Method for determining natural design principles of biological control circuits. - William S. Hlavacek; Michael A. Savageau (J. Intell. Fuzzy Syst., 1998)

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. - Michael L. Blinov; James R. Faeder; Byron Goldstein; William S. Hlavacek (Bioinform., 2004)

Graphical rule-based representation of signal-transduction networks. - James R. Faeder; Michael L. Blinov; William S. Hlavacek (SAC, 2005)

Rule-based modeling of biochemical networks. - James R. Faeder; Michael L. Blinov; Byron Goldstein; William S. Hlavacek (Complex., 2005)

Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites. - Fangping Mu; Pat J. Unkefer; Clifford J. Unkefer; William S. Hlavacek (Bioinform., 2006)

Graph Theory for Rule-Based Modeling of Biochemical Networks. - Michael L. Blinov; Jin Yang; James R. Faeder; William S. Hlavacek (Trans. Comp. Sys. Biology, 2006)

Carbon-fate maps for metabolic reactions. - Fangping Mu; Robert F. Williams; Clifford J. Unkefer; Pat J. Unkefer; James R. Faeder; William S. Hlavacek (Bioinform., 2007)

Simulation of large-scale rule-based models. - Joshua Colvin; Michael I. Monine; James R. Faeder; William S. Hlavacek; Daniel D. Von Hoff; Richard G. Posner (Bioinform., 2009)

GetBonNie for building, analyzing and sharing rule-based models. - Bin Hu 025; G. Matthew Fricke; James R. Faeder; Richard G. Posner; William S. Hlavacek (Bioinform., 2009)

Systems Biology Approaches for Developing Artificial Pathogen Detection Networks. - Anu Chaudhary; Geoffrey Waldo; William S. Hlavacek; Chang-Shung Tung (ALIFE, 2010)

RuleMonkey: software for stochastic simulation of rule-based models. - Joshua Colvin; Michael I. Monine; Ryan N. Gutenkunst; William S. Hlavacek; Daniel D. Von Hoff; Richard G. Posner (BMC Bioinform., 2010)

Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites. - Amy L. Bauer; William S. Hlavacek; Pat J. Unkefer; Fangping Mu (PLoS Comput. Biol., 2010)

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. - Fangping Mu; Clifford J. Unkefer; Pat J. Unkefer; William S. Hlavacek (Bioinform., 2011)

Hierarchical graphs for rule-based modeling of biochemical systems. - Nathan W. Lemons; Bin Hu; William S. Hlavacek (BMC Bioinform., 2011)

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. - Matthew S. Creamer; Edward C. Stites; Meraj Aziz; James A. Cahill; Chin Wee Tan; Michael E. Berens; Haiyong Han; Kimberly J. Bussey; Daniel D. Von Hoff; William S. Hlavacek; Richard G. Posner (BMC Syst. Biol., 2012)

Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells. - Dipak Barua; William S. Hlavacek (PLoS Comput. Biol., 2013)

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics. - Kristy Nowak-Lovato; Ludmil B. Alexandrov; Afsheen Banisadr; Amy L. Bauer; Alan R. Bishop; Anny Usheva; Fangping Mu; Elizabeth Hong-Geller; Kim Ø. Rasmussen; William S. Hlavacek; Boian S. Alexandrov (PLoS Comput. Biol., 2013)

Perspective on the q-bio Summer School and Conference: 2007-2014 and beyond. - Orna Resnekov; Brian Munsky; William S. Hlavacek (Quant. Biol., 2014)

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. - Brandon R. Thomas; Lily A. Chylek; Joshua Colvin; Suman Sirimulla; Andrew H. A. Clayton; William S. Hlavacek; Richard G. Posner (Bioinform., 2016)

TRuML: A Translator for Rule-Based Modeling Languages. - Ryan Suderman; William S. Hlavacek (BCB, 2017)

SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. - Marek Kochanczyk; William S. Hlavacek; Tomasz Lipniacki (Bioinform., 2017)

Prediction of Optimal Drug Schedules for Controlling Autophagy. - Afroza Shirin; Isaac S. Klickstein; Song Feng; Yen Ting Lin; William S. Hlavacek; Francesco Sorrentino 001 (CoRR, 2018)

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. - Keesha E. Erickson; Oleksii S. Rukhlenko; MD Shahinuzzaman; Kalina P. Slavkova; Yen Ting Lin; Ryan Suderman; Edward C. Stites; Marian Anghel; Richard G. Posner; Dipak Barua; Boris N. Kholodenko; William S. Hlavacek (PLoS Comput. Biol., 2019)

Bayesian inference using qualitative observations of underlying continuous variables. - Eshan D. Mitra; William S. Hlavacek (Bioinform., 2020)

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. - Fengkai Zhang; Lucian P. Smith; Michael L. Blinov; James R. Faeder; William S. Hlavacek; José Juan Tapia; Sarah M. Keating; Nicolas Rodriguez 001; Andreas Dräger; Leonard A. Harris; Andrew Finney; Bin Hu 025; et al. (J. Integr. Bioinform., 2020)

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit. - Jacob Neumann; Yen Ting Lin; Abhishek Mallela; Ely F. Miller; Joshua Colvin; Abell T. Duprat; Ye Chen; William S. Hlavacek; Richard G. Posner (Bioinform., 2022)