William S. Hlavacek

According to our database, William S. Hlavacek authored at least 26 papers between 1998 and 2022.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2022

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

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, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim

J. Integr. Bioinform., 2020

Bayesian inference using qualitative observations of underlying continuous variables.

Eshan D. Mitra, William S. Hlavacek

Bioinform., 2020

2019

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

2018

Prediction of Optimal Drug Schedules for Controlling Autophagy.

Afroza Shirin, Isaac S. Klickstein, Song Feng, Yen Ting Lin, William S. Hlavacek, Francesco Sorrentino

CoRR, 2018

2017

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

Marek Kochanczyk, William S. Hlavacek, Tomasz Lipniacki

Bioinform., 2017

TRuML: A Translator for Rule-Based Modeling Languages.

Ryan Suderman, William S. Hlavacek

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

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

2014

Perspective on the q-bio Summer School and Conference: 2007-2014 and beyond.

Orna Resnekov, Brian Munsky, William S. Hlavacek

Quant. Biol., 2014

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

Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells.

Dipak Barua, William S. Hlavacek

PLoS Comput. Biol., 2013

2012

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

2011

Hierarchical graphs for rule-based modeling of biochemical systems.

Nathan W. Lemons, Bin Hu, William S. Hlavacek

BMC Bioinform., 2011

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

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

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

Systems Biology Approaches for Developing Artificial Pathogen Detection Networks.

Anu Chaudhary, Geoffrey Waldo, William S. Hlavacek, Chang-Shung Tung

Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, 2010

2009

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

Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek

Bioinform., 2009

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

2007

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

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

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

Fangping Mu, Pat J. Unkefer, Clifford J. Unkefer, William S. Hlavacek

Bioinform., 2006

2005

Rule-based modeling of biochemical networks.

James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek

Complex., 2005

Graphical rule-based representation of signal-transduction networks.

James R. Faeder, Michael L. Blinov, William S. Hlavacek

Proceedings of the 2005 ACM Symposium on Applied Computing (SAC), 2005

2004

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

1998

Method for determining natural design principles of biological control circuits.

William S. Hlavacek, Michael A. Savageau

J. Intell. Fuzzy Syst., 1998