Weinberger Lab Publications
2017
- Aull, K. H., Tanner, E. J., Thomson, M. & Weinberger, L. S. (2017) Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch. Biophys. J. 112, 2428–2438.
- Saykally VR, Rast LI, Sasaki J, Jung SY, Bolovan-Fritts C, Weinberger LS. A Bioreactor Method to Generate High-titer, Genetically Stable, Clinical-isolate Human Cytomegalovirus. Bio Protoc. 2017 Nov 5;7(21). pii: e2589. doi: 10.21769/BioProtoc.2589.
- Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS. Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLosBiol.. 2017 Oct 18;15(10):e2000841. doi: 10.1371/journal.pbio.2000841. eCollection 2017 Oct
2016
- Rast LI, Rouzine IM, Rozhnova G, Bishop L, Weinberger AD, Weinberger LS (2016) Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals. PLoS Comput Biol 12(5): e1004799. doi:10.1371/journal.pcbi.1004799
- Tanner EJ, Kirkegaard KA, Weinberger LS (2016) Exploiting Genetic Interference for Antiviral Therapy. PLoS Genet 12(5): e1005986. doi:10.1371/journal.pgen.1005986
- Roy D. Dar, Sydney M. Shaffer, Abhyudai Singh, Brandon S. Razooky, Michael
L. Simpson, Arjun Raj, Leor S. Weinberger. Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels. PLOS One. doi:10.1371/journal.pone.0158298
2015
- Weinberger LS. A minimal fate-selection switch. Current Opinion in Cell Biology. doi:10.1016/j.ceb.2015.10.005
- Dar RD, Razooky BS, Weinberger LS, Cox CD, Simpson ML (2015) The Low Noise Limit in Gene Expression. PLoS ONE 10(10): e0140969. doi:10.1371/journal.pone.0140969
- Razooky BS, Pai A, Rouzine IM, Weinberger LS. A Hardwired HIV Latency Program. Cell. Volume 160, Issue 5, p990–1001, 26 February 2015.
Supplementary Information: Table S1
- Rouzine IM, Weinberger AD, Weinberger LS. An Evolutionary Role for HIV Latency in Enhancing Viral Transmission. Cell. Volume 160, Issue 5, p1002–1012, 26 February 2015.
Supplementary Information: Table S1 and S2
- Jung SY, Notton T, Fong E, Shusteff M, Weinberger LS. Spatial tuning of acoustofluidic pressure nodes by altering net sonic velocity enables high-throughput, efficient cell sorting. Lab on a Chip. 2015 Advance Article. Received 11 Nov 2014, Accepted 23 Dec 2014 First published online 07 Jan 2015.
2014
- Rouzine IM, Razooky BS, Weinberger LS. Stochastic variability in HIV affects viral eradication. Proc Natl Acad Sci. 111(37):13251-2. 2014 Sep 16. Epub 2014 Sep 8.
- Notton T, Sardanyes J, Weinberger AD, Weinberger LS. The case for transmissible antivirals to control population-wide infectious disease. Trends in Biotechnology. Cell Press. Published online July 10 2014. DOI: 10.1016/j.tibtech.2014.06.006.
- Dar RD, Hosmane NN, Arkin MR, Siliciano RF, Weinberger LS. Screening for noise in gene expression identifies drug synergies. Science. 20 June 2014: Vol. 344 no. 6190 pp. 1392-1396. PMCID: PMC4122234.
Supplementary Information: Table S1
- Reviewed in Research Highlights, Antivirals, in Nature Chemical Biology, Vol. 10 August 2014. "Turn up the noise".
- Selected as Research Highlight by Cell Volume 158, Issue 3, p469, 471, 31 July 2014. "Opening the HIV Mystery Box".
- Research Highlight, reviewed by Tan and Elledge in Genome Medicine 2014, 6:55. 29 July 2014. "When noise makes music: HIV reactivation with transcriptional noise enhancers".
- Selected as Research Highlight by Nature Biotechnology 32, 643 (2014) Published online 08 July 2014. "Screening for noise in gene expression identifies drug synergies".
- Selected as Research Highlight by Nature 510, 190. 12 June 2014. "Chemicals wake up dormant HIV"
- Rouzine IM, Coffin JM, Weinberger LS. Fifteen Years Later: Hard and Soft Selection Sweeps Confirm a Large Population Number for HIV In Vivo. PLoS Genet. 2014 Feb 20; 10(2):e1004179.
- Fong EJ, Johnston AC, Notton T, Jung SY, Rose KA, Weinberger LS, Shusteff M. Acoustic focusing with engineered node locations for high-performance microfluidic particle separation. Analyst. RSC Publishing. 2014: 139, 1192-1200.
2013
- Weinberger AD, Weinberger LS. Stochastic Fate Selection in HIV-infected Patients. Cell. 2013, Oct 24;155(3), 497-499.
- Gardner T, Bolovan-Fritts C, Teng M, Redmann V, Kraus T, Sperling R, Moran T, Britt W, Weinberger L, Tortorella D. Development of a high-throughput assay to measure the neutralization capability of anti-CMV antibodies. Clin Vaccine Immunol. April 2013 vol. 20 no. 4 540-550. PMCID PMC3623408.
Supplementary Information: Figure S1
- Rouzine IM, Weinberger LS. Design requirements for interfering particles to maintain coadaptive stability with HIV-1. J Virol. 2013 Feb;87(4):2081-93. doi: 10.1128/JVI.02741-12. PMCID: PMC3571494.
- Boehm D, Calvanese V, Dar RD, Xing S, Schroeder S, Martins L, Aull K, Li PC, Planelles V, Bradner JE, Zhou MM, F Siliciano RF, Weinberger L, Verdin E, Ott M. BET bromodomain-targeting compounds reactivate HIV from latency via a Tat-independent mechanism. Cell Cycle. 2013 Volume 12, Issue 3 February 1, 2013 Pages 452 - 462. PMCID: PMC358744.
2012
- Teng MW, Bolovan-Fritts C, Dar RD, Womack A, Shenk T, Simpson ML, Weinberger LS. An Endogenous Accelerator for Viral Gene Expression Provides a Fitness Advantage. Cell. Volume 151, Issue 7, 1569-1580, 21 December 2012.PMCID: PMC3552493.
Supplementary Information: Table S1
- Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM, Cox CD, Simpson ML, Weinberger LS. Transcriptional burst frequency and burst size are equally modulated across the human genome. Proc Natl Acad Sci USA. 2012 Oct 11. PMCID: PMC3491463.
- Singh A, Razooky BS, Dar RD, Weinberger LS. Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Molecular Systems Biology. 2012. Aug 28;8:607. PMCID: PMC3435505.
- Razooky BS, Gutierrez E, Terry VH, Spina CA, Groisman A, Weinberger LS. Microwell Devices with Finger-like Channels for Long-Term Imaging of HIV-1 Expression Kinetics in Primary Human Lymphocytes. Lab on a Chip. 2012. Oct 2;12(12):4305-4312.PMCID: PMC3589574.
2011
- Franz K, Singh A, Weinberger LS. Lentiviral vectors to study stochastic noise in gene expression. Methods in Enzymology. 2011; 497:603-22.
- Metzger V, Lloyd-Smith JO, Weinberger LS. Autonomous Targeting of Infectious Superspreaders using Engineered Transmissable Therapies. PLoS Computational Biology. 2011 Mar;7(3):e1002015. Epub 2011 Mar 17. PMCID: PMC3060167.
- Razooky BS, Weinberger LS. Mapping the architecture of the HIV-1 Tat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise. Methods. Razooky BS, Weinberger LS. 2011 Jan;53(1):68-77.
2010 and earlier
- Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS. Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J. 2010 Apr 21;98(8):L32-4.
- Weinberger AD, Perelson AS, Ribeiro RM, Weinberger LS. Accelerated immunodeficiency by anti-CCR5 treatment in HIV infection. PloS Comput Biol. 2009 Aug 5; 5(8):e1000467.
- Singh A, Weinberger LS. Stochastic gene expression as a molecular switch for viral latency. Curr Opin Microbiol. 2009 Jul 10; 12(4):460-6.
- Weinberger LS, Dar RD, Simpson ML. Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet. 2008 Apr; 40(4):466-70.
- Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive-feed back loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005 Jul; 122(2):169-82.
- Weinberger LS, Schaffer DV, Arkin AP. Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection. J Virol. 2003 Sep; 77(18):10028-36.
- Rosen HR, Ribeiro RR, Weinberger L, Wolf S, Chung M, Gretch DR, Perelson AS. Early hepatitis C viral kinetics correlate with long-term outcome in patients receiving high dose induction followed by combination interferon and ribavirin therapy. J Hepatol. 2002 Jul; 37(1):124-130.
- Mohri H, Perelson AS, Tung K, Ribeiro RM, Ramratnam B, Markowitz, Kost R, Hurley A, Weinberger L, Cesar D, Hellerstein MK, Ho DD. Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy. J Exp Med. 2001 Nov; 194(9):1277-87.
- Shiratori Y, Perelson AS, Weinberger L, Imazeki F, Yokosuka O, Nakata R, Ihori M, Hirota K, Ono N, Kuroda H, Motojima T, Nishigaki M, Omata M. Different turnover rate of hepatitis C virus clearance by different treatment regimen using interferon-beta. J Hepatol. 2000 Aug; 33(2):313-22.
- Jin X, Bauer DE, Tuttleton SE, Lewin S, Gettie A, Blanchard J, Irwin CE, Safrit JT, Mittler J, Weinberger L, Kostrikis LG, Zhang L, Perelson AS, Ho DD. Dramatic rise in plasma viremia after CD8(+) T cell depletion in simian immunodeficiency virus-infected macaques. J Exp Med. 1999 Mar; 189(6):991-