Weinberger Lab Publications

• Engineered deletions of HIV replicate conditionally to reduce disease in nonhuman primates

  Pitchai FNN*, Tanner, EJ*, Khetan N, Vasen G, Levrel C, Kumar AJ, Pandey S, Ordonez T, Barnette P, Spencer D, Jung SY, Glazier J, Thompson C, Harvey-Vera A, Son H, Strathdee SA, Holguin L, Urak R, Burnett J, Burgess W, Busman-Sahay K, Estes JD, Hessell A, Fennessey CM, Keele BF, Haigwood NL, Weinberger LS.

  Science 2024

  • News:

    • New York Times - Carl Zimmer - Aug 8 2024

    • Science - J Cohen - Aug 8 2024

    • Le Monde - M Gozlan - Oct 24 2024

• Single-cell RNA sequencing algorithms underestimate changes in transcriptional noise compared to single-molecule RNA imaging

Khetan N*, Zuckerman B.*, Calia GP*, Chen X, Arceo XG, Weinberger LS

Cell Reports Methods 2024

• Expression of thioredoxin-1 in the ASJ neuron corresponds with and enhances intrinsic regenerative capacity under lesion conditioning in C. elegans

  Grooms N W.F., Fitzgerald MQ., Zuckerman B, Ureña SE., Weinberger LS., Chung SH.

  bioRxiv 2023

• Comparative analysis between single-cell RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise

  Calia G P., Chen X, Zuckerman B, Weinberger LS.

  bioRxiv 2023

• Identification of a therapeutic interfering particle-A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance.

Chaturvedi S, Vasen G, Pablo M, Chen X, Beutler N, Kumar A, Tanner E, Illouz S, Rahgoshay D, Burnett J, Holguin L, Chen PY, Ndjamen B, Ott M, Rodick R, Rogers T, Smith DM, Weinberger LS.

Cell 2021

• A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions.

  Desai RV, Chen X, Martin B, Chaturvedi S, Hwang DW, Li W, Yu C, Ding S, Thomson M, Singer RH, Coleman RA, Hansen MMK, Weinberger LS.

  Science 2021

• Evaluation of Singer et al.: Technical points on analyzing viral replication kinetics in single cells.

  Chen X, Pablo M, Weinberger L

  Cell Syst 2021

• RanDeL-Seq: a High-Throughput Method to Map Viral cis- and trans-Acting Elements.

  Notton T, Glazier JJ, Saykally VR, Thompson CE, Weinberger LS.

  mBio 2021

• The HSV-1 ICP4 Transcriptional Auto-Repression Circuit Functions as a Transcriptional "Accelerator" Circuit.

  Chaturvedi S, Engel R, Weinberger L.

  Front Cell Infect Microbiol 2020

• Noise-driven cellular heterogeneity in circadian periodicity.

  Li Y, Shan Y, Desai RV, Cox KH, Weinberger LS, Takahashi JS.

  PNAS 2020

• HIV Latency: Stochastic across Multiple Scales.

  Hansen MMK, Martin B, Weinberger LS.

  Cell Host Microbe 2019

• Discovery and Engineering of a Therapeutic Interfering Particle (TIP): a combination self-renewing antiviral.

  Tanner EJ, Jung SY, Glazier J, Thompson C, Zhou Y, Martin B, Son HI, Riley JL, Weinberger LS.

  biorxiv 2019

• Disrupting Transcriptional Feedback Yields an Escape-Resistant Antiviral

  Chaturvedi S, Wolf M, Vardi N, Chan MF, Weinberger LS.

  Cell 2018

• Attacking Latent HIV with convertibleCAR-T Cells, a Highly Adaptable Killing Platform.

  Herzig E, Kim KC, Packard TA, Vardi N, Schwarzer R, Gramatica A, Deeks SG, Williams SR, Landgraf K, Killeen N, Martin DW, Weinberger LS, Greene WC.

  Cell 2019

• Post-Transcriptional Noise Control.

  Hansen MMK, Weinberger LS.

  Bioessays 2019

• Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability.

Hansen MMK, Desai RV, Simpson ML, Weinberger LS.

Cell Syst 2018

• Feedback-mediated signal conversion promotes viral fitness.

  Vardi N, Chaturvedi S, Weinberger LS.

  PNAS 2018

• A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization.

  Hansen MMK, Wen WY, Ingerman E, Razooky BS, Thompson CE, Dar RD, Chin CW, Simpson ML, Weinberger LS.

  Cell 2018

• Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean.

  Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS.

  PLos Biol 2017

• A Bioreactor Method to Generate High-titer, Genetically Stable, Clinical-isolate Human Cytomegalovirus.

  Saykally VR, Rast LI, Sasaki J, Jung SY, Bolovan-Fritts C, Weinberger LS.

  Bio Protoc 2017

• Fate-Regulating Circuits in Viruses: From Discovery to New Therapy Targets.

  Pai A, Weinberger LS.

  Annu Rev Virol 2017

• Transient Thresholding: A Mechanism Enabling Noncooperative Transcriptional Circuitry to Form a Switch.

  Aull, K. H., Tanner, E. J., Thomson, M. & Weinberger, L. S.

  Biophys J 2017

• Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels.

  Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS.

  PLOS One 2016

• Exploiting Genetic Interference for Antiviral Therapy.

  Tanner EJ, Kirkegaard KA, Weinberger LS.

  PLoS Genet 2016

• A minimal fate-selection switch.

  Weinberger LS.

  Current Opinion in Cell Biology 2015

• A Hardwired HIV Latency Program.

  Razooky BS, Pai A, Rouzine IM, Weinberger LS.

  Cell 2015

  • Supplementary Information: Table S1

  • Original Article with Supplementary Information Appended

• An Evolutionary Role for HIV Latency in Enhancing Viral Transmission.

  Rouzine IM, Weinberger AD, Weinberger LS.

  Cell 2015

  • Supplementary Information: Table S1 and S2

  • Original Article with Supplementary Information Appended

• Spatial tuning of acoustofluidic pressure nodes by altering net sonic velocity enables high throughput, efficient cell sorting.

  Jung SY, Notton T, Fong E, Shusteff M, Weinberger LS.

  Lab Chip 2015

• Stochastic variability in HIV affects viral eradication.

  Rouzine IM, Razooky BS, Weinberger LS.

  PNAS 2014

• Screening for noise in gene expression identifies drug synergies.

  Dar RD, Hosmane NN, Arkin MR, Siliciano RF, Weinberger LS.

  Science 2014

  • Supplementary Information: Table S1

  • Supplementary Information

    • Reviewed in Research Highlights, Antivirals, in Nature Chemical Biology, 2014. "Turn up the noise".

    • Selected as Research Highlight by Cell 2014. "Opening the HIV Mystery Box".

    • Research Highlight, reviewed by Tan and Elledge in Genome Medicine 2014. "When noise makes music: HIV reactivation with transcriptional noise enhancers".

    • Selected as Research Highlight by Nature Biotechnology 2014. "Screening for noise in gene expression identifies drug synergies".

    • Selected as Research Highlight by Nature 2014. "Chemicals wake up dormant HIV"

• The case for transmissible antivirals to control population-wide infectious disease.

  Notton T, Sardanyes J, Weinberger AD, Weinberger LS.

  Trends in Biotechnology Cell Press 2014

• Acoustic focusing with engineered node locations for high-performance microfluidic particle separation.

  Fong EJ, Johnston AC, Notton T, Jung SY, Rose KA, Weinberger LS, Shusteff M.

  Analyst RSC Publishing 2014

  • Supplementary Information

• Reply to Co-adaptive stability of interfering particles with HIV-1 when there is an evolutionary conflict.

  Rouzine IM, Weinberger LS.

  J Virol 2013

• The Low Noise Limit in Gene Expression.

  Dar RD, Razooky BS, Weinberger LS, Cox CD, Simpson ML.

  PLoS ONE 2015

  • Supplementary Information

• Design requirements for interfering particles to maintain coadaptive stability with HIV-1.

  Rouzine IM, Weinberger LS.

  J Virol 2013

  • Supplementary Information

• An Endogenous Accelerator for Viral Gene Expression Confers a Fitness Advantage.

  Teng MW, Bolovan-Fritts C, Dar RD, Womack A, Shenk T, Simpson ML, Weinberger LS.

  Cell 2012

  • Supplementary Information: Table S1

  • Original Article with Supplementary Information Appended

• Transcriptional burst frequency and burst size are equally modulated across the human genome.

  Dar RD, Razooky BS, Singh A, Trimeloni TV, McCollum JM, Cox CD, Simpson ML, Weinberger LS.

  PNAS 2012

  • Supplementary Information

• Microwell Devices with Finger-like Channels for Long-Term Imaging of HIV-1 Expression Kinetics in Primary Human Lymphocytes.

  Razooky BS, Gutierrez E, Terry VH, Spina CA, Groisman A, Weinberger LS.

  Lab on a Chip 2012

  • Supplementary Information

• Dynamics of protein noise can distinguish between alternate sources of gene-expression variability.

  Singh A, Razooky BS, Dar RD, Weinberger LS.

  Molecular Systems Biology 2012

  • Supplementary Information

• Fifteen Years Later: Hard and Soft Selection Sweeps Confirm a Large Population Number for HIV In Vivo.

  Rouzine IM, Coffin JM, Weinberger LS.

  PLoS Genet 2014

• Stochastic Fate Selection in HIV-infected Patients.

  Weinberger AD, Weinberger LS.

  Cell 2013

• Lentiviral vectors to study stochastic noise in gene expression.

  Franz K, Singh A, Weinberger LS.

  Methods in Enzymology 2011

• Mapping the architecture of the HIV-1 Tat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise.

  Razooky BS, Weinberger LS.

  Methods 2011

• Autonomous Targeting of Infectious Superspreaders using Engineered Transmissable Therapies.

  Metzger V, Lloyd-Smith JO, Weinberger LS.

  PLoS Computational Biology 2011

  • Supplementary Information

• Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression.

  Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS.

  Biophys J 2010

  • Supplementary Information

• Accelerated immunodeficiency by anti-CCR5 treatment in HIV infection.

  Weinberger AD, Perelson AS, Ribeiro RM, Weinberger LS.

  PloS Comput Biol 2009

  • Supplementary Figures: S1, S2, S3

  • Supplementary Information

• Stochastic Noise in gene expression as a molecular switch for viral latency.

  Singh A, Weinberger LS.

  Curr Opin Microbiol 2009

• Transient-mediated fate determination in a transcriptional circuit of HIV.

  Weinberger LS, Dar RD, Simpson ML.

  Nat Genet 2008

  • Supplementary Information

• An HIV feedback resistor: auto-regulatory circuit deactivator and noise buffer.

  Weinberger LS, Shenk T.

  PLoS Biol 2007

  • Supplementary Figures: S1, S2, S3, S4, S5

• Stochastic gene expression in a lentiviral positive-feed back loop: HIV-1 Tat fluctuations drive phenotypic diversity.

  Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV.

  Cell 2005

  • Supplementary Information

• Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection.

  Weinberger LS, Schaffer DV, Arkin AP.

  J Virol 2003

• Early hepatitis C viral kinetics correlate with long-term outcome in patients receiving high dose induction followed by combination interferon and ribavirin therapy.

  Rosen HR, Ribeiro RR, Weinberger L, Wolf S, Chung M, Gretch DR, Perelson AS.

  J Hepatol 2002

• Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy.

  Mohri H, Perelson AS, Tung K, Ribeiro RM, Ramratnam B, Markowitz M, Kost R, Hurley A, Weinberger L, Cesar D, Hellerstein MK, Ho DD.

  J Exp Med 2001

• Different turnover rate of hepatitis C virus clearance by different treatment regimen using interferon-beta.

  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.

  J Hepatol 2000