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Publications

Recent Publications

Linking a nuclear lncRNA to cytoplasmic lysosome integrity and cell death
Haibin Liu, Zhi-Ming Zheng
Proceedings of the National Academy of Sciences Feb 2022, 119 (8) e2123082119; DOI: 10.1073/pnas.2123082119

Intranuclear Positions of HIV-1 Proviruses Are Dynamic and Do Not Correlate with Transcriptional Activity.  
Burdick RC, Deleage C, Duchon A, Estes JD, Hu WS, Pathak VK.   
mBio. Jan 11;13(1): 2022 e0325621.  

Genome-wide regulation of KSHV RNA splicing by viral RNA-binding protein ORF57
Vladimir Majerciak, Alexei Lobanov, Maggie Cam, Zhi-Ming Zheng
bioRxiv 2022.01.28.478141; doi: https://doi.org/10.1101/2022.01.28.478141

Human Papillomavirus Type 16 Circular RNA Is Barely Detectable for the Claimed Biological Activity.
Yu L, Zheng ZM.
mBio. 2022 Jan 18;13(1):e0359421. doi: 10.1128/mbio.03594-21. Epub ahead of print. PMID: 35038914; PMCID: PMC8764516.

Why the HIV reservoir never runs dry: Clonal expansion and the characterisitcs of HIV-infected cells challenge strategies to cure and control HIV infection
Lau CY, Adan MA, Maldarelli F
Viruses 13: 2512, 2021.

 
INSTIs and NNRTIs potently inhibit HIV-1 polypurine tract mutants in a single round infection assay
Smith SJ, Ferris A, Zhao X, Pauly G, Schneider JP, Burke TR, Jr, Hughes SH
Viruses 13: 2501, 2021.
 
New approaches to multi-parametric HIV-1 genetics using multiple displacement amplification: Determining the what, how, and where of the HIV-1 reservoir
Patro SC, Niyongabo A, Maldarelli F, Kearney MF
Viruses 13: 2475, 2021.
 
Therapeutic implications of ongoing alveolar viral replication in COVID-19
McGonagle D, Kearney MF, O'Regan A, O'Donnell JS, Quartuccio L, Watad A, Bridgewood C
Lancet Rheumatol Dec 1: doi 10.1016/S2665-9913(21)00322-2, 2021.
 
Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem
Nikolaitchik OA, Liu S, Kitzrow JP, Liu Y, Rawson JMO, Shakya S, Cheng Z, Pathak VK, Hu W-S, Musier-Forsyth K
Proc Natl Acad Sci USA 118: e2114494118, 2021.
 
Plasma membrane anchoring and Gag:Gag multimerization on viral RNA are critical properties of HIV-1 Gag required to mediate efficient genome packaging
Duchon A, Santos S, Chen J, Brown M, Nikolaitchik OA, Tai S, Chao JA, Freed EO, Pathak VK, Hu W-S
mBio Dec 7: doi 10.1128/mbio.03254-21, 2021.
 
RNA granules in antiviral innate immunity, a KSHV journey
Sharma N, Zheng Z-M
Front Microbiol Dec 2: doi 10.3389/fmicb.2021.794431, 2021.
 
Human immunodeficiency viruses: Replication
Ott M, Freed EO
In: Fields Virology, 7th edition, Vol 3: RNA Viruses (Knipe DM, Howley PM, eds), Lippincott, Williams, and Wilkins, in press November 2021.
 
Mitchell JL, Pollara J, Dietze K, Edwards RW, Nohara J, N'guessan KF, Zemil M, Buranapraditkun S, Takata H, Li Y, Muir R, Kroon E, Pinyakorn S, Jha S, Manasnayakorn S, Chottanapund S, Thantiworasit P, Prueksakaew P, Ratnaratorn N, Nuntapinit B, Fox L, Tovanabutra S, Paquin-Proulx D, Wieczorek L, Polonis VR, Maldarelli F, Haddad EK, Phanuphak P, Sacdalan CP, Rolland M, Phanuphak N, Ananworanich J, Vasan S, Ferrari G, Trautmann L
J Clin Invest Nov 11: doi 10.1172/JCI150937, 2021.
 
A combination of amino acid mutations leads to resistance to multiple nucleoside analogs in reverse transcriptases from HIV-1 subtypes B and C
Boyer PL, Rehm CA, Sneller MC, Mican J, Caplan MR, Dewar R, Ferris AL, Clark P, Johnson A, Maldarelli F, Hughes SH
Antimicrob Agents Chemother Nov 1: doi 10.1128/AAC.01500-21, 2021.
 
Zhang L, Richards A, Barrasa MI, Hughes SH, Young RA, Jaenisch R
Proc Natl Acad Sci USA 118: e2114995118, 2021.
 
Rafting through the palms: S-acylation of SARS-CoV-2 spike protein induces lipid reorganization
Vilmen G, Banerjee A, Freed EO
Dev Cell 56: 2787-2789, 2021.
 
Environmental pollutants, mucosal barriers, and pathogen susceptibility; The case for aflatoxin B1 as a risk factor for HIV transmission and pathogenesis
Madeen EP, Maldarelli F, Groopman JD
Pathogens 10: 1229, 2021.
 
Ecdysoneless protein regulates viral and cellular mRNA splicing to promote cervical oncogenesis
Mirza S, Kalluchi A, Raza M, Saleem I, Mohapatra B, Pal D, Ouellette MM, Qiu F, Yu L, Lobanov A, Zheng ZM, Zhang Y, Alsaleem MA, Rakha EA, Band H, Rowley MJ, Band V
Mol Cancer Res Oct 20: doi 10.1158/1541-7786.MCR-21-0567, 2021.
 
Clonal expansion of infected CD4+ T cells in people living with HIV
Coffin JM, Hughes SH
Viruses 13: 2078, 2021.
 
Majdoul S, Compton AA
Nat Rev Immunol Oct 13: doi 10.1038/s41577-021-00626-8, 2021.
 
Mellors JW, Guo S, Naqvi A, Brandt LD, Su L, Sun Z, Joseph KW, Demirov D, Halvas EK, Butcher D, Scott B, Hamilton A, Heil M, Karim B, Wu X, Hughes SH
Sci Adv 7: eabi8795, 2021.
 
Levin JG, Rein A
Proc Natl Acad Sci USA 118: e2115344118, 2021.
 
RNA helicase DDX6 in P-bodies is essential for the assembly of stress granules
Majerciak V, Zhou T, Zheng Z-M
bioRxiv Sep 25: doi 10.1101/2021.09.24.461736, 2021.
 
Human papillomavirus type 16 circular RNA is barely detectable for the claimed transformation activity
Yu, L, Zheng Z-M
bioRxiv Sep 22: doi 10.1101/2021.09.22.449294v1, 2021.
 
SERINC proteins potentiate antiviral type I IFN production and proinflammatory signaling pathways
Zeng C, Waheed AA, Li T, Yu J, Zheng Y-M, Yount J, Wen H, Freed EO, Liu S-L
Sci Signal 14: eabc7611, 2021.
 
Merati TP, Karyana M, Tjitra E, Kosasih H, Aman AT, Alisjahbana B, Lokida D, Arlinda D, Maldarelli F, Neal A, Arif M, Gasem MH, Lukman N, Sudarmono P, Lau CY, Hadi U, Lisdawati V, Wulan WN, Lane HC, Siddiqui S
Am J Trop Med Hyg 105: 960-5zhi-ming, 2021.
 
Puthenveetil R, Lun CM, Murphy RE, Healy LB, Vilmen G, Christenson ET, Freed EO, Banerjee A
J Biol Chem 297: 101112, 2021.
 
Prevalence and risk of residual viremia after ART in low- and middle-income countries: A cross-sectional study
Gatechompol S, Zheng L, Bao Y, Avihingsanon A, Kerr SJ, Kumarasamy N, Hakim JG, Maldarelli F, Gorelick RJ, Welker JL, Lifson JD, Hosseinipour MC, Eron JJ, Ruxrungtham K
Medicine (Baltimore) 100: e26817, 2021.
 
SARS-CoV-2 viremia is associated with COVID-19 severity and predicts clinical outcomes
Jacobs JL, Bain W, Naqvi A, Staines B, Castanha PMS, Yang H, Boltz VF, Barratt-Boyes S, Marques ETA, Mitchell SL, Methé B, Olonisakin TF, Haidar G, Burke TW, Petzold E, Denny T, Woods CW, McVerry BJ, Lee JS, Watkins SC, St Croix CM, Morris A, Kearney MF, Ladinsky MS, Bjorkman PJ, Kitsios G, Mellors JW
Clin Infect Dis Aug 10: ciab686, 2021.

Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures

Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke TR Jr, Cherepanov P, Maertens GN
Nat Commun 12: 4996, 2021.
 
Zhang L, Richards A, Barrasa MI, Hughes SH, Young RA, Jaenisch R
Proc Natl Acad Sci USA 118: e2109497118, 2021.
 
Maturation of HIV-1
Hikichi Y, Freed EO
Science 373: 621-622, 2021.
 
Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Yu L, Majerciak V, Xue XY, Uberoi A, Lobanov A, Chen X, Cam M, Hughes SH, Lambert PF, Zheng Z-M
PLoS Pathog 17: e1009812.
 
Immune reconstitution following allogenic stem cell transplantation in HIV infected individuals: Years of living danger-ously
Lange C, Maldarelli F
Clin Infect Dis Jun 22: doi 10.1093/cid/ciab565, 2021.
 
Dong H, Shu X, Xu Q, Zhu C, Kaufmann AM, Zheng Z-M, Albers AE, Qian X
Virol Sin Jun 21: doi 10.1007/s12250-021-00413-8, 2021.
 
Crystal structure of a retroviral polyprotein: Prototype foamy virus protease-reverse transcriptase (PR-RT)
Harrison JJEK, Tuske S, Das K, Ruiz FX, Bauman JD, Boyer P, DeStefano JJ, Hughes SH, Eddy A
Viruses 13: 1495, 2021.
 
SARS-CoV-2: From its discovery to genome structure, transcription, and replication
Brant AC, Tian W, Majerciak V, Yang W, Zheng Z-M
Cell Biosci 11: 136, 2021. 
 
HIVIntact: A python-based tool for HIV-1 genome intactness inference
Wright IA, Bale MJ, Shao W, Hu W-S, Coffin JM, van Zyl GU, Kearney MF
Retrovirology 18: 16, 2021.
 
Brandt LD, Guo S, Joseph KW, Jacobs JL, Naqvi A, Coffin JM, Kearney MF, Halvas EK, Wu X, Hughes SH, Mellors JW
Viruses 13: 1235, 2021.
 
Zhang L, Richards A, Barrasa MI, Hughes SH, Young RA, Jaenisch R.
Proc Natl Acad Sci USA 118: e2105968118, 2021.
 
Capoferri AA, Shao W, Spindler J, Coffin JM, Rausch JW, Kearney MF
medRxiv Jun 4: doi 10.1101/2021.06.01.21258185, 2021.
 
Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2
Shi G, Chiramel AI, Majdoul S, Lai KK, Das S, Beare PA, Andresson T, Best SM, Compton AA
bioRxiv Apr 16: doi 10.1101/2021.04.15.440067, 2021.
 
Boltz VF, Ceriani C, Rausch JW, Shao W, Bale MJ, Keele BF, Hoh R, Milush JM, Deeks SG, Maldarelli F, Kearney MF, Coffin JM
Viruses 13: 799, 2021.
 
Mendonça L, Sun D, Ning J, Liu J, Kotecha A, Olek M, Frosio T, Fu X, Himes BA, Kleinpeter AB, Freed EO, Zhou J, Aiken C, Zhang P
Commun Biol 4: 481, 2021.
 
Coffin JM, Bale MJ, Wells D, Guo S, Luke B, Zerbato JM, Sobolewski MD, Sia T, Shao W, Wu X, Maldarelli F, Kearney MF, Mellors JW, Hughes SH
PLoS Pathog 17: e1009141, 2021.
 
Early emergence and long-term persistence of HIV-infected T-cell clones in children
Bale MJ, Katusiime MG, Wells D, Wu X, Spindler J, Halvas EK, Cyktor JC, Wiegand A, Shao W, Cotton MF, Hughes SH, Mellors JW, Coffin JM, van Zyl GU, Kearney MF
mBio 12: e00568-21, 2021.
 
Rein A
Viruses 13: 491, 2021.
 
Banday AR, Onabajo OO, Lin SH, Obajemu A, Vargas JM, Delviks-Frankenberry KA, Lamy P, Bayanjargal A, Zettelmeyer C, Florez-Vargas O, Pathak VK, Dyrskjøt L, Prokunina-Olsson L
Commun Biol 4: 386, 2021.
 
Lun CM, Waheed AA, Majadly A, Powell N, Freed EO
mBio 12: e00219-21, 2021.
 
Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR Jr, Hughes SH

ACS Infect Dis 7: 1469-1482, 2021.

Mallery DL, Kleinpeter AB, Renner N, Rifat Faysal KM, Novikova M, Kiss L, Wilson MSC, Ahsan B, Ke Z, Briggs JAG, Saiardi A, Böcking T, Freed EO*, James LC* (*Joint corresponding author)
Sci Adv 7: eabe4716, 2021.
 
Li C, Burdick RC, Nagashima K, Hu W-S, Pathak VK
Proc Natl Acad Sci USA 118: e2019467118, 2021.
 
Coomer CA, Rahman K, Compton AA
Trends Genet 37: 406-410, 2021.
 
Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR Jr, Hughes SH
Viruses 13: 205, 2021.
 
Rawson JMO, Duchon A, Nikolaitchik OA, Pathak VK, Hu W-S
Viruses 13: 173, 2021.
 
Burdick RC, Pathak VK
Signal Transduct Target Ther 6: 13, 2021.
 
Hikichi Y, Van Duyne R, Pham P, Groebner JL, Wiegand A, Mellors JW, Kearney MF, Freed EO
mBio 12: e03134-20, 2021.
 
Liu H, Xu J, Yang Y, Wang X, Wu E, Majerciak V, Zhang T, Steenbergen RDM, Wang H-K, Banerjee NS, Li Y, Lu W, Meyers C, Zhu J, Xie X, Chow LT, Zheng Z-M
Proc Natl Acad Sci USA 118: e2014195118, 2021.
 
Shi G, Kenney AD, Kudryashova E, Zani A, Zhang L, Lai KK, Hall-Stoodley L, Robinson RT, Kudryashov DS, Compton AA, Yount JS
EMBO J 40: e106501, 2021.
 
Smith SJ, Pauly GT, Hewlett K, Schneider JP, Hughes SH
Chem Biol Drug Des 97: 4-17, 2021.
 
Umunnakwe CN, Duchon A, Nikolaitchik OA, Abdul Rahman S, Liu Y, Chen J, Tai S, Pathak VK, Hu W-S
J Mol Biol 433: 166718, 2021.
 
Yu L, Lobanov A, Majerciak V, Mirza S, Band V, Liu H, Cam M, Zheng Z-M
bioRxiv Jun 27: doi 10.1101/2020.06.25.171959v1, 2020.