4.6 Article

Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

Trends in modeling Biomedical Complex Systems

Luciano Milanesi et al.

BMC BIOINFORMATICS (2009)

Article Chemistry, Physical

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

Hong Qian et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2009)

Article Physics, Fluids & Plasmas

Quantifying stochastic effects in biochemical reaction networks using partitioned leaping

Leonard A. Harris et al.

PHYSICAL REVIEW E (2009)

Article Multidisciplinary Sciences

Toward a microscopic model of bidirectional synaptic plasticity

Gastone C. Castellani et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Adiabatic coarse-graining and simulations of stochastic biochemical networks

N. A. Sinitsyn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biochemical Research Methods

Integrating Extrinsic and Intrinsic Cues into a Minimal Model of Lineage Commitment for Hematopoietic Progenitors

Santhosh Palani et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Mathematical & Computational Biology

Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory

William J. Heuett et al.

BMC SYSTEMS BIOLOGY (2008)

Article Mathematical & Computational Biology

Identification of gene interactions associated with disease from gene expression data using synergy networks

John Watkinson et al.

BMC SYSTEMS BIOLOGY (2008)

Article Automation & Control Systems

Stochastic modeling and control of biological systems: The lactose regulation system of Escherichia coli

A. Agung Julius et al.

IEEE TRANSACTIONS ON AUTOMATIC CONTROL (2008)

Article Automation & Control Systems

The finite state projection approach for the analysis of stochastic noise in gene networks

Brian Munsky et al.

IEEE TRANSACTIONS ON AUTOMATIC CONTROL (2008)

Article Chemistry, Physical

Coarse graining of master equations with fast and slow states

Simone Pigolotti et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

An efficient and exact stochastic simulation method to analyze rare events in biochemical systems

Hiroyuki Kuwahara et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks

Alexander Slepoy et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Biochemistry & Molecular Biology

Colored extrinsic fluctuations and stochastic gene expression

Vahid Shahrezaei et al.

MOLECULAR SYSTEMS BIOLOGY (2008)

Article Genetics & Heredity

Stochastic switching as a survival strategy in fluctuating environments

Murat Acar et al.

NATURE GENETICS (2008)

Article Physics, Fluids & Plasmas

Population extinction in a time-modulated environment

Michael Assaf et al.

PHYSICAL REVIEW E (2008)

Article Physics, Multidisciplinary

Noise enhanced persistence in a biochemical regulatory network with feedback control

Michael Assaf et al.

PHYSICAL REVIEW LETTERS (2008)

Article Multidisciplinary Sciences

Network properties of genes harboring inherited disease mutations

Igor Feldman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

The thermal impulse response of Escherichial coli

Eli Paster et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

Analytical distributions for stochastic gene expression

Vahid Shahrezaei et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Multidisciplinary Sciences

The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae

Jerome T. Mettetal et al.

SCIENCE (2008)

Article Biochemical Research Methods

TABASCO: A single molecule, base-pair resolved gene expression simulator

Sriram Kosuri et al.

BMC BIOINFORMATICS (2007)

Article Biophysics

Noise-limited frequency signal transmission in gene circuits

Cheemeng Tan et al.

BIOPHYSICAL JOURNAL (2007)

Article Medicine, General & Internal

Detection of intracellular bacterial communities in human urinary tract infection

David A. Rosen et al.

PLOS MEDICINE (2007)

Article Biochemical Research Methods

Operating regimes of signaling cycles: Statics, dynamics, and noise filtering

Carlos Gomez-Uribe et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Multidisciplinary Sciences

Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities

Maxim N. Artyomov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Physics, Fluids & Plasmas

Response to a temperature modulation as a signature of chemical mechanisms

H. Berthoumieux et al.

PHYSICAL REVIEW E (2007)

Article Biochemistry & Molecular Biology

Negative autoregulation by FAS mediates robust fetal erythropoiesis

Merav Socolovsky et al.

PLOS BIOLOGY (2007)

Article Biochemistry & Molecular Biology

An HIV feedback resistor: Auto-regulatory circuit deactivator and noise buffer

Leor S. Weinberger et al.

PLOS BIOLOGY (2007)

Article Physics, Multidisciplinary

The Berry phase and the pump flux in stochastic chemical kinetics

N. A. Sinitsyn et al.

Review Chemistry, Physical

Stochastic simulation of chemical kinetics

Daniel T. Gillespie

ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2007)

Review Biotechnology & Applied Microbiology

Innovation - A robustness-based approach to systems-oriented drug design

Hiroaki Kitano

NATURE REVIEWS DRUG DISCOVERY (2007)

Article Multidisciplinary Sciences

Filamentation by Escherichia coli subverts innate defenses during urinary tract infection

Sheryl S. Justice et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemical Research Methods

Few crucial links assure checkpoint efficiency in the yeast cell-cycle network

Gautier Stoll et al.

BIOINFORMATICS (2006)

Article Biotechnology & Applied Microbiology

Deviant effects in molecular reaction pathways

Michael S. Samoilov et al.

NATURE BIOTECHNOLOGY (2006)

Article Biochemistry & Molecular Biology

Understanding the dynamic behavior of genetic regulatory networks by functional decomposition

William Longabaugh et al.

CURRENT GENOMICS (2006)

Review Biochemistry & Molecular Biology

Bistability in bacteria

David Dubnau et al.

MOLECULAR MICROBIOLOGY (2006)

Article Multidisciplinary Sciences

An excitable gene regulatory circuit induces transient cellular differentiation

GM Süel et al.

NATURE (2006)

Article Chemistry, Physical

The finite state projection algorithm for the solution of the chemical master equation

B Munsky et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Immunology

Coordinate expression of fimbriae in uropathogenic Escherichia coli

JA Snyder et al.

INFECTION AND IMMUNITY (2005)

Article Biochemistry & Molecular Biology

H-NS is a part of a thermally controlled mechanism for bacterial gene regulation

S Ono et al.

BIOCHEMICAL JOURNAL (2005)

Article Multidisciplinary Sciences

Contact-dependent inhibition of growth in Escherichia coli

SK Aoki et al.

SCIENCE (2005)

Article Biology

Diversity in times of adversity: probabilistic strategies in microbial survival games

DM Wolf et al.

JOURNAL OF THEORETICAL BIOLOGY (2005)

Article Multidisciplinary Sciences

Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations

M Samoilov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Chemistry, Physical

The slow-scale stochastic simulation algorithm

Y Cao et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Review Physiology

More than just a barrier: urothelium as a drug target for urinary bladder pain

LA Birder

AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY (2005)

Article Urology & Nephrology

Cool (TRPM8) and hot (TRPV1) receptors in the bladder and male genital tract

RJ Stein et al.

JOURNAL OF UROLOGY (2004)

Article Chemistry, Physical

Efficient formulation of the stochastic simulation algorithm for chemically reacting systems

Y Cao et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Immunology

Transcriptome of uropathogenic Eschetichia coli during urinary tract infection

JA Snyder et al.

INFECTION AND IMMUNITY (2004)

Article Chemistry, Physical

Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method

M Rathinam et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

Article Multidisciplinary Sciences

Intracellular bacterial biofilm-like pods in urinary tract infections

GG Anderson et al.

SCIENCE (2003)

Article Multidisciplinary Sciences

Self-perpetuating epigenetic pili switches in bacteria

A Hernday et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Chemistry, Physical

Signal processing by simple chemical systems

M Samoilov et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2002)

Article Biochemical Research Methods

The mutual information: Detecting and evaluating dependencies between variables

R Steuer et al.

BIOINFORMATICS (2002)

Article Biochemistry & Molecular Biology

Molecular regulation of urothelial renewal and host defenses during infection with uropathogenic Escherichia coli

IU Mysorekar et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2002)

Article Medicine, General & Internal

Widespread distribution of urinary tract infections caused by a multidrug-resistant Escherichia coli clonal group

AR Manges et al.

NEW ENGLAND JOURNAL OF MEDICINE (2001)

Article Chemistry, Physical

Approximate accelerated stochastic simulation of chemically reacting systems

DT Gillespie

JOURNAL OF CHEMICAL PHYSICS (2001)

Article Health Care Sciences & Services

Urinary tract infection among women aged 40 to 65: Behavioral and sexual risk factors

B Foxman et al.

JOURNAL OF CLINICAL EPIDEMIOLOGY (2001)

Article Multidisciplinary Sciences

Bad bugs and beleaguered bladders:: Interplay between uropathogenic Escherichia coli and innate host defenses

MA Mulvey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Article Biochemistry & Molecular Biology

Type 1 pilus-mediated bacterial invasion of bladder epithelial cells

JJ Martinez et al.

EMBO JOURNAL (2000)

Article Chemistry, Physical

Efficient exact stochastic simulation of chemical systems with many species and many channels

MA Gibson et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2000)

Article Physics, Multidisciplinary

Pumped biochemical reactions, nonequilibrium circulation, and stochastic resonance

H Qian et al.

PHYSICAL REVIEW LETTERS (2000)