William S. Hlavacek

Publication Activity (10 Years)

Years Active: 1998-2022
Publications (10 Years): 8

Top Topics

Markup Language

Arabidopsis Thaliana

Markov Chain Monte Carlo

Top Venues

PLoS Comput. Biol.

Publications

Jacob Neumann, Yen Ting Lin, Abhishek Mallela, Ely F. Miller, Joshua Colvin, Abell T. Duprat, Ye Chen, William S. Hlavacek, Richard G. Posner
Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit. Bioinform. 38 (6) (2022)
Eshan D. Mitra, William S. Hlavacek
Bayesian inference using qualitative observations of underlying continuous variables. Bioinform. 36 (10) (2020)
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
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J. Integr. Bioinform. 17 (2-3) (2020)
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
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLoS Comput. Biol. 15 (1) (2019)
Afroza Shirin, Isaac S. Klickstein, Song Feng, Yen Ting Lin, William S. Hlavacek, Francesco Sorrentino
Prediction of Optimal Drug Schedules for Controlling Autophagy. CoRR (2018)
Ryan Suderman, William S. Hlavacek
TRuML: A Translator for Rule-Based Modeling Languages. BCB (2017)
Marek Kochanczyk, William S. Hlavacek, Tomasz Lipniacki
SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces. Bioinform. 33 (22) (2017)
Brandon R. Thomas, Lily A. Chylek, Joshua Colvin, Suman Sirimulla, Andrew H. A. Clayton, William S. Hlavacek, Richard G. Posner
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. Bioinform. 32 (5) (2016)
Orna Resnekov, Brian Munsky, William S. Hlavacek
Perspective on the q-bio Summer School and Conference: 2007-2014 and beyond. Quant. Biol. 2 (1) (2014)
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
Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics. PLoS Comput. Biol. 9 (1) (2013)
Dipak Barua, William S. Hlavacek
Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells. PLoS Comput. Biol. 9 (9) (2013)
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
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Syst. Biol. 6 (2012)
Fangping Mu, Clifford J. Unkefer, Pat J. Unkefer, William S. Hlavacek
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. Bioinform. 27 (11) (2011)
Nathan W. Lemons, Bin Hu, William S. Hlavacek
Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinform. 12 (2011)
Amy L. Bauer, William S. Hlavacek, Pat J. Unkefer, Fangping Mu
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites. PLoS Comput. Biol. 6 (11) (2010)
Anu Chaudhary, Geoffrey Waldo, William S. Hlavacek, Chang-Shung Tung
Systems Biology Approaches for Developing Artificial Pathogen Detection Networks. ALIFE (2010)
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkunst, William S. Hlavacek, Daniel D. Von Hoff, Richard G. Posner
RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinform. 11 (2010)
Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek
GetBonNie for building, analyzing and sharing rule-based models. Bioinform. 25 (11) (2009)
Joshua Colvin, Michael I. Monine, James R. Faeder, William S. Hlavacek, Daniel D. Von Hoff, Richard G. Posner
Simulation of large-scale rule-based models. Bioinform. 25 (7) (2009)
Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek
Carbon-fate maps for metabolic reactions. Bioinform. 23 (23) (2007)
Fangping Mu, Pat J. Unkefer, Clifford J. Unkefer, William S. Hlavacek
Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites. Bioinform. 22 (24) (2006)
Michael L. Blinov, Jin Yang, James R. Faeder, William S. Hlavacek
Graph Theory for Rule-Based Modeling of Biochemical Networks. Trans. Comp. Sys. Biology 7 (2006)
James R. Faeder, Michael L. Blinov, William S. Hlavacek
Graphical rule-based representation of signal-transduction networks. SAC (2005)
James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek
Rule-based modeling of biochemical networks. Complex. 10 (4) (2005)
Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinform. 20 (17) (2004)
William S. Hlavacek, Michael A. Savageau
Method for determining natural design principles of biological control circuits. J. Intell. Fuzzy Syst. 6 (1) (1998)