Hlavacek:Publications

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(Recent work)
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==Recent work==
==Recent work==
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*Mu F, Unkefer CJ, Unkefer PJ, Hlavacek WS (2011) Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. [http://bioinformatics.oxfordjournals.org/ Bioinformatics]  
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*Chylek LA, Wilson BS, Hlavacek WS (2012) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Los Alamos Technical Report LA-UR-12-23058 [[media:LA-UR-12-23058.pdf|pdf]]
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*Lemons NW, Hu B, Hlavacek WS (2011) Hierarchical graphs for rule-based modeling of biochemical systems. [http://www.biomedcentral.com/bmcbioinformatics BMC Bioinformatics] '''12''':45 PMID 21288338
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*Chylek LA, Stites EC, Posner RG, Hlavacek WS (2012) Innovations of the rule-based modeling approach. Los Alamos Technical Report LA-UR-12-10375 [[media:LA-UR-12-10375.pdf|pdf]]
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*Bauer AL, Hlavacek WS, Unkefer PJ, Mu F (2010) Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. [http://www.ploscompbiol.org PLoS Comput Biol] '''6''':e1001007 PMID 21124945
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*Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Von Hoff DD, Hlavacek WS, Posner RG (2012) Visualization, annotation and simulation of a large rule-based model for ErbB receptor signaling. BMC Syst Biol 6:107 PMID 22913808
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*Yang J, Meng X, Hlavacek WS (2010) Rule-based modelling and simulation of biochemical systems with molecular finite automata. [http://scitation.aip.org/IET-SYB IET Syst Biol] '''4''', 453-466 PMID 21073243
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*Barua D, Hlavacek WS, Lipniacki T (2012) A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J Immunol 189:646-658. PMID 22711887
==Selected publications==
==Selected publications==
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*Wall ME, Hlavacek WS, Savageau MA (2004) Design of gene circuits: lessons from bacteria. [http://www.nature.com/nrg/index.html Nat Rev Genet] '''5''', 34-42 PMID 14708014
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*Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (2003) The complexity of complexes in signal transduction. [http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0290 Biotechnol Bioeng] '''84''', 783-794. PMID 14708119
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*Wall ME, Hlavacek WS, Savageau MA (2004) Design of gene circuits: lessons from bacteria. [http://www.nature.com/nrg/index.html Nat Rev Genet] '''5''', 34-42. PMID 14708014
 +
 
 +
*Goldstein B, Faeder JR, Hlavacek WS (2004) Mathematical and computational models of immune-receptor signalling. [http://www.nature.com/nri/index.html Nat Rev Immunol] '''4''', 445-456. PMID 15173833
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*Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. [http://bioinformatics.oxfordjournals.org/ Bioinformatics] '''20''', 3289-3291. PMID 15217809
*Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. [http://stke.sciencemag.org/ Sci STKE] '''2006''', re6. PMID 16849649
*Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. [http://stke.sciencemag.org/ Sci STKE] '''2006''', re6. PMID 16849649

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Recent work

  • Chylek LA, Wilson BS, Hlavacek WS (2012) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Los Alamos Technical Report LA-UR-12-23058 pdf
  • Chylek LA, Stites EC, Posner RG, Hlavacek WS (2012) Innovations of the rule-based modeling approach. Los Alamos Technical Report LA-UR-12-10375 pdf
  • Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, Von Hoff DD, Hlavacek WS, Posner RG (2012) Visualization, annotation and simulation of a large rule-based model for ErbB receptor signaling. BMC Syst Biol 6:107 PMID 22913808
  • Barua D, Hlavacek WS, Lipniacki T (2012) A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J Immunol 189:646-658. PMID 22711887

Selected publications

  • Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (2003) The complexity of complexes in signal transduction. Biotechnol Bioeng 84, 783-794. PMID 14708119
  • Goldstein B, Faeder JR, Hlavacek WS (2004) Mathematical and computational models of immune-receptor signalling. Nat Rev Immunol 4, 445-456. PMID 15173833
  • Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. PMID 15217809
  • Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (2006) Rules for modeling signal-transduction systems. Sci STKE 2006, re6. PMID 16849649
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