Abhyudai Singh | University of Delaware (original) (raw)

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Papers by Abhyudai Singh

Research paper thumbnail of Transcriptional Bursting from the HIV1 Promoter Is a Significant Source of Stochastic Noise in HIV1 Gene Expression

Biophysical journal, Jan 1, 2010

Research paper thumbnail of Stochastic gene expression as a molecular switch for viral latency

Current Opinion in Microbiology, Jan 1, 2009

Stochastic ‘noise’ arises from random thermal fluctuations in the concentration of protein, RNA, ... more Stochastic ‘noise’ arises from random thermal fluctuations in the concentration of protein, RNA, or other molecules within the cell and is an unavoidable aspect of life at the single-cell level. Evidence is accumulating that this biochemical noise crucially influences cellular auto-regulatory circuits and can ‘flip’ genetic switches to drive probabilistic fate decisions in bacteria, viruses, cancer, and stem cells. Here, we review how stochastic gene expression in key auto-regulatory proteins can control fate determination between latency and productive replication in both phage-λ and HIV-1. We highlight important new studies that synthetically manipulate auto-regulatory circuitry and noise, to bias HIV-1's ability to enter proviral latency. We argue that an appreciation of noise in gene expression may shed light on the mystery of animal virus latency and that strategies to manipulate noise may have impact on anti-viral therapeutics.

Research paper thumbnail of Stochastic Analysis of Gene Regulatory Networks Using Moment Closure

American Control Conference, 2007. …, Jan 1, 2007

Research paper thumbnail of Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks

Biophysical journal, Jan 1, 2009

Research paper thumbnail of Moment Closure for the Stochastic Logistic Model 1

Research paper thumbnail of Moment closure techniques for stochastic models in population biology

American Control Conference, 2006, Jan 1, 2006

Research paper thumbnail of A Derivative Matching Approach to Moment Closure for the Stochastic Logistic Model

Bulletin of Mathematical Biology, Jan 1, 2007

Research paper thumbnail of Lognormal Moment Closures for Biochemical Reactions

Decision and Control, 2006 45th …, Jan 1, 2006

Research paper thumbnail of Regulation of nonlinear systems using conditional integrators

… Journal of Robust and Nonlinear Control, Jan 1, 2005

This paper studies the regulation of nonlinear systems using conditional integrators. Previous wo... more This paper studies the regulation of nonlinear systems using conditional integrators. Previous work introduced the tool of conditional integrators that provide integral action inside a boundary layer while acting as stable systems outside, leading to improvement in transient response while achieving asymptotic regulation in the presence of unknown constant disturbances or parameter uncertainties. The approach, however, is restricted to a sliding mode control framework. This paper extends this tool to a fairly general class of state feedback control laws, with the stipulation that we know a Lyapunov function for the closed-loop system. Asymptotic regulation with improvement in transient response is done by using the Lyapunov redesign technique to implement the state feedback control as a saturated high-gain feedback and introducing a conditional integrator to provide integral action inside a boundary layer. Improvement in the transient response using conditional integrators is demonstrated with an experimental application to the pendubot. Copyright © 2005 John Wiley & Sons, Ltd.

Research paper thumbnail of Stochastic models for chemically reacting systems using polynomial stochastic hybrid systems

International Journal of Robust and …, Jan 1, 2005

INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL Int. J. Robust Nonlinear Control 2005; 15:6... more INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL Int. J. Robust Nonlinear Control 2005; 15:669–689 Published online 15 September 2005 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/rnc.1017 ... Stochastic models for chemically ...

Research paper thumbnail of Transcriptional Bursting from the HIV1 Promoter Is a Significant Source of Stochastic Noise in HIV1 Gene Expression

Biophysical journal, Jan 1, 2010

Research paper thumbnail of Stochastic gene expression as a molecular switch for viral latency

Current Opinion in Microbiology, Jan 1, 2009

Stochastic ‘noise’ arises from random thermal fluctuations in the concentration of protein, RNA, ... more Stochastic ‘noise’ arises from random thermal fluctuations in the concentration of protein, RNA, or other molecules within the cell and is an unavoidable aspect of life at the single-cell level. Evidence is accumulating that this biochemical noise crucially influences cellular auto-regulatory circuits and can ‘flip’ genetic switches to drive probabilistic fate decisions in bacteria, viruses, cancer, and stem cells. Here, we review how stochastic gene expression in key auto-regulatory proteins can control fate determination between latency and productive replication in both phage-λ and HIV-1. We highlight important new studies that synthetically manipulate auto-regulatory circuitry and noise, to bias HIV-1's ability to enter proviral latency. We argue that an appreciation of noise in gene expression may shed light on the mystery of animal virus latency and that strategies to manipulate noise may have impact on anti-viral therapeutics.

Research paper thumbnail of Stochastic Analysis of Gene Regulatory Networks Using Moment Closure

American Control Conference, 2007. …, Jan 1, 2007

Research paper thumbnail of Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks

Biophysical journal, Jan 1, 2009

Research paper thumbnail of Moment Closure for the Stochastic Logistic Model 1

Research paper thumbnail of Moment closure techniques for stochastic models in population biology

American Control Conference, 2006, Jan 1, 2006

Research paper thumbnail of A Derivative Matching Approach to Moment Closure for the Stochastic Logistic Model

Bulletin of Mathematical Biology, Jan 1, 2007

Research paper thumbnail of Lognormal Moment Closures for Biochemical Reactions

Decision and Control, 2006 45th …, Jan 1, 2006

Research paper thumbnail of Regulation of nonlinear systems using conditional integrators

… Journal of Robust and Nonlinear Control, Jan 1, 2005

This paper studies the regulation of nonlinear systems using conditional integrators. Previous wo... more This paper studies the regulation of nonlinear systems using conditional integrators. Previous work introduced the tool of conditional integrators that provide integral action inside a boundary layer while acting as stable systems outside, leading to improvement in transient response while achieving asymptotic regulation in the presence of unknown constant disturbances or parameter uncertainties. The approach, however, is restricted to a sliding mode control framework. This paper extends this tool to a fairly general class of state feedback control laws, with the stipulation that we know a Lyapunov function for the closed-loop system. Asymptotic regulation with improvement in transient response is done by using the Lyapunov redesign technique to implement the state feedback control as a saturated high-gain feedback and introducing a conditional integrator to provide integral action inside a boundary layer. Improvement in the transient response using conditional integrators is demonstrated with an experimental application to the pendubot. Copyright © 2005 John Wiley & Sons, Ltd.

Research paper thumbnail of Stochastic models for chemically reacting systems using polynomial stochastic hybrid systems

International Journal of Robust and …, Jan 1, 2005

INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL Int. J. Robust Nonlinear Control 2005; 15:6... more INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL Int. J. Robust Nonlinear Control 2005; 15:669–689 Published online 15 September 2005 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/rnc.1017 ... Stochastic models for chemically ...

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