Probabilistic control of HIV latency and transactivation by the Tat gene circuit

HIV latency in isolated patient CD4 + T cells may be due to blocks in HIV transcriptional elongation, completion, and splicing

(2018) Steven A. Yukl et al.   Science Translational Medicine

CD8+ lymphocyte control of SIV infection during antiretroviral therapy

(2018) Youfang Cao et al.   PLoS Pathogens

Interval dosing with the HDAC inhibitor vorinostat effectively reverses HIV latency

(2017) Nancie M. Archin et al.   JOURNAL OF CLINICAL INVESTIGATION

Proviral Latency, Persistent Human Immunodeficiency Virus Infection, and the Development of Latency Reversing Agents

(2017) David M. Margolis et al.   JOURNAL OF INFECTIOUS DISEASES

In Vivo Suppression of HIV Rebound by Didehydro-Cortistatin A, a “Block-and-Lock” Strategy for HIV-1 Treatment

(2017) Cari F. Kessing et al.   Cell Reports

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

(2017) Brandon S. Razooky et al.   PLOS BIOLOGY

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

(2016) Youfang Cao et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Epigenetics and Genetics of Viral Latency

(2016) Paul M. Lieberman   Cell Host & Microbe

Accurate Chemical Master Equation Solution Using Multi-Finite Buffers

(2016) Youfang Cao et al.   MULTISCALE MODELING & SIMULATION

In vivo analysis of the effect of panobinostat on cell-associated HIV RNA and DNA levels and latent HIV infection

(2016) Perry Tsai et al.   Retrovirology

Reversal of Latency as Part of a Cure for HIV-1

(2016) Thomas Aagaard Rasmussen et al.   TRENDS IN MICROBIOLOGY

Residual Viremia in Treated HIV+ Individuals

(2016) Jessica M. Conway et al.   PLoS Computational Biology

Glucose Metabolism in T Cells and Monocytes: New Perspectives in HIV Pathogenesis

(2016) Clovis S. Palmer et al.   EBioMedicine

Landscape and flux theory of non-equilibrium dynamical systems with application to biology

(2015) Jin Wang   ADVANCES IN PHYSICS

A Hardwired HIV Latency Program

(2015) Brandon S. Razooky et al.   CELL

The Remarkable Stability of the Latent Reservoir for HIV-1 in Resting Memory CD4+T Cells

(2015) Janet M. Siliciano et al.   JOURNAL OF INFECTIOUS DISEASES

Precise Quantitation of the Latent HIV-1 Reservoir: Implications for Eradication Strategies

(2015) Amanda M. Crooks et al.   JOURNAL OF INFECTIOUS DISEASES

Regulation of HIV-1 Latency by Chromatin Structure and Nuclear Architecture

(2015) Marina Lusic et al.   JOURNAL OF MOLECULAR BIOLOGY

HIV-1 Virion Production from Single Inducible Proviruses following T-Cell ActivationEx Vivo

(2015) John K. Bui et al.   JOURNAL OF VIROLOGY

Post-treatment control of HIV infection

(2015) Jessica M. Conway et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Tat Inhibitor Didehydro-Cortistatin A Prevents HIV-1 Reactivation from Latency

(2015) Guillaume Mousseau et al.   mBio

Modeling the Effects of Vorinostat In Vivo Reveals both Transient and Delayed HIV Transcriptional Activation and Minimal Killing of Latently Infected Cells

(2015) Ruian Ke et al.   PLoS Pathogens

HIV Reactivation from Latency after Treatment Interruption Occurs on Average Every 5-8 Days—Implications for HIV Remission

(2015) Mykola Pinkevych et al.   PLoS Pathogens

The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo

(2015) Ole S. Søgaard et al.   PLoS Pathogens

The Histone Deacetylase Inhibitor Vorinostat (SAHA) Increases the Susceptibility of Uninfected CD4+ T Cells to HIV by Increasing the Kinetics and Efficiency of Postentry Viral Events

(2014) M. B. Lucera et al.   JOURNAL OF VIROLOGY

Spatial confinement is a major determinant of the folding landscape of human chromosomes

(2014) Gamze Gürsoy et al.   NUCLEIC ACIDS RESEARCH

Predicting the outcomes of treatment to eradicate the latent reservoir for HIV-1

(2014) Alison L. Hill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Progressive contraction of the latent HIV reservoir around a core of less-differentiated CD4+ memory T Cells

(2014) S. Jaafoura et al.   Nature Communications

Activation of HIV Transcription with Short-Course Vorinostat in HIV-Infected Patients on Suppressive Antiretroviral Therapy

(2014) Julian H. Elliott et al.   PLoS Pathogens

Modeling the within-host dynamics of HIV infection

(2013) Alan S Perelson et al.   BMC BIOLOGY

Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability

(2013) Benjamin E. L. Lauffer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reactivation of latent HIV by histone deacetylase inhibitors

(2013) Kotaro Shirakawa et al.   TRENDS IN MICROBIOLOGY

Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression

(2013) J. Karn et al.   Cold Spring Harbor Perspectives in Medicine

Comparative Analysis of Measures of Viral Reservoirs in HIV-1 Eradication Studies

(2013) Susanne Eriksson et al.   PLoS Pathogens

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

An Analog of the Natural Steroidal Alkaloid Cortistatin A Potently Suppresses Tat-Dependent HIV Transcription

(2012) Guillaume Mousseau et al.   Cell Host & Microbe

Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection

(2012) N. M. Archin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

T-Cell Receptor Signaling Enhances Transcriptional Elongation from Latent HIV Proviruses by Activating P-TEFb through an ERK-Dependent Pathway

(2011) Young Kyeung Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

Host factors mediating HIV-1 replication

(2011) Brian M. Friedrich et al.   VIRUS RESEARCH

Stochastic Bistability and Bifurcation in a Mesoscopic Signaling System with Autocatalytic Kinase

(2010) Lisa M. Bishop et al.   BIOPHYSICAL JOURNAL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Kinetic paths, time scale, and underlying landscapes: A path integral framework to study global natures of nonequilibrium systems and networks

(2010) Jin Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Adiabatic and Non-Adiabatic Non-Equilibrium Stochastic Dynamics of Single Regulating Genes

(2010) Haidong Feng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2010) Brandon S. Razooky et al.   METHODS

Intracellular transactivation of HIV can account for the decelerating decay of virus load during drug therapy

(2010) Christian L Althaus et al.   Molecular Systems Biology

Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda

(2010) Y. Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The molecular biology of HIV latency: breaking and restoring the Tat-dependent transcriptional circuit

(2010) Jonathan Karn   Current Opinion in HIV and AIDS

Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity

(2009) Hong Qian et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

(2009) Frederic D. Bushman et al.   PLoS Pathogens

Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability

(2008) Youfang Cao et al.   BMC Systems Biology

Transient-mediated fate determination in a transcriptional circuit of HIV

(2008) Leor S Weinberger et al.   NATURE GENETICS

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA