Neurobiol Aging. 2013 Apr;34(4):1060-8. PubMed PMID: 23040664; PubMed Central PMCID: PMC4011558.

Kosloski LM, Kosmacek EA, Olson KE, Mosley RL, Gendelman HE. GM-CSF induces neuroprotective and anti-inflammatory responses in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine intoxicated mice. J Neuroimmunol. 2013 Dec 15;265(1-2):1-10. PubMed PMID: 24210793; PubMed Central PMCID: PMC3872482.

Liu Y, Sajja BR, Gendelman HE, Boska MD. Mouse brain fixation to preserve In vivo manganese enhancement for ex vivo manganese-enhanced MRI. J Magn Reson Imaging. 2013 Aug;38(2):482-7. PubMed PMID: 23349027; PubMed Central PMCID: PMC3638066.

Marcondes MC, Spina C, Bustamante E, Fox H. Increased toll-like receptor signaling pathways characterize CD8+ cells in rapidly progressive SIV infection. Biomed Res Int. 2013;2013:796014. PubMed PMID: 23484159; PubMed Central PMCID: PMC3591242.

Martinez-Skinner AL, Veerubhotla RS, Liu H, Xiong H, Yu F, McMillan JM, Gendelman HE. Functional proteome of macrophage carried nanoformulated antiretroviral therapy demonstrates enhanced particle carrying capacity. J Proteome Res. 2013 May 3;12(5):2282-94. PubMed PMID: 23544708; PubMed Central PMCID: PMC3664030.

Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nat Rev Genet. 2013 Oct;14(10):719-32. PubMed PMID: 24045689; PubMed Central PMCID: PMC3940161.

Nowacek A, Kadiu I, McMillan J, Gendelman HE. Immunoisolation of nanoparticles containing endocytic vesicles for drug quantitation. Methods Mol Biol. 2013;991:41-6. PubMed PMID: 23546657; PubMed Central PMCID: PMC3930998.

Olszowy PP, Burns A, Ciborowski PS. Pressure-assisted sample preparation for proteomic analysis. Anal Biochem. 2013 Jul 1;438(1):67-72. PubMed PMID: 23545193; PubMed Central PMCID: PMC3761939.

Patti GJ, Tautenhahn R, Rinehart D, Cho K, Shriver LP, Manchester M, Nikolskiy I, Johnson CH, Mahieu NG, Siuzdak G. A view from above: cloud plots to visualize global metabolomic data. Anal Chem. 2013 Jan 15;85(2):798-804. PubMed PMID: 23206250; PubMed Central PMCID: PMC3716252.

Puligujja P, McMillan J, Kendrick L, Li T, Balkundi S, Smith N, Veerubhotla RS, Edagwa BJ, Kabanov AV, Bronich T, Gendelman HE, Liu XM. Macrophage folate receptor-targeted antiretroviral therapy facilitates drug entry, retention, antiretroviral activities and biodistribution for reduction of human immunodeficiency virus infections. Nanomedicine. 2013 Nov;9(8):1263-73. PubMed PMID: 23680933; PubMed Central PMCID: PMC3779529.

Purnell PR, Fox HS. Autophagy-mediated turnover of dynamin- related protein 1. BMC Neurosci. 2013 Aug 9;14:86. PubMed PMID: 23937156; PubMed Central PMCID: PMC3750610.

Sandkovsky U, Robertson KR, Meza JL, High RR, Bonasera SJ, Fisher CM, Marsh AJ, Sheehy MK, Fox HS, Swindells S. Pilot study of younger and older HIV-infected adults using traditional and novel functional assessments. HIV Clin Trials. 2013 Jul- Aug;14(4):165-74. PubMed PMID: 23924589; PubMed Central PMCID: PMC3931515.

Schweitzer CJ, Jagadish T, Haverland N, Ciborowski P, Belshan M. Proteomic analysis of early HIV-1 nucleoprotein complexes. J Proteome Res. 2013 Feb 1;12(2):559-72. PubMed PMID: 23282062; PubMed Central PMCID: PMC3564510.

Villeneuve L, Tiede LM, Morsey B, Fox HS. Quantitative proteomics reveals oxygen-dependent changes in neuronal mitochondria affecting function and sensitivity to rotenone. J Proteome Res. 2013 Oct 4;12(10):4599-606. PubMed PMID: 23971408; PubMed Central PMCID: PMC3909963.

Williams J, Sayles HR, Meza JL, Sayre P, Sandkovsky U, Gendelman HE, Flexner C, Swindells S. Long-acting parenteral nanoformulated antiretroviral therapy: interest and attitudes of HIV-infected patients. Nanomedicine (Lond). 2013 Nov;8(11):1807-13. PubMed PMID: 23611617; PubMed Central PMCID: PMC3987826.

Wilson TW, Fox HS, Robertson KR, Sandkovsky U, O'Neill J, Heinrichs-Graham E, Knott NL, Swindells S. Abnormal MEG oscillatory activity during visual processing in the prefrontal cortices and frontal eye-fields of the aging HIV brain. PLoS One. 2013;8(6):e66241. PubMed PMID: 23840428; PubMed Central PMCID: PMC3688779.

Wilson TW, Heinrichs-Graham E, Robertson KR, Sandkovsky U, O'Neill J, Knott NL, Fox HS, Swindells S. Functional brain abnormalities during finger-tapping in HIV-infected older adults: a magnetoencephalography study. J Neuroimmune Pharmacol. 2013 Sep;8(4):965-74. PubMed PMID: 23749418; PubMed Central PMCID: PMC3809128.

Winkler JM, Fox HS. Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer's disease. BMC Syst Biol. 2013 Jun 26;7:51. PubMed PMID: 23803348; PubMed Central PMCID: PMC3702487.

Yang J, Hu D, Xia J, Liu J, Zhang G, Gendelman HE, Boukli NM, Xiong H. Enhancement of NMDA receptor-mediated excitatory postsynaptic currents by gp120-treated macrophages: implications for HIV-1-associated neuropathology. J Neuroimmune Pharmacol. 2013 Sep;8(4):921-33. PubMed PMID: 23660833; PubMed Central PMCID: PMC3740075.

Yang L, Chao J, Kook YH, Gao Y, Yao H, Buch SJ. Involvement of miR-9/MCPIP1 axis in PDGF-BB-mediated neurogenesis in neuronal progenitor cells. Cell Death Dis. 2013 Dec 12;4:e960. PubMed PMID: 24336080; PubMed Central PMCID: PMC3877557.

Yao H, Duan M, Yang L, Buch S. Nonmuscle myosin light-chain kinase mediates microglial migration induced by HIV Tat: involvement of β1 integrins. FASEB J. 2013 Apr;27(4):1532-48. PubMed PMID: 23292072; PubMed Central PMCID: PMC3606530.

Zhang J, Liu J, Fox HS, Xiong H. N-methyl-D-aspartate receptor- mediated axonal injury in adult rat corpus callosum. J Neurosci Res. 2013 Feb;91(2):240-8. PubMed PMID: 23161705; PubMed Central PMCID: PMC3546500.

Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc. 2013 Mar;8(3):451-60. PubMed PMID: 23391889; PubMed Central PMCID: PMC3666335.

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Bathena SP, Huang J, Epstein AA, Gendelman HE, Boska MD, Alnouti Y. Rapid and reliable quantitation of amino acids and myo-inositol in mouse brain by high performance liquid chromatography and tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2012 Apr 15;893-894:15-20. PubMed PMID: 22425384; PubMed Central PMCID: PMC3322302.

Bethel-Brown C, Yao H, Hu G, Buch S. Platelet-derived growth factor (PDGF)-BB-mediated induction of monocyte chemoattractant protein 1 in human astrocytes: implications for HIV-associated neuroinflammation. J Neuroinflammation. 2012 Dec 1;9:262. PubMed PMID: 23198981; PubMed Central PMCID: PMC3526410.

Caswell CC, Gaines JM, Ciborowski P, Smith D, Borchers CH, Roux CM, Sayood K, Dunman PM, Roop Ii RM. Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol. 2012 Jul;85(2):345-60. PubMed PMID: 22690807; PubMed Central PMCID: PMC3391331.

Dash PK, Gendelman HE, Roy U, Balkundi S, Alnouti Y, Mosley RL, Gelbard HA, McMillan J, Gorantla S, Poluektova LY. Long- acting nanoformulated antiretroviral therapy elicits potent antiretroviral and neuroprotective responses in HIV-1-infected humanized mice. AIDS. 2012 Nov 13;26(17):2135-44. PubMed PMID: 22824628; PubMed Central PMCID: PMC4024396.

Dempsey K, Thapa I, Bastola D, Ali H. Functional identification in correlation networks using gene ontology edge annotation. Int J Comput Biol Drug Des. 2012;5(3-4):222-44. PubMed PMID: 23013651.

Fox HS, Gendelman HE. Commentary: Animal models of neuroAIDS. J Neuroimmune Pharmacol. 2012 Jun;7(2):301-5. PubMed PMID: 22549136; PubMed Central PMCID: PMC3915784.

Gorantla S, Gendelman HE, Poluektova LY. Can humanized mice reflect the complex pathobiology of HIV-associated neurocognitive disorders? J Neuroimmune Pharmacol. 2012 Jun;7(2):352-62. PubMed PMID: 22222956; PubMed Central PMCID: PMC3782112.

Gorantla S, Poluektova L, Gendelman HE. Rodent models for HIV-associated neurocognitive disorders. Trends Neurosci. 2012 Mar;35(3):197-208. PubMed PMID: 22305769; PubMed Central PMCID: PMC3294256.

Haney MJ, Suresh P, Zhao Y, Kanmogne GD, Kadiu I, Sokolsky- Papkov M, Klyachko NL, Mosley RL, Kabanov AV, Gendelman HE, Batrakova EV. Blood-borne macrophage-neural cell interactions hitchhike on endosome networks for cell-based nanozyme brain delivery. Nanomedicine (Lond). 2012 Jun;7(6):815-33. PubMed PMID: 22236307; PubMed Central PMCID: PMC3384770.

Hu G, Yao H, Chaudhuri AD, Duan M, Yelamanchili SV, Wen H, Cheney PD, Fox HS, Buch S. Exosome-mediated shuttling of microRNA-29 regulates HIV Tat and morphine-mediated neuronal dysfunction. Cell Death Dis. 2012 Aug 30;3:e381. PubMed PMID: 22932723; PubMed Central PMCID: PMC3434655.

Jagadish T, Pottiez G, Fox HS, Ciborowski P. Plasma gelsolin accumulates in macrophage nodules in brains of simian immunodeficiency virus infected rhesus macaques. J Neurovirol. 2012 Apr;18(2):113-9. PubMed PMID: 22403026; PubMed Central PMCID: PMC3794665.

Kadiu I, Narayanasamy P, Dash PK, Zhang W, Gendelman HE. Biochemical and biologic characterization of exosomes and microvesicles as facilitators of HIV-1 infection in macrophages. J Immunol. 2012 Jul 15;189(2):744-54. PubMed PMID: 22711894; PubMed Central PMCID: PMC3786185.

Kanmogne GD, Singh S, Roy U, Liu X, McMillan J, Gorantla S, Balkundi S, Smith N, Alnouti Y, Gautam N, Zhou Y, Poluektova L, Kabanov A, Bronich T, Gendelman HE. Mononuclear phagocyte intercellular crosstalk facilitates transmission of cell-targeted nanoformulated antiretroviral drugs to human brain endothelial cells. Int J Nanomedicine. 2012;7:2373-88. PubMed PMID: 22661891; PubMed Central PMCID: PMC3357981.

Kassmeier MD, Mondal K, Palmer VL, Raval P, Kumar S, Perry GA, Anderson DK, Ciborowski P, Jackson S, Xiong Y, Swanson PC. VprBP binds full-length RAG1 and is required for B-cell development and V(D)J recombination fidelity. EMBO J. 2012 Feb 15;31(4):945-58. PubMed PMID: 22157821; PubMed Central PMCID: PMC3280554.

Kuhl C, Tautenhahn R, Böttcher C, Larson TR, Neumann S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem. 2012 Jan 3;84(1):283-9. PubMed PMID: 22111785; PubMed Central PMCID: PMC3658281.

Landis SC, Amara SG, Asadullah K, Austin CP, Blumenstein R, Bradley EW, Crystal RG, Darnell RB, Ferrante RJ, Fillit H, Finkelstein R, Fisher M, Gendelman HE, Golub RM, Goudreau JL, Gross RA, Gubitz AK, Hesterlee SE, Howells DW, Huguenard J, Kelner K, Koroshetz W, Krainc D, Lazic SE, Levine MS, Macleod MR, McCall JM, Moxley RT 3rd, Narasimhan K, Noble LJ, Perrin S, Porter JD, Steward O, Unger E, Utz U, Silberberg SD. A call for transparent reporting to optimize the predictive value of preclinical research. Nature. 2012 Oct 11;490(7419):187-91. PubMed PMID: 23060188; PubMed Central PMCID: PMC3511845.

Liu J, Xu C, Chen L, Xu P, Xiong H. Involvement of Kv13 and p38 MAPK signaling in HIV-1 glycoprotein 120-induced microglia neurotoxicity. Cell Death Dis. 2012 Jan 19;3:e254. PubMed PMID: 22258405; PubMed Central PMCID: PMC3270274.

Liu Y, Sajja BR, Uberti MG, Gendelman HE, Kielian T, Boska MD. Landmark optimization using local curvature for point-based nonlinear rodent brain image registration. Int J Biomed Imaging. 2012;2012:635207. PubMed PMID: 21966289; PubMed Central PMCID: PMC3180176.

Panopoulos AD, Yanes O, Ruiz S, Kida YS, Diep D, Tautenhahn R, Herrerías A, Batchelder EM, Plongthongkum N, Lutz M, Berggren WT, Zhang K, Evans RM, Siuzdak G, Izpisua Belmonte JC. The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell Res. 2012 Jan;22(1):168-77. PubMed PMID: 22064701; PubMed Central PMCID: PMC3252494.

Patti GJ, Tautenhahn R, Siuzdak G. Meta-analysis of untargeted metabolomic data from multiple profiling experiments. Nat Protoc. 2012 Feb 16;7(3):508-16. PubMed PMID: 22343432; PubMed Central PMCID: PMC3683249.

Patti GJ, Yanes O, Shriver LP, Courade JP, Tautenhahn R, Manchester M, Siuzdak G. Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin. Nat Chem Biol. 2012 Jan 22;8(3):232-4. PubMed PMID: 22267119; PubMed Central PMCID: PMC3567618.

Patti GJ, Yanes O, Siuzdak G. Innovat ion: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol. 2012 Mar 22;13(4):263-9. PubMed PMID: 22436749; PubMed Central PMCID: PMC3682684.

Pendyala G, Buescher JL, Fox HS. Methamphetamine and inflammatory cytokines increase neuronal Na+/K+-ATPase isoform 3: relevance for HIV associated neurocognitive disorders. PLoS One. 2012;7(5):e37604. PubMed PMID: 22662178; PubMed Central PMCID: PMC3360751.

Pendyala G, Ninemire C, Fox HS. Protective role for the disulfide isomerase PDIA3 in methamphetamine neurotoxicity. PLoS One. 2012;7(6):e38909. PubMed PMID: 22715419; PubMed Central PMCID: PMC3371042.

Peng F, Yao H, Akturk HK, Buch S. Platelet-derived growth factor CC-mediated neuroprotection against HIV Tat involves TRPC- mediated inactivation of GSK 3beta. PLoS One. 2012;7(10):e47572. PubMed PMID: 23077641; PubMed Central PMCID: PMC3471979.

Peng H, Wu Y, Duan Z, Ciborowski P, Zheng JC. Proteolytic processing of SDF-1α by matrix metalloproteinase-2 impairs CXCR4 signaling and reduces neural progenitor cell migration. Protein Cell. 2012 Nov;3(11):875-82. PubMed PMID: 23143873; PubMed Central PMCID: PMC3973535.

Pottiez G, Ciborowski P. Elucidating protein inter- and intramolecular interacting domains using chemical cross-linking and matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry. Anal Biochem. 2012 Feb 15;421(2):712-8. PubMed PMID: 22226790; PubMed Central PMCID: PMC3287059.

Pottiez G, Jagadish T, Yu F, Letendre S, Ellis R, Duarte NA, Grant I, Gendelman HE, Fox HS, Ciborowski P. Plasma proteomic profiling in HIV-1 infected methamphetamine abusers. PLoS One. 2012;7(2):e31031. PubMed PMID: 22359561; PubMed Central PMCID: PMC3281056.

Pottiez G, Wiederin J, Fox HS, Ciborowski P. Comparison of 4- plex to 8-plex iTRAQ quantitative measurements of proteins in human plasma samples. J Proteome Res. 2012 Jul 6;11(7):3774- 81. PubMed PMID: 22594965; PubMed Central PMCID: PMC3390908.

Roy A, Ghosh A, Jana A, Liu X, Brahmachari S, Gendelman HE, Pahan K. Sodium phenylbutyrate controls neuroinflammatory and antioxidant activities and protects dopaminergic neurons in mouse models of Parkinson's disease. PLoS One. 2012;7(6):e38113. PubMed PMID: 22723850; PubMed Central PMCID: PMC3377667.

Roy U, McMillan J, Alnouti Y, Gautum N, Smith N, Balkundi S, Dash P, Gorantla S, Martinez-Skinner A, Meza J, Kanmogne G, Swindells S, Cohen SM, Mosley RL, Poluektova L, Gendelman HE. Pharmacodynamic and antiretroviral activities of combination nanoformulated antiretrovirals in HIV-1-infected human peripheral blood lymphocyte-reconstituted mice. J Infect Dis. 2012 Nov 15;206(10):1577-88. PubMed PMID: 22811299; PubMed Central PMCID: PMC3570176.

Saunders JA, Estes KA, Kosloski LM, Allen HE, Dempsey KM, Torres-Russotto DR, Meza JL, Santamaria PM, Bertoni JM, Murman DL, Ali HH, Standaert DG, Mosley RL, Gendelman HE. CD4+ regulatory and effector/memory T cell subsets profile motor dysfunction in Parkinson's disease. J Neuroimmune Pharmacol. 2012 Dec;7(4):927-38. PubMed PMID: 23054369; PubMed Central PMCID: PMC3515774.

Stone DK, Kiyota T, Mosley RL, Gendelman HE. A model of nitric oxide induced α-synuclein misfolding in Parkinson's disease. Neurosci Lett. 2012 Aug 15;523(2):167-73. PubMed PMID: 22776646; PubMed Central PMCID: PMC3408780.

Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G. An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol. 2012 Sep;30(9):826-8. PubMed PMID: 22965049; PubMed Central PMCID: PMC3666346.

Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G. XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem. 2012 Jun 5;84(11):5035-9. PubMed PMID: 22533540; PubMed Central PMCID: PMC3703953.

Wiederin JL, Yu F, Donahoe RM, Fox HS, Ciborowski P, Gendelman HE. Changes in the plasma proteome follows chronic opiate administration in simian immunodeficiency virus infected rhesus macaques. Drug Alcohol Depend. 2012 Jan 1;120(1- 3):105-12. PubMed PMID: 21821369; PubMed Central PMCID: PMC3245805.

Winkler JM, Chaudhuri AD, Fox HS. Translating the brain transcriptome in neuroAIDS: from non-human primates to humans. J Neuroimmune Pharmacol. 2012 Jun;7(2):372-9. PubMed PMID: 22367717; PubMed Central PMCID: PMC3354039.

Yao H, Duan M, Yang L, Buch S. Platelet-derived growth factor- BB restores human immunodeficiency virus Tat-cocaine- mediated impairment of neurogenesis: role of TRPC1 channels. J Neurosci. 2012 Jul 18;32(29):9835-47. PubMed PMID: 22815499; PubMed Central PMCID: PMC3438664.

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Balkundi S, Nowacek AS, Veerubhotla RS, Chen H, Martinez- Skinner A, Roy U, Mosley RL, Kanmogne G, Liu X, Kabanov AV, Bronich T, McMillan J, Gendelman HE. Comparative manufacture and cell-based delivery of antiretroviral nanoformulations. Int J Nanomedicine. 2011;6:3393-404. PubMed PMID: 22267924; PubMed Central PMCID: PMC3260033.

Bethel-Brown C, Yao H, Callen S, Lee YH, Dash PK, Kumar A, Buch S. HIV-1 Tat-mediated induction of platelet-derived growth factor in astrocytes: role of early growth response gene 1. J Immunol. 2011 Apr 1;186(7):4119-29. PubMed PMID: 21368226; PubMed Central PMCID: PMC3110059.

Bokhari SM, Hegde R, Callen S, Yao H, Adany I, Li Q, Li Z, Pinson D, Yeh HW, Cheney PD, Buch S. Morphine potentiates neuropathogenesis of SIV infection in rhesus macaques. J Neuroimmune Pharmacol. 2011 Dec;6(4):626-39. PubMed PMID: 21431470; PubMed Central PMCID: PMC3270698.

Bressani RF, Nowacek AS, Singh S, Balkundi S, Rabinow B, McMillan J, Gendelman HE, Kanmogne GD. Pharmacotoxicology of monocyte-macrophage nanoformulated antiretroviral drug uptake and carriage. Nanotoxicology. 2011 Dec;5(4):592-605. PubMed PMID: 21175298; PubMed Central PMCID: PMC3715104.

Chatterjee N, Callen S, Seigel GM, Buch SJ. HIV-1 Tat-mediated neurotoxicity in retinal cells. J Neuroimmune Pharmacol. 2011 Sep;6(3):399-408. PubMed PMID: 21274647; PubMed Central PMCID: PMC3321305.

Chen L, Liu J, Xu C, Keblesh J, Zang W, Xiong H. HIV-1gp120 induces neuronal apoptosis through enhancement of 4-aminopyridine-sensitive outward K+ currents. PLoS One. 2011;6(10):e25994. PubMed PMID: 22016798; PubMed Central PMCID: PMC3189248.

Constantino AA, Huang Y, Zhang H, Wood C, Zheng JC. HIV-1 clade B and C isolates exhibit differential replication: relevance to macrophage-mediated neurotoxicity. Neurotox Res. 2011 Oct;20(3):277-88. PubMed PMID: 21336667; PubMed Central PMCID: PMC3407549.

Dash PK, Gorantla S, Gendelman HE, Knibbe J, Casale GP, Makarov E, Epstein AA, Gelbard HA, Boska MD, Poluektova LY. Loss of neuronal integrity during progressive HIV-1 infection of humanized mice. J Neurosci. 2011 Mar 2;31(9):3148-57. PubMed PMID: 21368026; PubMed Central PMCID: PMC3059783.

Dhillon NK, Li F, Xue B, Tawfik O, Morgello S, Buch S, Ladner AO. Effect of cocaine on human immunodeficiency virus-mediated pulmonary endothelial and smooth muscle dysfunction. Am J Respir Cell Mol Biol. 2011 Jul;45(1):40-52. PubMed PMID: 20808207; PubMed Central PMCID: PMC3145070.

Gong N, Liu J, Reynolds AD, Gorantla S, Mosley RL, Gendelman HE. Brain ingress of regulatory T cells in a murine model of HIV-1 encephalitis. J Neuroimmunol. 2011 Jan;230(1-2):33-41. PubMed PMID: 20846730; PubMed Central PMCID: PMC3003943.

Greving MP, Patti GJ, Siuzdak G. Nanostructure-initiator mass spectrometry metabolite analysis and imaging. Anal Chem. 2011 Jan 1;83(1):2-7. PubMed PMID: 21049956; PubMed Central PMCID: PMC3012143.

Haney MJ, Zhao Y, Li S, Higginbotham SM, Booth SL, Han HY, Vetro JA, Mosley RL, Kabanov AV, Gendelman HE, Batrakova EV. Cell-mediated transfer of catalase nanoparticles from macrophages to brain endothelial, glial and neuronal cells. Nanomedicine (Lond). 2011 Sep;6(7):1215-30. PubMed PMID: 21449849; PubMed Central PMCID: PMC3166447.

Holguin A, Banda M, Willen EJ, Malama C, Chiyenu KO, Mudenda VC, Wood C. HIV-1 effects on neuropsychological performance in a resource-limited country, Zambia. AIDS Behav. 2011 Nov;15(8):1895-901. PubMed PMID: 21744118; PubMed Central PMCID: PMC3314062.

Huang J, Gautam N, Bathena SP, Roy U, McMillan J, Gendelman HE, Alnouti Y. UPLC-MS/MS quantification of nanoformulated ritonavir, indinavir, atazanavir, and efavirenz in mouse serum and t issues. J Chromatogr B Analyt Technol Biomed Life Sci. 2011 Aug 1;879(23):2332-8. PubMed PMID: 21752731; PubMed Central PMCID: PMC3144699.

Hutter-Saunders JA, Mosley RL, Gendelman HE. Pathways towards an effective immunotherapy for Parkinson's disease. Expert Rev Neurother. 2011 Dec;11(12):1703-15. PubMed PMID: 22091596; PubMed Central PMCID: PMC3263336.

Kadiu I, Gendelman HE. Human immunodeficiency virus type 1 endocytic trafficking through macrophage bridging conduits facilitates spread of infection. J Neuroimmune Pharmacol. 2011 Dec;6(4):658-75. PubMed PMID: 21789505; PubMed Central PMCID: PMC3232570.

Kadiu I, Gendelman HE. Macrophage bridging conduit trafficking of HIV-1 through the endoplasmic reticulum and Golgi network. J Proteome Res. 2011 Jul 1;10(7):3225-38. PubMed PMID: 21563830; PubMed Central PMCID: PMC3128463.

Kadiu I, Nowacek A, McMillan J, Gendelman HE. Macrophage endocytic trafficking of antiretroviral nanoparticles. Nanomedicine (Lond). 2011 Aug;6(6):975-94. PubMed PMID: 21417829; PubMed Central PMCID: PMC3184214.

Kraft-Terry SD, Engebretsen IL, Bastola DK, Fox HS, Ciborowski P, Gendelman HE. Pulsed stable isotope labeling of amino acids in cell culture uncovers the dynamic interactions between HIV-1 and the monocyte-derived macrophage. J Proteome Res. 2011 Jun 3;10(6):2852-62. PubMed PMID: 21500866; PubMed Central PMCID: PMC3108467.

Lei YJ, Makhaola K, Pittayakhajonwut D, Wood C, Angeletti PC. Human papillomavirus 16 variants from Zambian women with normal pap smears. J Med Virol. 2011 Jul;83(7):1230-7. PubMed PMID: 21567426.

Malik S, Khalique H, Buch S, Seth P. A growth factor attenuates HIV-1 Tat and morphine induced damage to human neurons: implication in HIV/AIDS-drug abuse cases. PLoS One. 2011 Mar 24;6(3):e18116. PubMed PMID: 21483469; PubMed Central PMCID: PMC3063804.

Mermis J, Gu H, Xue B, Li F, Tawfik O, Buch S, Bartolome S, O'Brien-Ladner A, Dhillon NK. Hypoxia-inducible factor-1 α/platelet derived growth factor axis in HIV-associated pulmonary vascular remodeling. Respir Res. 2011 Aug 5;12:103. PubMed PMID: 21819559; PubMed Central PMCID: PMC3163194.

Minhas V, Crabtree KL, Chao A, Wojcicki JM, Sifuniso AM, Nkonde C, Kankasa C, Mitchell CD, Wood C. The Zambia Children's KS-HHV8 Study: rationale, study design, and study methods. Am J Epidemiol. 2011 May 1;173(9):1085-92. PubMed PMID: 21447476; PubMed Central PMCID: PMC3121218.

Nowacek AS, Balkundi S, McMillan J, Roy U, Martinez-Skinner A, Mosley RL, Kanmogne G, Kabanov AV, Bronich T, Gendelman HE. Analyses of nanoformulated antiretroviral drug charge, size, shape and content for uptake, drug release and antiviral activities in human monocyte-derived macrophages. J Control Release. 2011 Mar 10;150(2):204-11. PubMed PMID: 21108978; PubMed Central PMCID: PMC3065529.

Pendyala G, Trauger SA, Siuzdak G, Fox HS. Short communication: quantitative proteomic plasma profiling reveals activation of host defense to oxidative stress in chronic SIV and methamphetamine comorbidity. AIDS Res Hum Retroviruses.2011 Feb;27(2):179-82. PubMed PMID: 20929344; PubMed Central PMCID: PMC3045074.

Shah A, Singh DP, Buch S, Kumar A. HIV-1 envelope protein gp120 up regulates CCL5 production in astrocytes which can be circumvented by inhibitors of NF-κB pathway. Biochem Biophys Res Commun. 2011 Oct 14;414(1):112-7. PubMed PMID: 21945445; PubMed Central PMCID: PMC3204359.

Shah A, Verma AS, Patel KH, Noel R, Rivera-Amill V, Silverstein PS, Chaudhary S, Bhat HK, Stamatatos L, Singh DP, Buch S, Kumar A. HIV-1 gp120 induces expression of IL-6 through a nuclear factor-kappa B-dependent mechanism: suppression by gp120 specific small interfering RNA. PLoS One. 2011;6(6):e21261. PubMed PMID: 21712995; PubMed Central PMCID: PMC3119684.

Shriver LP, Manchester M. Inhibit ion of fatty acid metabolism ameliorates disease activity in an animal model of multiple sclerosis. Sci Rep. 2011;1:79. PubMed PMID: 22355598; PubMed Central PMCID: PMC3216566.

Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 28: new features for data integration and network visualization. Bioinformatics. 2011 Feb 1;27(3):431-2. PubMed PMID: 21149340; PubMed Central PMCID: PMC3031041.

Tautenhahn R, Patti GJ, Kalisiak E, Miyamoto T, Schmidt M, Lo FY, McBee J, Baliga NS, Siuzdak G. metaXCMS: second-order analysis of untargeted metabolomics data. Anal Chem. 2011 Feb 1;83(3):696-700. PubMed PMID: 21174458; PubMed Central PMCID: PMC3654666.

Tiede LM, Cook EA, Morsey B, Fox HS. Oxygen matters: t issue culture oxygen levels affect mitochondrial function and structure as well as responses to HIV viroproteins. Cell Death Dis. 2011 Dec 22;2:e246. PubMed PMID: 22190005; PubMed Central PMCID: PMC3253381.

Wen H, Lu Y, Yao H, Buch S. Morphine induces expression of platelet-derived growth factor in human brain microvascular endothelial cells: implication for vascular permeability. PLoS One. 2011;6(6):e21707. PubMed PMID: 21738771; PubMed Central PMCID: PMC3125302.

Xu C, Liu J, Chen L, Liang S, Fujii N, Tamamura H, Xiong H. HIV-1 gp120 enhances outward potassium current via CXCR4 and cAMP-dependent protein kinase A signaling in cultured rat microglia. Glia. 2011 Jun;59(6):997-1007. PubMed PMID: 21438014; PubMed Central PMCID: PMC3077451.

Yanes O, Tautenhahn R, Patti GJ, Siuzdak G. Expanding coverage of the metabolome for global metabolite profiling. Anal Chem. 2011 Mar 15;83(6):2152-61. PubMed PMID: 21329365; PubMed Central PMCID: PMC3285547.

Yao H, Duan M, Hu G, Buch S. Platelet-derived growth factor B chain is a novel target gene of cocaine-mediated Notch1 signaling: implications for HIV-associated neurological disorders. J Neurosci. 2011 Aug 31;31(35):12449-54. PubMed PMID: 21880906; PubMed Central PMCID: PMC3283138.

Yao H, Kim K, Duan M, Hayashi T, Guo M, Morgello S, Prat A, Wang J, Su TP, Buch S. Cocaine hijacks σ1 receptor to initiate induction of activated leukocyte cell adhesion molecule: implication for increased monocyte adhesion and migration in the CNS. J Neurosci. 2011 Apr 20;31(16):5942-55. PubMed PMID: 21508219; PubMed Central PMCID: PMC3410749.

Yelamanchili SV, Chaudhuri AD, Flynn CT, Fox HS. Upregulation of cathepsin D in the caudate nucleus of primates with experimental parkinsonism. Mol Neurodegener. 2011 Jul 21;6:52. PubMed PMID: 21777416; PubMed Central PMCID: PMC3160400.

Zhang J, Liu J, Katafiasz B, Fox H, Xiong H. HIV-1 gp120-induced axonal injury detected by accumulation of β-amyloid precursor protein in adult rat corpus callosum. J Neuroimmune Pharmacol. 2011 Dec;6(4):650-7. PubMed PMID: 21286834; PubMed Central PMCID: PMC3165079.

Zhao Y, Haney MJ, Klyachko NL, Li S, Booth SL, Higginbotham SM, Jones J, Zimmerman MC, Mosley RL, Kabanov AV, Gendelman HE, Batrakova EV. Polyelectrolyte complex optimization for macrophage delivery of redox enzyme nanoparticles. Nanomedicine (Lond). 2011 Jan;6(1):25-42. PubMed PMID: 21182416; PubMed Central PMCID: PMC3037278.

Zhao Y, Haney MJ, Mahajan V, Reiner BC, Dunaevsky A, Mosley RL, Kabanov AV, Gendelman HE, Batrakova EV. Active Targeted Macrophage-mediated Delivery of Catalase to Affected Brain Regions in Models of Parkinson's Disease. J Nanomed Nanotechnol. 2011 Sep 10;S4PubMed PMID: 22288024; PubMed Central PMCID: PMC3267477.

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Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nat Methods. 2010 Oct;7(10):801-5. PubMed PMID: 20936779; PubMed Central PMCID: PMC2967489.

Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and t issue embryological classes. Bioinformatics. 2010 Sep 15;26(18):i531-9. PubMed PMID: 20823318; PubMed Central PMCID: PMC2935424.

Clingerman KJ, Spray S, Flynn C, Fox HS. A technique for intracisternal collection and administration in a rhesus macaque. Lab Anim (NY). 2010 Oct;39(10):307-11. PubMed PMID: 20859278.

Fox HS. Advances in the "omics" for diagnosis, pathogenesis, and therapeutic development. J Neuroimmune Pharmacol. 2010 Mar;5(1):1-3. PubMed PMID: 20143174; PubMed Central PMCID: PMC2862255.

Kraft-Terry S, Gerena Y, Wojna V, Plaud-Valentin M, Rodriguez Y, Ciborowski P, Mayo R, Skolasky R, Gendelman HE, Meléndez LM. Proteomic analyses of monocytes obtained from Hispanic women with HIV-associated dementia show depressed antioxidants. Proteomics Clin Appl. 2010 Sep;4(8-9):706-14. PubMed PMID: 21137088; PubMed Central PMCID: PMC3098323.

Kuijpers M, van Gassen KL, de Graan PN, Gruol D. Chronic exposure to the chemokine CCL3 enhances neuronal network activity in rat hippocampal cultures. J Neuroimmunol. 2010 Dec 15;229(1-2):73-80. PubMed PMID: 20678811; PubMed Central PMCID: PMC2991474.

Marcondes MC, Flynn C, Watry DD, Zandonatti M, Fox HS. Methamphetamine increases brain viral load and activates natural killer cells in simian immunodeficiency virus-infected monkeys. Am J Pathol. 2010 Jul;177(1):355-61. PubMed PMID: 20489154; PubMed Central PMCID: PMC2893678.

Patti GJ, Shriver LP, Wassif CA, Woo HK, Uritboonthai W, Apon J, Manchester M, Porter FD, Siuzdak G. Nanostructure-initiator mass spectrometry (NIMS) imaging of brain cholesterol metabolites in Smith-Lemli-Opitz syndrome. Neuroscience. 2010 Oct 27;170(3):858-64. PubMed PMID: 20670678; PubMed Central PMCID: PMC2952448.

Patti GJ, Woo HK, Yanes O, Shriver L, Thomas D, Uritboonthai W, Apon JV, Steenwyk R, Manchester M, Siuzdak G. Detection of carbohydrates and steroids by cation-enhanced nanostructure- initiator mass spectrometry (NIMS) for biofluid analysis and t issue imaging. Anal Chem. 2010 Jan 1;82(1):121-8. PubMed PMID: 19961200; PubMed Central PMCID: PMC2802282.

Pendyala G, Trauger SA, Siuzdak G, Fox HS. Quantitative plasma proteomic profiling identifies the vitamin E binding protein afamin as a potential pathogenic factor in SIV induced CNS disease. J Proteome Res. 2010 Jan;9(1):352-8. PubMed PMID: 19908921; PubMed Central PMCID: PMC2801767.

Peng F, Yao H, Bai X, Zhu X, Reiner BC, Beazely M, Funa K, Xiong H, Buch S. Platelet-derived growth factor-mediated induction of the synaptic plasticity gene Arc/Arg31. J Biol Chem. 2010 Jul 9;285(28):21615-24. PubMed PMID: 20452974; PubMed Central PMCID: PMC2898451.

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K,Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010 Mar 5;140(5):744-52. PubMed PMID: 20211142; PubMed Central PMCID: PMC2836267.

Wiederin JL, Donahoe RM, Anderson JR, Yu F, Fox HS, Gendelman HE, Ciborowski PS. Plasma proteomic analysis of simian immunodeficiency virus infection of rhesus macaques. J Proteome Res. 2010 Sep 3;9(9):4721-31. PubMed PMID: 20677826; PubMed Central PMCID: PMC3285256.

Yang Y, Yao H, Lu Y, Wang C, Buch S. Cocaine potentiates astrocyte toxicity mediated by human immunodeficiency virus (HIV-1) protein gp120. PLoS One. 2010 Oct 15;5(10):e13427. PubMed PMID: 20976166; PubMed Central PMCID: PMC2955538.

Yao H, Yang Y, Kim KJ, Bethel-Brown C, Gong N, Funa K, Gendelman HE, Su TP, Wang JQ, Buch S. Molecular mechanisms involving sigma receptor-mediated induction of MCP-1: implication for increased monocyte transmigration. Blood. 2010 Jun 10;115(23):4951-62. PubMed PMID: 20354174; PubMed Central PMCID: PMC2890169.

Yelamanchili SV, Chaudhuri AD, Chen LN, Xiong H, Fox HS. MicroRNA-21 dysregulates the expression of MEF2C in neurons in monkey and human SIV/HIV neurological disease. Cell Death Dis. 2010;1:e77. PubMed PMID: 21170291; PubMed Central PMCID: PMC3002786. 

Yelamanchili SV, Fox HS. Defining larger roles for "tiny" RNA molecules: role of miRNAs in neurodegeneration research. J Neuroimmune Pharmacol. 2010 Mar;5(1):63-9. PubMed PMID: 19757077; PubMed Central PMCID: PMC2881294.


Alirezaei M, Fox HS, Flynn CT, Moore CS, Hebb AL, Frausto RF, Bhan V, Kiosses WB, Whitton JL, Robertson GS, Crocker SJ. Elevated ATG5 expression in autoimmune demyelination and multiple sclerosis. Autophagy. 2009 Feb;5(2):152-8. PubMed PMID: 19066443; PubMed Central PMCID: PMC2779564.

Cho J, Nelson TE, Bajova H, Gruol DL. Chronic CXCL10 alters neuronal properties in rat hippocampal culture. J Neuroimmunol. 2009 Feb 15;207(1-2):92-100. PubMed PMID: 19167097; PubMed Central PMCID: PMC2817940.

Crews B, Wikoff WR, Patti GJ, Woo HK, Kalisiak E, Heideker J, Siuzdak G. Variability analysis of human plasma and cerebral spinal fluid reveals statistical significance of changes in mass spectrometry-based metabolomics data. Anal Chem. 2009 Oct 15;81(20):8538-44. PubMed PMID: 19764780; PubMed Central PMCID: PMC3058611.

Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. Evolutionarily conserved herpes viral protein interaction networks. PLoS Pathog. 2009 Sep;5(9):e1000570. PubMed PMID: 19730696; PubMed Central PMCID: PMC2731838.

Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis- induced neural dysfunction. J Neurosci. 2009 Oct 7;29(40):12467-76. PubMed PMID: 19812322; PubMed Central PMCID: PMC2802851.

Kalisiak J, Trauger SA, Kalisiak E, Morita H, Fokin VV, Adams MW, Sharpless KB, Siuzdak G. Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach. J Am Chem Soc. 2009 Jan 14;131(1):378-86. PubMed PMID: 19055353; PubMed Central PMCID: PMC2735399.

Marcondes MC, Flynn C, Huitron-Rezendiz S, Watry DD, Zandonatti M, Fox HS. Early antiretroviral treatment prevents the development of central nervous system abnormalities in simian immunodeficiency virus-infected rhesus monkeys. AIDS. 2009 Jun 19;23(10):1187-95. PubMed PMID: 19455015; PubMed Central PMCID: PMC2698130.

Pendyala G, Trauger SA, Kalisiak E, Ellis RJ, Siuzdak G, Fox HS. Cerebrospinal f luid proteomics reveals potential pathogenic changes in the brains of SIV-infected monkeys. J Proteome Res. 2009 May;8(5):2253-60. PubMed PMID: 19281240; PubMed Central PMCID: PMC2682714.

RamachandraRao SP, Zhu Y, Ravasi T, McGowan TA, Toh I, Dunn SR, Okada S, Shaw MA, Sharma K. Pirfenidone is renoprotective in diabetic kidney disease. J Am Soc Nephrol. 2009 Aug;20(8):1765-75. PubMed PMID: 19578007; PubMed Central PMCID: PMC2723978.

Truong P, Heydari S, Garidou L, McGavern DB. Persistent viral infection elevates central nervous system MHC class I through chronic production of interferons. J Immunol. 2009 Sep 15;183(6):3895-905. PubMed PMID: 19717517.

Wikoff WR, Kalisak E, Trauger S, Manchester M, Siuzdak G. Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response. J Proteome Res. 2009 Jul;8(7):3578-87. PubMed PMID: 19496611; PubMed Central PMCID: PMC3437991.

Woo HK, Go EP, Hoang L, Trauger SA, Bowen B, Siuzdak G,Northen TR. Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom. 2009 Jun;23(12):1849-55. PubMed PMID: 19449318; PubMed Central PMCID: PMC3052201.

Yanes O, Woo HK, Northen TR, Oppenheimer SR, Shriver L, Apon J, Estrada MN, Potchoiba MJ, Steenwyk R, Manchester M, Siuzdak G. Nanostructure initiator mass spectrometry: tissue imaging and direct biofluid analysis. Anal Chem. 2009 Apr 15;81(8):2969-75. PubMed PMID: 19301920; PubMed Central PMCID: PMC2676195.

Yao H, Peng F, Fan Y, Zhu X, Hu G, Buch SJ. TRPC channel- mediated neuroprotection by PDGF involves Pyk2/ERK/CREB pathway. Cell Death Differ. 2009 Dec;16(12):1681-93. PubMed PMID: 19680266; PubMed Central PMCID: PMC2783976.

 Presentations at national and international meetings

Dempsey, K. and Ali, H. Evaluation of Essential Genes in Correlation Networks using Measures of Centrality. 4th Annual 2011 BIBM Workshop on Biomolecular Network Analysis: November 2011. Atlanta, GA.

Dempsey, K, Bhowmick, S. and Ali, H. Function-preserving filters for sampling in biological networks. 2012 International Conference on Computational Science (ICCS 2012).  June 4-6, 2012: Omaha, NE.

Dempsey, K. Duraisamy, K, Bhowmick, S. and Ali, H. The Development of Parallel Adaptive Sampling Algorithms for Analyzing Biological Networks. 11th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2012). May 21, 2012: Shanghai, China.

Dempsey, K, Duraisamy, K, Ali, H, and Bhowmick, S. A Parallel Graph Sampling Algorithm for Analyzing Gene Correlation Networks. International Conference on Computational Science 2011. June 1-3, 2011. Singapore.

Dempsey, K. Thapa, I, Bastola, D. and Ali, H. Identifying Modular Function via Edge Annotation in Gene Correlation Networks using Gene Ontology Search. 2011 BIBM Workshop on Data Mining for Biomarker Discovery: November 2011. Atlanta, GA.

Duraisamy, K, Dempsey, K, Ali, H, and Bhowmick, S. A noise reducing sampling approach for uncovering critical properties in large scale biological networks. High Performance Computing and Simulation 2011 International Conference (HPCS): July 4-8,2011. Istanbul, Turkey.

Halappanavar, M, Bhowmick, S, Dempsey, K, Ali, H. and Feo, J. A Novel Multi-threaded Algorithm for Extracting Maximal Chordal Subgraphs. The 41st   International Conference on Parallel Processing (ICPP 2012). September 10-13, 2012. Pittsburgh, PA.  

Liu J, Wang J, Chen LN, Xiong H. Co-morbid effects of HIV-1gp120 and Methamphetamine on neuronal physiology & animal behavior: role of voltage-gated K channels.  18th SNIP Conference, Honolulu, Hawaii, April 25-28, 2012.

Liu J, Xu P, Collins C, Liu H, Xie J, Xiong  H. Involvement of KV 1.3 in HIV-1 Tat-associated microglial neurotoxicity. Symposium for Chinese Neuroscientists worldwide 2010.  Xi’an, China, May 25-30, 2012.

Liu J, Xu P, Xu CS, Liu H, Xie J, Xiong H. HIV-1 Tat induces microglial neurotoxicity via voltage-gated Kv 1.3 channels. 11th International Symposium on Neurovirology held jointly with 2012 Conference on HIV in the Nervous System. NYC, NY, May 29-June 2, 2012.

Marsh A, Sheehy M, Fisher C, High R, Sandkovsky U, Fox H, Meza J, Swindells S. Chronic HIV Infection and Aging in NeuroAIDS (CHAIN): Gender differences in sexual function. 2nd International Workshop on HIV & Aging, Baltimore, MD, October 27-28, 2011, poster.

Wilson TW, Sandkovsky US, O’Neill J, Knott NL, Fox HS, Swindells S. Hyperactivation of frontal and prefrontal cortices during movement planning in older HIV-infected patients.  XIX International AIDS Conference (AIDS 2012), Washington, DC, July 22-27, 2012, abstract WEPE074, poster.

Xia JX, Liu JN Xiong H. Potentiation of NMDA receptor-mediated EPSCs by D-serine: Implications for HIV-1-assopciated neurotoxicity.  18th SNIP Conference, Honolulu, Hawaii, April 25-28, 2012.

Zhang J, Liu J, Kruchowsky J, Fox H, Xiong H. Microglia activation induces axonal injury in corpus callosum.  42nd Annual Meeting Society for Neuroscience. New Orleans, LA, Oct 13-17, 2012.

Zhou Y, Kasiyanov A, Xiong  H. HIV-1gp120 alteration of synaptic transmission and plasticity in rat hippocampal slices: Implications for HIV-1-associated neurocognitive decline. Symposium for Chinese Neuroscientists worldwide 2010. Xi’an, China, May 25-30, 2012.

Zhou Y, Kasiyanov A, Liu J, Dong J, Xiong H. Inhibition of long-term potentiation by HIV-1gp120 in rat hippocampal slices. 11th International Symposium on Neurovirology held jointly with 2012 Conference on HIV in the Nervous System. NYC, NY, May 29-June 2, 2012.

Book chapters:

Ciborowski P and Silberring J. Co-editors.  The cross-roads of proteomics and analytical chemistry.  Elsevier, Inc. – signed contract

Pottiez G and Ciborowski P.  Proteomic Profiling of Cerebrospinal Fluid. In: Expression Profiling in Neuroscience. (Y. Karamanos, ed.) Humana Press, Inc. 2010 – invited contributor.

Haverland N, and Ciborowski P.  Protein Profiling of the Brain: Proteomics of Isolated Tissues and Cells. In: Expression Profiling in Neuroscience. (Y. Karamanos, ed.) Humana press, Inc. 2010 – invited contributor.

Wojtkiewicz M and Ciborowski P.  Profiling of HIV proteins in Cerebrospinal Fluid.  In: Expression Profiling in Neuroscience. (Y. Karamanos, ed.) Humana press, Inc. 2010 – invited contributor.

Pottiez G, Wiederin J and Ciborowski P.  Metabolomics and Proteomics In: NeuroAIDS and Proteomics and neuroAIDS diagnostics.  In: The Neurology of AIDS, 3rd. ed, (HE Gendelman and T. Ikezu, eds.), Springer, Inc. 2010.

Wojtkiewich M, Barnett K and Ciborowski P. Protein identification by mass spectrometry: Proteomics. In: Current Laboratory Methods in Neuroscience Research.  H. Xiong and HE. Gendelman, Eds.  Springer, 2012.