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List of works by William S Hlavacek

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

scientific article published on 17 October 2005

A quantitative approach for studying IgE-FcepsilonRI aggregation

scientific article published on 01 September 2002

Allergen Valency, Dose, and FcεRI Occupancy Set Thresholds for Secretory Responses to Pen a 1 and Motivate Design of Hypoallergens.

scientific article published on 30 December 2016

An Interaction Library for the FcεRI Signaling Network

scientific article

Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics

scientific article

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

scientific article

Carbon-fate maps for metabolic reactions.

scientific article published on 12 October 2007

Completely uncoupled and perfectly coupled gene expression in repressible systems

scientific article published in February 1997

Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1

scientific article

Computational model for autophagic vesicle dynamics in single cells ⬇️

scientific article published on November 29, 2012

Depicting signaling cascades

scientific article published on 01 February 2006

Determinants of bistability in induction of the Escherichia coli lac operon.

scientific article

Dynamics of the nucleated polymerization model of prion replication

scientific article published on 04 October 2006

Editorial: Selected papers from the Third q-bio Conference on Cellular Information Processing

scientific article published on 01 November 2010

Enhanced dimerization drives ligand-independent activity of mutant epidermal growth factor receptor in lung cancer

scientific article

Generalizing Gillespie's Direct Method to Enable Network-Free Simulations.

scientific article published on 28 March 2018

GetBonNie for building, analyzing and sharing rule-based models.

scientific article published on 25 March 2009

Hierarchical graphs for rule-based modeling of biochemical systems

scientific article

How to deal with large models?

scientific article published on 20 January 2009

Improved predictions of transcription factor binding sites using physicochemical features of DNA.

scientific article

Kinetic Monte Carlo method for rule-based modeling of biochemical networks.

scientific article

Kinetic proofreading model.

scientific article published on January 2008

Mitochondrial morphological features are associated with fission and fusion events

scientific article

Modeling biomolecular site dynamics in immunoreceptor signaling systems.

scientific article

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

scientific article published in January 2019

Modeling for (physical) biologists: an introduction to the rule-based approach

scientific article (publication date: July 2015)

Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates

scientific article

Modeling the early signaling events mediated by FcepsilonRI.

scientific article

Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells

scientific article

On imposing detailed balance in complex reaction mechanisms.

scientific article

Optimal aggregation of FcεRI with a structurally defined trivalent ligand overrides negative regulation driven by phosphatases.

scientific article

Phosphorylation site dynamics of early T-cell receptor signaling

scientific article

Prediction of Optimal Drug Schedules for Controlling Autophagy

scientific article published in Scientific Reports

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds.

scientific article

Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites

scientific article

PyBioNetFit and the Biological Property Specification Language

scientific article published on 28 August 2019

Q-bio 2007: a watershed moment in modern biology

scientific article published on 4 December 2007

Recruitment of the adaptor protein Grb2 to EGFR tetramers

scientific article

Relaxation oscillations and hierarchy of feedbacks in MAPK signaling

scientific article

Rule-based modeling of biochemical networks

article published in 2005

Rule-based modeling of biochemical systems with BioNetGen

scientific article

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

scientific article published on 30 September 2013

RuleMonkey: software for stochastic simulation of rule-based models

scientific article

Rules for coupled expression of regulator and effector genes in inducible circuits

scientific article published in January 1996

SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

scientific article published on 17 July 2017

Scaffold-mediated nucleation of protein signaling complexes: elementary principles.

scientific article

Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks

scientific article published on 01 June 2019

Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform

scientific article published on 27 March 2013

Special section dedicated to The Sixth q-bio Conference: meeting report and preface

scientific article published on 4 June 2013

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling.

scientific article

Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits

scientific article published in May 1995

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

scientific article published on 06 July 2020

The Brucella TIR-like protein TcpB interacts with the death domain of MyD88

scientific journal article

The Seventh q-bio Conference: meeting report and preface

scientific article published on 30 July 2014

The complexity of cell signaling and the need for a new mechanics

scientific article

The complexity of complexes in signal transduction.

scientific article

The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems

scientific article

The eighth q-bio conference: meeting report and special issue preface

scientific article published on 30 December 2015

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation

scientific article published on 14 November 2017

Use of mechanistic models to integrate and analyze multiple proteomic datasets

scientific article

Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics

scientific article published on 08 June 2018

Using both qualitative and quantitative data in parameter identification for systems biology models

scientific article published in Nature Communications

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites

scientific article

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