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  1. 1.   How to recover from a bad start: adaptation of HIV-1 transcription start site mutants during serial passaging in culture
  2. Nikolaitchik,Olga; Chameettachal,Akhil; Islam,Mohammad Saiful; Keele,Brandon; Delviks-Frankenberry, Krista; Pathak,Vinay; Hu,Wei-Shau; Cheng,Zetao
  3. Journal of Virology. 2025, May 07; e0015925.
  1. 2.   ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events
  2. Regev,Clil; Jang,Hyunbum; Nussinov,Ruth
  3. Journal of Molecular Biology. 2025, Apr 09; 169130.
  1. 3.   Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350
  2. Joyce, M Gordon; Bu, Wei; Chen, Wei-Hung; Gillespie, Rebecca A; Andrews, Sarah F; Wheatley, Adam K; Tsybovsky,Yaroslav; Jensen, Jaime L; Stephens,Tyler; Prabhakaran, Madhu; Fisher, Brian E; Narpala, Sandeep R; Bagchi, Meghna; McDermott, Adrian B; Nabel, Gary J; Kwong, Peter D; Mascola, John R; Cohen, Jeffrey I; Kanekiyo, Masaru
  3. Immunity. 2025, Feb 11; 58(2): 295-308.e5. .
  1. 4.   Genomic profiles and clinical presentation of chordoma
  2. Koka, Hela; Zhou,Weiyin; McMaster, Mary L; Bai, Jiwei; Luo,Wen; Klein, Alyssa; Zhang, Tongwu; Hua,Xing; Li, Xin; Wang,Difei; Xiong, Yujia; Jones,Kristine; Vogt,Aurelie; Hicks,Belynda; Parry, Dilys; Goldstein, Alisa M; Yang, Xiaohong R
  3. Acta Neuropathologica Communications. 2024, Aug 12; 12(1): 129.
  1. 5.   Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy
  2. Lian, Xiaodong; Seiger, Kyra W; Parsons, Elizabeth M; Gao, Ce; Sun, Weiwei; Gladkov, Gregory T; Roseto, Isabelle C; Einkauf, Kevin B; Osborn, Matthew R; Chevalier, Joshua M; Jiang, Chenyang; Blackmer, Jane; Carrington,Mary; Rosenberg, Eric S; Lederman, Michael M; McMahon, Deborah K; Bosch, Ronald J; Jacobson, Jeffrey M; Gandhi, Rajesh T; Peluso, Michael J; Chun, Tae-Wook; Deeks, Steven G; Yu, Xu G; Lichterfeld, Mathias
  3. Cell Host & Microbe. 2022, Dec 28; 31
  1. 6.   Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition
  2. Chen, Wei-Hung; Kim, JungHyun; Bu, Wei; Board, Nathan L; Tsybovsky,Yaroslav; Wang,Yanmei; Hostal, Anna; Andrews, Sarah F; Gillespie, Rebecca A; Choe, Misook; Stephens, Tyler; Yang, Eun Sung; Pegu, Amarendra; Peterson, Caroline E; Fisher, Brian E; Mascola, John R; Pittaluga, Stefania; McDermott, Adrian B; Kanekiyo, Masaru; Joyce, M Gordon; Cohen, Jeffrey I
  3. Immunity. 2022, Nov 8; 55(11): 2135-2148.
  1. 7.   Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats
  2. Joseph, Kevin W; Halvas, Elias K; Brandt, Leah D; Patro,Sean; Rausch,Jason; Chopra, Abha; Mallal, Simon; Kearney,Mary; Coffin, John M; Mellors, John W
  3. Journal of Virology. 2022, Jun 08; e0012222.
  1. 8.   Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR
  2. Brandt, Leah D; Guo,Amber; Joseph, Kevin W; Jacobs, Jana L; Naqvi, Asma; Coffin, John M; Kearney,Mary; Halvas, Elias K; Wu,Xiaolin; Hughes,Stephen; Mellors, John W
  3. Viruses. 2021, Jul; 13(7):
  1. 9.   The epigenetic regulator LSH maintains fork protection and genomic stability via MacroH2A deposition and RAD51 filament formation
  2. Xu,Xiaoping; Ni, Kai; He,Yafeng; Ren, Jianke; Sun, Chongkui; Liu, Yie; Aladjem, Mirit; Burkett, Sandra; Finney, Richard; Ding, Xia; Sharan,Shyam; Muegge,Kathrin
  3. Nature communications. 2021, Jun 10; 12(1):
  1. 10.   Antibody-mediated depletion of viral reservoirs is limited in SIV-infected macaques treated early with antiretroviral therapy
  2. Swanstrom,Adrienne; Immonen,Taina; Oswald,Kelli; Pyle,Cathi; Thomas,James; Bosche,Bj; Silipino,Lorna; Hull,Mike; Newman,Laura; Coalter, Vicky; Wiles,Adam; Wiles,Rodney; Kiser,Jacob; Morcock,David; Shoemaker,Rebecca; Fast,Randy; Breed,Matthew; Kramer,Josh; Donohue,Duncan; Malys,Tyler; Fennessey,Christine; Trubey,Charles; Deleage,Claire; Estes, Jacob D.; Lifson,Jeffrey; Keele,Brandon; Del Prete,Greg
  3. The Journal of Clinical Investigation. 2021, Mar 15; 131(6):
  1. 11.   The D2 and D3 sublineages of human papillomavirus 16-positive cervical cancer in Guatemala differ in integration rate and age of diagnosis
  2. Lou,Hong; Boland,Joseph; Torres-Gonzalez, Edmundo; Albanez, Anaseidy; Zhou,Weiyin; Steinberg,Mia; Diaw, Lena; Mitchell, Jason; Roberson, David; Cullen,Michael; Garland,Lisa; Bass,Sara; Burk, Robert D; Yeager,Meredith; Wentzensen, Nicolas; Schiffman, Mark; Alvirez Freites, Enrique; Gharzouzi, Eduardo; Mirabello, Lisa; Dean, Michael
  3. Cancer research. 2020, SEP 15; 80(18): 3803-3809.
  1. 12.   Lentiviral gene therapy for X-linked chronic granulomatous disease
  2. Kohn, Donald B; Booth, Claire; Kang, Elizabeth M; Pai, Sung-Yun; Shaw, Kit L; Santilli, Giorgia; Armant, Myriam; Buckland, Karen F; Choi, Uimook; De Ravin, Suk See; Dorsey, Morna J; Kuo, Caroline Y; Leon-Rico, Diego; Rivat, Christine; Izotova, Natalia; Gilmour, Kimberly; Snell, Katie; Dip, Jinhua Xu-Bayford; Darwish, Jinan; Morris, Emma C; Terrazas, Dayna; Wang, Leo D; Bauser, Christopher A; Paprotka, Tobias; Kuhns,Doug; Gregg, John; Raymond, Hayley E; Everett, John K; Honnet, Geraldine; Biasco, Luca; Newburger, Peter E; Bushman, Frederic D; Grez, Manuel; Gaspar, H Bobby; Williams, David A; Malech, Harry L; Galy, Anne; Thrasher, Adrian J
  3. Nature medicine. 2020, Jan 27; pii: 10.1038/s41591-019-0735-5.
  1. 13.   Cellular RNA surveillance in health and disease
  2. Wolin,Sandra; Maquat, Lynne E.
  3. Science (New York, N.Y.). 2019, Nov 15; 366(6467): 822-826.
  1. 14.   Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
  2. Schneider,Tom; Jejjala, Vishnu
  3. PloS one. 2019, OCT 31; 14(10): e0222419.
  1. 15.   RNA Packaging in HIV
  2. Rein,Alan
  3. Trends in microbiology. 2019, Aug; 27(8): 715-723.
  1. 16.   Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II
  2. Wang, Wei; Walmacq, Celine; Chong, Jenny; Kashlev, Mikhail; Wang, Dong
  3. Proceedings of the National Academy of Sciences of the United States of America. 2018, Mar 13; 115(11): E2538-E2545.
  1. 17.   Next-generation in situ hybridization approaches to define and quantify HIV and SIV reservoirs in tissue microenvironments
  2. Deleage, Claire; Chan, Chi N.; Busman-Sahay, Kathleen; Estes, Jake
  3. Retrovirology. 2018, Jan 9; 15(1): 4.
  1. 18.   Crystal structures of beta-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding
  2. Tsutsui, Y.; Ramakrishnan, B.; Qasba, P. K.
  3. Journal of Biological Chemistry. 2013, 1-Nov; 288(44): 31963-70.
  1. 19.   Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's beta-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology
  2. Connelly, L.; Jang, H.; Arce, F. T.; Capone, R.; Kotler, S. A.; Ramachandran, S.; Kagan, B. L.; Nussinov, R.; Lal, R.
  3. Journal of Physical Chemistry B. 2012, Feb; 116(5): 1728-1735.
  1. 20.   XMRV and prostate cancer-a 'final' perspective
  2. Sfanos, K. S.; Aloia, A. L.; De Marzo, A. M.; Rein, A.
  3. Nature Reviews Urology. 2012, Feb; 9(2): 111-118.
  1. 21.   Cre-mediated recombination can induce apoptosis in vivo by activating the p53 DNA damage-induced pathway
  2. Zhu, J. J.; Nguyen, M. T.; Nakamura, E.; Yang, J. M.; Mackem, S.
  3. Genesis. 2012, Feb; 50(2): 102-111.
  1. 22.   Filarial Lymphatic Pathology Reflects Augmented Toll-Like Receptor-Mediated, Mitogen-Activated Protein Kinase-Mediated Proinflammatory Cytokine Production
  2. Babu, S.; Anuradha, R.; Kumar, N. P.; George, P. J.; Kumaraswami, V.; Nutman, T. B.
  3. Infection and Immunity. 2011, Nov; 79(11): 4600-4608.
  1. 23.   Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals
  2. Machado, J. P.; Johnson, W. E.; O'Brien, S. J.; Vasconcelos, V.; Antunes, A.
  3. Bmc Evolutionary Biology. 2011, Nov; 11
  1. 24.   Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
  2. Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O.
  3. Nature Protocols. 2011, Sep; 6(9): 1341-1354.
  1. 25.   The TY3 Gag3 Spacer Controls Intracellular Condensation and Uncoating
  2. Clemens, K.; Larsen, L.; Zhang, M.; Kuznetsov, Y.; Bilanchone, V.; Randall, A.; Harned, A.; DaSilva, R.; Nagashima, K.; McPherson, A.; Baldi, P.; Sandmeyer, S.
  3. Journal of Virology. 2011, Apr; 85(7): 3055-3066.
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