William S. Hlavacek

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