Cooperativity in Cellular Biochemical Processes: Noise-Enhanced Sensitivity, Fluctuating Enzyme, Bistability with Nonlinear Feedback, and Other Mechanisms for Sigmoidal Responses

A perturbation analysis of rate theory of self-regulating genes and signaling networks

(2011) Pei-Zhe Shi et al.   JOURNAL OF CHEMICAL PHYSICS

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems—an analytical theory

(2011) Hong Qian   NONLINEARITY

Role of Fluctuations in Ligand Binding Cooperativity of Membrane Receptors

(2011) Lizhe Zhu et al.   PHYSICAL REVIEW LETTERS

Stochastic theory of nonequilibrium steady states and its applications. Part I

(2011) Xue-Juan Zhang et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics

(2011) Hao Ge et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

The dynamics of zeroth-order ultrasensitivity: A critical phenomenon in cell biology

(2011) Qingdao Huang et al.   Discrete and Continuous Dynamical Systems-Series S

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

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

Nonessential Sites Improve Phosphorylation Switch

(2010) Liming Wang et al.   BIOPHYSICAL JOURNAL

Complex Kinetics of Fluctuating Enzymes: Phase Diagram Characterization of a Minimal Kinetic Scheme

(2010) Wei Min et al.   Chemistry-An Asian Journal

Two-component signaling circuit structure and properties

(2010) Mark Goulian   CURRENT OPINION IN MICROBIOLOGY

The Chemical Master Equation Approach to Nonequilibrium Steady-State of Open Biochemical Systems: Linear Single-Molecule Enzyme Kinetics and Nonlinear Biochemical Reaction Networks

(2010) Hong Qian et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

(2010) Jie Liang et al.   JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY

Cyclic Conformational Modification of an Enzyme: Serial Engagement, Energy Relay, Hysteretic Enzyme, and Fischer’s Hypothesis†

(2010) Hong Qian   JOURNAL OF PHYSICAL CHEMISTRY B

Cellular Biology in Terms of Stochastic Nonlinear Biochemical Dynamics: Emergent Properties, Isogenetic Variations and Chemical System Inheritability

(2010) Hong Qian   JOURNAL OF STATISTICAL PHYSICS

Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond

(2010) H. Ge et al.   Journal of the Royal Society Interface

Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network

(2010) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Calcium Signals Driven by Single Channel Noise

(2010) Alexander Skupin et al.   PLoS Computational Biology

Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits

(2009) Tolga Çağatay et al.   CELL

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

(2009) Jayajit Das et al.   CELL

Fluctuating Enzyme and Its Biological Functions: Positive Cooperativity without Multiple States

(2009) Hong Qian et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses

(2009) Andrzej M. Kierzek et al.   Molecular BioSystems

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

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

Thermodynamic Limit of a Nonequilibrium Steady State: Maxwell-Type Construction for a Bistable Biochemical System

(2009) Hao Ge et al.   PHYSICAL REVIEW LETTERS

Exploring the roles of noise in the eukaryotic cell cycle

(2009) S. Kar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciding fate in adverse times: Sporulation and competence inBacillus subtilis

(2009) Daniel Schultz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Poincare-Hill cycle map of rotational random walk: locating the stochastic limit cycle in a reversible Schnakenberg model

(2009) M. Vellela et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Single-Molecule Approach to Molecular Biology in Living Bacterial Cells

(2008) X. Sunney Xie et al.   Annual Review of Biophysics

Temporal Cooperativity and Sensitivity Amplification in Biological Signal Transduction†

(2008) Hong Qian et al.   BIOCHEMISTRY

Cooperativity and Specificity in Enzyme Kinetics: A Single-Molecule Time-Based Perspective

(2008) Hong Qian   BIOPHYSICAL JOURNAL

The stochastic nature of biochemical networks

(2008) Vahid Shahrezaei et al.   CURRENT OPINION IN BIOTECHNOLOGY

Sensitivity amplification in the phosphorylation-dephosphorylation cycle: Nonequilibrium steady states, chemical master equation, and temporal cooperativity

(2008) Hao Ge et al.   JOURNAL OF CHEMICAL PHYSICS

Capturing cooperativity

(2008)   Nature Chemical Biology

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

A genetic timer through noise-induced stabilization of an unstable state

(2008) M. Turcotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution

(2007) Ping Ao et al.   MEDICAL HYPOTHESES