Exposures

A Primer on Modular Mass Action Modelling with CellML

Tutorial models for a book chapter by Cooling, M. T. submitted to Springer, edited by Choi, S.

Adrian, Chandler, Hodgkin, 1970

Voltage clamp experiments in striated muscle fibres

Aguda, 1999

A quantitative analysis of the kinetics of the G2 DNA damage checkpoint system

Aguda, Tang, 1999

The kinetic origins of the restriction point in the mammalian cell cycle

Albrecht, Colegrove, Friel, 2002

Differential Regulation of ER Ca2+ Uptake and Release Rates Accounts for Multiple Modes of Ca2+-induced Ca2+ Release

Albrecht, Colegrove, Hongpaisan, Pivovarova, Andrews, Friel, 2001

Multiple Modes of Calcium-induced Calcium Release in Sympathetic Neurons I: Attenuation of Endoplasmic Reticulum Ca2+ Accumulation at Low [Ca2+]i during Weak Depolarisation

Aon, Cortassa, 2002

Coherent and robust modulation of a metabolic network by cytoskeletal organization and dynamics

Aslanidi, Boyett, Dobrzynski, Li, Zhang, 2009

Mechanisms of transition from normal to reentrant electrical activity in a model of rabbit atrial tissue: interaction of tissue heterogeneity and anisotropy

Aslanidi, Stewart, Boyett, Zhang, 2009

Optimal velocity and safety of discontinuous conduction through the heterogeneous Purkinje-ventricular junction

Asthagiri, Lauffenburger, 2001

A Compuational Study of Feedback Effects on Signal Dynamics in a Mitogen-Activated Protein Kinase (MAPK) Pathway Model

Bagci, Vodovotz, Billiar, Ermentrout, Bahar, 2006

Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores

Bagci, Vodovotz, Billiar, Ermentrout, Bahar, 2008

Computational insights on the competing effects of nitric oxide in regulating apoptosis

Bakker, Mensonides, Teusink, van Hoek, Michels, Westerhoff, 2000

Compartmentation protects trypanosomes from the dangerous design of glycolysis

Bakker, Michels, Opperdoes, Westerhoff, 1997

Glycolysis in Bloodstream Form Trypanosoma brucei Can Be Understood in Terms of the Kinetics of the Glycolytic Enzymes

Barberis, Klipp, Vanoni, Alberghina, 2007

Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network

Baylor, Hollingworth, Chandler, 2002

Comparison of Simulated and Measured Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog

Beard, 2005

A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation

Beeler, Reuter, 1977

Reconstruction of the action potential of ventricular myocardial fibres

Ben-Tal, 2006

Simplified models for gas exchange in the human lungs

Benson, Aslanidi, Zhang, Holden, 2008

The canine virtual ventricular wall: a platform for dissecting pharmacological effects on propagation and arrhythmogenesis

Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002

A computationally efficient electrophysiological model of human ventricular cells

Bertram, Arnot, Zamponi, 2002

Role for G protein Gbetagamma isoform specificity in synaptic signal processing: a computational study

Bertram, Previte, Sherman, Kinard, Satin, 2000

The Phantom Burster Model for Pancreatic Beta Cells

Bertram, Satin, Pedersen, Luciani, Sherman, 2007

Intra- and inter-islet synchronization of metabolically driven insulin secretion

Bertram, Satin, Zhang, Smolen, Sherman, 2004

Calcium and Glycolysis Mediate Multiple Bursting Modes in Pancreatic Islets

Bertram, Sherman, 2004

A Calcium-based Phantom Bursting Model for Pancreatic Islets

Bertram, Smolen, Sherman, Mears, Atwater, Martin, Soria, 1995

A role for calcium release-activated current (CRAC) in cholinergic modulation of electrical activity in pancreatic beta-cells

Bhalla, Iyengar, 1999

Emergent Properties of Networks of Biological Signaling Pathways

Bindschadler, Sneyd, 2001

A Bifurcation Analysis of Two Coupled Calcium Oscillators

Bingzheng, Zhenye, Liansong, 1990

A mathematical model of the regulation system of the secretion of glucocorticoids

Bondarenko, Szigeti, Bett, Kim, Rasmusson, 2004

A Computer Model for the Action Potential of Mouse Ventricular Myocytes

Bonhoeffer, Rembiszewski, Ortiz, Nixon, 2000

Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection

Borghans, Dupont, Goldbeter, 1997

Complex intracellular calcium oscillations. A theoretical exploration of possible mechanisms

Boyett, Zhang, Garny, Holden, 2001

Control of the pacemaker activity of the sinoatrial node by intracellular Ca2+. Experiments and modelling

Brightman, Fell, 2000

Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells.

Brown, Choe, Shanahan, Czeisler, 1997

A mathematical model of diurnal variations in human plasma melatonin levels

Bueno, 2007

Mathematical modeling and spectral simulation of genetic diseases in the human heart

Bugbuster Systems Model

 

Butera, Rinzel, Smith, 1999

Models of Respiratory Rhythm Generation in the Pre-Botzinger Complex. I. Bursting Pacemaker Neurons

Calzone, Thieffry, Tyson, Novak, 2007

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

Campbell, Chandra, 2006

Functions of Stretch Activation in Heart Muscle

Cartwright, Husain, 1986

A model for the control of testosterone secretion

Chang, Fujita, 1999

A kinetic model of the thiazide-sensitive Na-Cl cotransporter

Chang, Fujita, 1999

A numerical model of the renal distal tubule

Chang, Fujita, 2001

A numerical model of acid-base transport in rat distal tubule

Chassagnole, Rais, Quentin, Fell, Mazat, 2001

An integrated study of Threonine-pathway enzyme kinetics in Escherichia coli

Chay, 1997

Effects of extracellular calcium on electrical bursting and intracellular and luminal calcium oscillations in insulin secreting pancreatic beta-cells

Chay, Lee, Fan, 1995

Appearance of Phase-locked Wenchbach-like Rhythms, Devil's Staircase and Universality in Intracellular Calcium Spikes in Non-excitable Cell Models

Chen, Calzone, Csikasz-Nagy, Cross, Novak, Tyson, 2004

Integrative Analysis of Cell Cycle Control in Budding Yeast

Chen, Csikasz-Nagy, Gyorffy, Val, Novak, Tyson, 2000

Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle

Chen, Popel, 2006

Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells

Chen, Popel, 2006

Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells

Cheng, Brown, Loeb, 2000

Virtual muscle: a computational approach to understanding the effects of muscle properties on motor control

Ciliberto, Novak, Tyson, 2003

Mathematical Model of the Morphogenesis Checkpoint in Budding Yeast

Ciliberto, Petrus, Tyson, Sible, 2003

A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus

Ciliberto, Tyson, 2000

Mathematical Model for Early Development of the Sea Urchin Embryo

Clancy, Rudy, 2001

Cellular consequences of HERG mutations in the long QT syndrome: precursors to sudden cardiac death

Clancy, Rudy, 2002

Na Channel Mutation That Causes Both Brugada Syndrome and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism

Cloutier, Bolger, Lowry, Wellstead, 2009

An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements

Cloutier, Wellstead, 2009

The control systems structures of energy metabolism

Colegrove, Albrecht, Friel, 2000

Quantitive Analysis of Mitochondrial Ca2+ Uptake and Release Pathways in Sympathetic Neurons Reconstruction of the Recovery after Depolarisation-evoked [Ca2+] Elevations

Cooling, Hunter, Crampin, 2008

 

Cooling, Hunter, Crampin, 2009. Dual Calcium Protocol

 

Cooling, Hunter, Crampin, 2009. Shen Calcium Protocol

 

Cooling, Hunter, Crampin, 2009. Tomida Calcium Protocol

 

Corrias, Buist, 2007

A quantitative model of gastric smooth muscle cellular activation

Corrias, Buist, 2008

Quantitative cellular description of gastric slow wave activity

Cortassa, Aon, Marban, Winslow, O'Rourke, 2003

An Integrated Model of Cardiac Mitrochondrial Energy Metabolism and Calcium Dynamics

Cortassa, Aon, Winslow, O'Rourke, 2004

A mitochondrial oscillator dependent on reactive oxygen species

Costa, Holmes, McCulloch, 2001

Modelling Cardiac Mechanical Properties In Three Dimensions

Courtemanche, Ramirez, Nattel, 1998

Ionic mechanisms underlying human atrial action potential properties: insights from a mathematical model

Creating a Systems Model from SVPs - a Tutorial

 

Cronwright, Rohwer, Prior, 2002

Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae

Csikasz-Nagy, Battogtokh, Chen, Novak, Tyson, 2006

Analysis of a generic model of eukaryotic cell-cycle regulation: budding yeast taken from the original model code

Cui, Kaandorp, 2006

Mathematical modeling of calcium homeostasis in yeast cells

Cui, Kaandorp, 2008

Simulating Complex Calcium-Calcineurin Signaling Network

Cui, Kaandorp, Lloyd, 2008

Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli

Curien, Ravanel, Dumas, 2003

A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana

Dash, Bassingthwaighte, 2004

Blood HbO2 and HbCO2 dissociation curves at varied O2, CO2, pH, 2,3-DPG and temperature levels

Dawson, Lea, Irvine, 2003

Kinetic model of the inositol trisphosphate receptor that shows both steady-state and quantal patterns of Ca2+ release from intracellular stores

De Paor, Timmons, 1986

A feedback oscillator model for circulatory autoregulation

De Vries, Sherman, 2000

Channel Sharing in Pancreatic Beta-Cells Revisited: Enhancement of Emergent Bursting by Noise

De Vries, Sherman, 2001

From Spikers to Bursters Via Coupling: Help from Heterogeneity

De Young, Keizer, 1992

A single-pool inositol 1,4,5-triphosphate-receptor-based model for agonist-stimulated oscillations in Ca 2+ concentration

Decker, Heijman, Silva, Hund, Rudy, 2009

Properties and ionic mechanisms of action potential adaptation, restitution, and accommodation in canine epicardium

Demir, Clark, Giles, 1999

Parasympathetic modulation of sinoatrial node pacemaker activity in rabbit heart: a unifying model

Demir, Clark, Giles, Murphey, 1994

A Mathematical Model of a Rabbit Sinoatrial Node Cell

Demiray, 1981

Large deformation analysis of some soft biological tissues

Dempsher, Gann, Phair, 1984

A mechanistic model of ACTH-stimulated cortisol secretion

DiFrancesco, Noble, 1985

A Model of Cardiac Electrical Activity Incorporating Ionic Pumps and Concentration Changes

Dixit, Perelson, 2004

Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay

Dokos, Celler, Lovell, 1996

Ion currents underlying sinoatrial node pacemaker activity: a new single cell mathematical model

Dougherty, Wright, Yew, 2005

Computational model of the cAMP-mediated sensory response and calcium-dependent adaptation in vertebrate olfactory receptor neurons

Drouhard, Roberge, 1987

Revised formulation of the Hodgkin-Huxley representation of the sodium current in cardiac cells

Dumaine, Towbin, Brugada, Vatta, Nesterenko, Nesterenko, Brugada, Brugada, Antzelevitch, 1999

Ionic mechanisms responsible for the electrocardiographic phenotype of the Brugada Syndrome are temperature dependent

Dupont, Berridge, Goldbetter, 1991

Signal-induced Ca2+ oscillations: Properties of a model based on (Ca2+)-induced Ca2+ release

Dupont, Goldbeter, 1992

Protein phosphorylation driven by intracellular calcium oscillations: A kinetic analysis

Earm, Noble, 1990

A Model of the Single Atrial Cell: Relation between Calcium Current and Calcium Release

Ebihara, Johnson, 1980

Fast sodium current in cardiac muscle: A quantitative description

Egli, Bertram, Sellix, Freeman, 2004

Rhythmic secretion of prolactin in rats: action of oxytocin coordinated by vasoactive intestinal polypeptide of suprachiasmatic nucleus origin